Starting phenix.real_space_refine on Tue Aug 26 02:52:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fne_50591/08_2025/9fne_50591.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fne_50591/08_2025/9fne_50591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fne_50591/08_2025/9fne_50591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fne_50591/08_2025/9fne_50591.map" model { file = "/net/cci-nas-00/data/ceres_data/9fne_50591/08_2025/9fne_50591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fne_50591/08_2025/9fne_50591.cif" } resolution = 4.0 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= -0.000 sd= 1.000 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 86 5.49 5 Mg 1 5.21 5 S 104 5.16 5 C 20190 2.51 5 N 5846 2.21 5 O 6477 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32706 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1708 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 210} Chain: "B" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1790 Classifications: {'peptide': 236} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 220} Chain: "C" Number of atoms: 8678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 8678 Classifications: {'peptide': 1121} Link IDs: {'PTRANS': 59, 'TRANS': 1061} Chain: "D" Number of atoms: 9897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1265, 9897 Classifications: {'peptide': 1265} Link IDs: {'PCIS': 2, 'PTRANS': 55, 'TRANS': 1207} Chain breaks: 2 Chain: "E" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 684 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 6, 'TRANS': 82} Chain: "F" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2543 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 8, 'TRANS': 309} Chain: "J" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 726 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 7, 'TRANS': 81} Chain: "O" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 879 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "P" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 884 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "Y" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2383 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 296} Chain: "X" Number of atoms: 2531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2531 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 314} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19247 SG CYS D 890 104.158 105.110 145.269 1.00 68.63 S ATOM 19809 SG CYS D 967 105.310 103.572 141.920 1.00 72.76 S ATOM 19851 SG CYS D 974 102.100 105.675 142.210 1.00 58.75 S ATOM 19870 SG CYS D 977 105.406 107.338 142.409 1.00 73.73 S ATOM 12674 SG CYS D 60 78.720 57.069 102.644 1.00103.93 S ATOM 12692 SG CYS D 62 79.564 53.890 100.851 1.00114.18 S ATOM 12801 SG CYS D 75 78.794 53.694 104.574 1.00119.36 S ATOM 12827 SG CYS D 78 82.005 55.254 103.415 1.00121.85 S Time building chain proxies: 7.75, per 1000 atoms: 0.24 Number of scatterers: 32706 At special positions: 0 Unit cell: (188.16, 190.4, 168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 104 16.00 P 86 15.00 Mg 1 11.99 O 6477 8.00 N 5846 7.00 C 20190 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: 2.97 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 974 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 977 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 890 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 967 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 60 " Number of angles added : 12 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7366 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 49 sheets defined 42.7% alpha, 15.5% beta 29 base pairs and 54 stacking pairs defined. Time for finding SS restraints: 4.14 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 removed outlier: 3.656A pdb=" N LEU A 34 " --> pdb=" O PHE A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 203 through 225 removed outlier: 3.898A pdb=" N ARG A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 45 removed outlier: 3.981A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 removed outlier: 3.577A pdb=" N GLY B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 224 Processing helix chain 'C' and resid 45 through 57 removed outlier: 4.286A pdb=" N SER C 51 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 69 Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 109 through 117 Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 235 through 243 Processing helix chain 'C' and resid 246 through 256 removed outlier: 3.962A pdb=" N MET C 250 " --> pdb=" O SER C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 273 Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 300 through 312 Processing helix chain 'C' and resid 325 through 342 Processing helix chain 'C' and resid 371 through 396 removed outlier: 3.685A pdb=" N THR C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.641A pdb=" N LEU C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 425 removed outlier: 3.625A pdb=" N VAL C 415 " --> pdb=" O ILE C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 444 Processing helix chain 'C' and resid 523 through 530 removed outlier: 3.801A pdb=" N ARG C 529 " --> pdb=" O ASP C 525 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS C 530 " --> pdb=" O GLU C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 567 Processing helix chain 'C' and resid 581 through 585 removed outlier: 3.672A pdb=" N ILE C 585 " --> pdb=" O THR C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 603 Processing helix chain 'C' and resid 622 through 630 removed outlier: 4.053A pdb=" N GLY C 630 " --> pdb=" O ALA C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 770 through 774 removed outlier: 3.515A pdb=" N ALA C 773 " --> pdb=" O GLU C 770 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASP C 774 " --> pdb=" O VAL C 771 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 770 through 774' Processing helix chain 'C' and resid 806 through 817 Processing helix chain 'C' and resid 847 through 849 No H-bonds generated for 'chain 'C' and resid 847 through 849' Processing helix chain 'C' and resid 918 through 932 removed outlier: 4.250A pdb=" N ILE C 922 " --> pdb=" O ASN C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 948 Processing helix chain 'C' and resid 951 through 954 Processing helix chain 'C' and resid 972 through 982 Processing helix chain 'C' and resid 1027 through 1032 Processing helix chain 'C' and resid 1060 through 1071 Processing helix chain 'C' and resid 1072 through 1082 removed outlier: 3.710A pdb=" N LEU C1076 " --> pdb=" O ALA C1072 " (cutoff:3.500A) Processing helix chain 'C' and resid 1086 through 1100 removed outlier: 3.833A pdb=" N VAL C1091 " --> pdb=" O THR C1087 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1121 removed outlier: 3.767A pdb=" N LYS C1113 " --> pdb=" O PRO C1109 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 7 Processing helix chain 'D' and resid 16 through 23 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 84 through 90 removed outlier: 3.734A pdb=" N VAL D 87 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 147 through 187 Processing helix chain 'D' and resid 190 through 228 removed outlier: 3.615A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 257 through 268 removed outlier: 3.581A pdb=" N ILE D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 Processing helix chain 'D' and resid 286 through 305 removed outlier: 4.213A pdb=" N LEU D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG D 291 " --> pdb=" O GLN D 287 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.515A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 340 through 361 Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 393 through 397 removed outlier: 3.754A pdb=" N ARG D 397 " --> pdb=" O PRO D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 407 Processing helix chain 'D' and resid 411 through 417 removed outlier: 3.580A pdb=" N LEU D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 482 through 491 removed outlier: 3.829A pdb=" N VAL D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 579 through 590 Processing helix chain 'D' and resid 614 through 623 Processing helix chain 'D' and resid 645 through 651 removed outlier: 3.607A pdb=" N GLN D 649 " --> pdb=" O ASP D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 676 Processing helix chain 'D' and resid 688 through 703 Processing helix chain 'D' and resid 704 through 724 removed outlier: 3.950A pdb=" N THR D 724 " --> pdb=" O PHE D 720 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 761 Processing helix chain 'D' and resid 765 through 792 Processing helix chain 'D' and resid 796 through 804 Processing helix chain 'D' and resid 809 through 817 Processing helix chain 'D' and resid 844 through 880 removed outlier: 3.876A pdb=" N ALA D 863 " --> pdb=" O LEU D 859 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU D 864 " --> pdb=" O ALA D 860 " (cutoff:3.500A) Processing helix chain 'D' and resid 944 through 954 Processing helix chain 'D' and resid 975 through 979 Processing helix chain 'D' and resid 993 through 1004 removed outlier: 4.071A pdb=" N VAL D 997 " --> pdb=" O ALA D 993 " (cutoff:3.500A) Processing helix chain 'D' and resid 1005 through 1007 No H-bonds generated for 'chain 'D' and resid 1005 through 1007' Processing helix chain 'D' and resid 1028 through 1037 Processing helix chain 'D' and resid 1118 through 1126 removed outlier: 3.572A pdb=" N VAL D1122 " --> pdb=" O ASP D1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 1127 through 1145 removed outlier: 3.535A pdb=" N GLN D1132 " --> pdb=" O PRO D1128 " (cutoff:3.500A) Processing helix chain 'D' and resid 1151 through 1162 removed outlier: 4.016A pdb=" N ILE D1155 " --> pdb=" O HIS D1151 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D1157 " --> pdb=" O LYS D1153 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE D1158 " --> pdb=" O HIS D1154 " (cutoff:3.500A) Processing helix chain 'D' and resid 1184 through 1196 removed outlier: 3.707A pdb=" N ALA D1196 " --> pdb=" O ARG D1192 " (cutoff:3.500A) Processing helix chain 'D' and resid 1210 through 1216 removed outlier: 3.660A pdb=" N LEU D1216 " --> pdb=" O THR D1212 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1228 removed outlier: 3.668A pdb=" N ALA D1224 " --> pdb=" O SER D1220 " (cutoff:3.500A) Processing helix chain 'D' and resid 1229 through 1241 Processing helix chain 'D' and resid 1248 through 1255 Processing helix chain 'D' and resid 1261 through 1264 Processing helix chain 'D' and resid 1265 through 1270 removed outlier: 3.556A pdb=" N ASN D1270 " --> pdb=" O SER D1266 " (cutoff:3.500A) Processing helix chain 'D' and resid 1276 through 1283 Processing helix chain 'E' and resid 30 through 34 removed outlier: 3.562A pdb=" N THR E 33 " --> pdb=" O LEU E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 47 through 66 removed outlier: 4.954A pdb=" N TYR E 53 " --> pdb=" O ALA E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 98 Processing helix chain 'F' and resid 149 through 159 Processing helix chain 'F' and resid 164 through 174 Processing helix chain 'F' and resid 182 through 206 removed outlier: 3.738A pdb=" N GLU F 206 " --> pdb=" O ALA F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 237 removed outlier: 3.545A pdb=" N ASN F 237 " --> pdb=" O LEU F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 246 removed outlier: 4.237A pdb=" N VAL F 241 " --> pdb=" O ASN F 237 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL F 242 " --> pdb=" O LEU F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 272 Processing helix chain 'F' and resid 280 through 300 removed outlier: 4.223A pdb=" N TYR F 284 " --> pdb=" O LYS F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 329 removed outlier: 4.001A pdb=" N VAL F 313 " --> pdb=" O HIS F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 341 Processing helix chain 'F' and resid 346 through 355 Processing helix chain 'F' and resid 372 through 376 Processing helix chain 'F' and resid 386 through 403 Processing helix chain 'F' and resid 406 through 417 Processing helix chain 'F' and resid 426 through 435 Processing helix chain 'F' and resid 437 through 453 Processing helix chain 'F' and resid 454 through 463 removed outlier: 4.815A pdb=" N VAL F 460 " --> pdb=" O SER F 456 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LEU F 461 " --> pdb=" O ARG F 457 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP F 463 " --> pdb=" O GLN F 459 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 89 Processing helix chain 'J' and resid 90 through 111 Processing helix chain 'Y' and resid 3 through 21 removed outlier: 4.411A pdb=" N VAL Y 15 " --> pdb=" O LEU Y 11 " (cutoff:3.500A) Proline residue: Y 16 - end of helix Processing helix chain 'Y' and resid 26 through 34 Processing helix chain 'Y' and resid 36 through 49 removed outlier: 3.559A pdb=" N MET Y 49 " --> pdb=" O ASP Y 45 " (cutoff:3.500A) Processing helix chain 'Y' and resid 85 through 101 removed outlier: 4.232A pdb=" N ASP Y 101 " --> pdb=" O ARG Y 97 " (cutoff:3.500A) Processing helix chain 'Y' and resid 107 through 123 Processing helix chain 'Y' and resid 141 through 153 Processing helix chain 'Y' and resid 217 through 223 removed outlier: 4.075A pdb=" N ALA Y 221 " --> pdb=" O PRO Y 217 " (cutoff:3.500A) Processing helix chain 'Y' and resid 250 through 255 removed outlier: 3.985A pdb=" N TYR Y 254 " --> pdb=" O TRP Y 250 " (cutoff:3.500A) Processing helix chain 'Y' and resid 276 through 288 removed outlier: 3.798A pdb=" N PHE Y 287 " --> pdb=" O PHE Y 283 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY Y 288 " --> pdb=" O ILE Y 284 " (cutoff:3.500A) Processing helix chain 'Y' and resid 296 through 317 Processing helix chain 'X' and resid 4 through 19 Processing helix chain 'X' and resid 24 through 32 Processing helix chain 'X' and resid 40 through 58 Processing helix chain 'X' and resid 79 through 84 Processing helix chain 'X' and resid 91 through 102 Processing helix chain 'X' and resid 107 through 124 Processing helix chain 'X' and resid 150 through 163 Processing helix chain 'X' and resid 235 through 245 removed outlier: 3.515A pdb=" N ALA X 245 " --> pdb=" O ARG X 241 " (cutoff:3.500A) Processing helix chain 'X' and resid 262 through 269 Processing helix chain 'X' and resid 291 through 303 removed outlier: 3.774A pdb=" N TYR X 302 " --> pdb=" O GLU X 298 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY X 303 " --> pdb=" O ILE X 299 " (cutoff:3.500A) Processing helix chain 'X' and resid 311 through 327 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 6.648A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS A 173 " --> pdb=" O GLU A 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.222A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 removed outlier: 3.523A pdb=" N SER A 166 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 10 removed outlier: 6.801A pdb=" N ARG B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B 14 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 8 through 10 removed outlier: 6.668A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE B 189 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.587A pdb=" N TYR B 96 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 134 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AB1, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.862A pdb=" N GLY B 103 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB3, first strand: chain 'C' and resid 30 through 31 removed outlier: 6.722A pdb=" N VAL C 30 " --> pdb=" O ALA C 964 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 94 through 103 removed outlier: 6.655A pdb=" N PHE C 125 " --> pdb=" O PRO C 101 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE C 103 " --> pdb=" O PRO C 123 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ALA C 122 " --> pdb=" O ASP C 147 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASP C 147 " --> pdb=" O ALA C 122 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU C 124 " --> pdb=" O MET C 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 157 through 159 Processing sheet with id=AB6, first strand: chain 'C' and resid 367 through 370 removed outlier: 6.241A pdb=" N SER C 168 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 175 through 182 removed outlier: 4.331A pdb=" N HIS C 191 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 203 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU C 204 " --> pdb=" O ARG C 216 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 345 through 346 Processing sheet with id=AB9, first strand: chain 'C' and resid 496 through 497 removed outlier: 3.575A pdb=" N THR C 505 " --> pdb=" O LEU C 522 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLN C 518 " --> pdb=" O LYS C 509 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N GLU C 511 " --> pdb=" O THR C 516 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR C 516 " --> pdb=" O GLU C 511 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 496 through 497 Processing sheet with id=AC2, first strand: chain 'C' and resid 532 through 533 removed outlier: 5.925A pdb=" N VAL C 550 " --> pdb=" O PHE C 561 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N PHE C 561 " --> pdb=" O VAL C 550 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL C 552 " --> pdb=" O VAL C 559 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL C 559 " --> pdb=" O VAL C 552 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 633 through 634 removed outlier: 6.887A pdb=" N VAL C 633 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG C 678 " --> pdb=" O ASP C 695 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 659 through 662 removed outlier: 3.578A pdb=" N GLU C 643 " --> pdb=" O THR C 650 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 667 through 668 Processing sheet with id=AC6, first strand: chain 'C' and resid 699 through 700 Processing sheet with id=AC7, first strand: chain 'C' and resid 998 through 999 removed outlier: 6.187A pdb=" N ILE C 726 " --> pdb=" O ILE C 886 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS C 888 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE C 727 " --> pdb=" O ILE C 907 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N ILE C 906 " --> pdb=" O ASN C 709 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU C 711 " --> pdb=" O ILE C 906 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LEU C 908 " --> pdb=" O LEU C 711 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ALA C 713 " --> pdb=" O LEU C 908 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N THR C1015 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 739 through 751 removed outlier: 4.027A pdb=" N GLY C 840 " --> pdb=" O TYR C 863 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA C 865 " --> pdb=" O VAL C 838 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N VAL C 838 " --> pdb=" O ALA C 865 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N LYS C 867 " --> pdb=" O GLY C 836 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N GLY C 836 " --> pdb=" O LYS C 867 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 759 through 760 Processing sheet with id=AD1, first strand: chain 'C' and resid 792 through 794 removed outlier: 3.635A pdb=" N VAL C 794 " --> pdb=" O LEU C 828 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 935 through 936 Processing sheet with id=AD3, first strand: chain 'C' and resid 1033 through 1035 removed outlier: 7.832A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1057 through 1059 removed outlier: 3.812A pdb=" N GLN C1057 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 422 " --> pdb=" O GLN C1057 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1127 through 1129 removed outlier: 3.545A pdb=" N ASP D1244 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 24 through 27 removed outlier: 7.753A pdb=" N HIS D 94 " --> pdb=" O TYR D 25 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLU D 27 " --> pdb=" O HIS D 94 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N GLU D 96 " --> pdb=" O GLU D 27 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASP D 315 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 10.774A pdb=" N ALA D 99 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 10.164A pdb=" N VAL D 313 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 234 through 235 removed outlier: 7.169A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 328 through 329 removed outlier: 6.440A pdb=" N PHE D 335 " --> pdb=" O ILE F 359 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 611 through 612 removed outlier: 7.719A pdb=" N TYR D 612 " --> pdb=" O ARG D 636 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 885 through 887 Processing sheet with id=AE2, first strand: chain 'D' and resid 896 through 899 Processing sheet with id=AE3, first strand: chain 'D' and resid 1052 through 1058 Processing sheet with id=AE4, first strand: chain 'D' and resid 1181 through 1183 removed outlier: 4.846A pdb=" N ARG D1165 " --> pdb=" O VAL D1207 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1272 through 1275 removed outlier: 3.507A pdb=" N GLN D1272 " --> pdb=" O THR E 104 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 39 through 45 Processing sheet with id=AE7, first strand: chain 'Y' and resid 24 through 25 removed outlier: 3.859A pdb=" N VAL Y 24 " --> pdb=" O ILE Y 70 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Y' and resid 62 through 63 removed outlier: 6.348A pdb=" N ASP Y 62 " --> pdb=" O THR Y 73 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Y' and resid 196 through 201 removed outlier: 7.166A pdb=" N ASN Y 184 " --> pdb=" O LEU Y 180 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU Y 180 " --> pdb=" O ASN Y 184 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N TYR Y 186 " --> pdb=" O VAL Y 178 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N VAL Y 178 " --> pdb=" O TYR Y 186 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLU Y 188 " --> pdb=" O ILE Y 176 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU Y 159 " --> pdb=" O ASP Y 207 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASP Y 207 " --> pdb=" O GLU Y 159 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N TYR Y 161 " --> pdb=" O ILE Y 205 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE Y 205 " --> pdb=" O TYR Y 161 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Y' and resid 270 through 273 removed outlier: 7.413A pdb=" N THR Y 241 " --> pdb=" O LEU Y 294 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU Y 294 " --> pdb=" O THR Y 241 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'X' and resid 62 through 66 Processing sheet with id=AF3, first strand: chain 'X' and resid 207 through 211 removed outlier: 3.608A pdb=" N GLY X 199 " --> pdb=" O ARG X 208 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ARG X 194 " --> pdb=" O THR X 190 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR X 190 " --> pdb=" O ARG X 194 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TYR X 196 " --> pdb=" O VAL X 188 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N VAL X 188 " --> pdb=" O TYR X 196 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL X 198 " --> pdb=" O TRP X 186 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'X' and resid 271 through 274 removed outlier: 3.884A pdb=" N THR X 271 " --> pdb=" O THR X 286 " (cutoff:3.500A) 1429 hydrogen bonds defined for protein. 4095 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 54 stacking parallelities Total time for adding SS restraints: 8.51 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9888 1.34 - 1.45: 4676 1.45 - 1.57: 18511 1.57 - 1.69: 170 1.69 - 1.81: 184 Bond restraints: 33429 Sorted by residual: bond pdb=" C GLU D1004 " pdb=" N PRO D1005 " ideal model delta sigma weight residual 1.339 1.375 -0.036 3.40e-02 8.65e+02 1.13e+00 bond pdb=" N PRO D 642 " pdb=" CA PRO D 642 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.31e-02 5.83e+03 9.69e-01 bond pdb=" C PRO Y 218 " pdb=" N PRO Y 219 " ideal model delta sigma weight residual 1.329 1.341 -0.012 1.18e-02 7.18e+03 9.62e-01 bond pdb=" C3' DG O 58 " pdb=" C2' DG O 58 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 8.49e-01 bond pdb=" CA VAL Y 78 " pdb=" CB VAL Y 78 " ideal model delta sigma weight residual 1.527 1.539 -0.012 1.31e-02 5.83e+03 8.35e-01 ... (remaining 33424 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 45237 1.78 - 3.56: 400 3.56 - 5.34: 25 5.34 - 7.12: 3 7.12 - 8.89: 1 Bond angle restraints: 45666 Sorted by residual: angle pdb=" C ALA E 49 " pdb=" N LEU E 50 " pdb=" CA LEU E 50 " ideal model delta sigma weight residual 122.15 131.04 -8.89 2.83e+00 1.25e-01 9.88e+00 angle pdb=" N GLY E 31 " pdb=" CA GLY E 31 " pdb=" C GLY E 31 " ideal model delta sigma weight residual 110.77 116.51 -5.74 1.93e+00 2.68e-01 8.85e+00 angle pdb=" N PRO Y 218 " pdb=" CA PRO Y 218 " pdb=" C PRO Y 218 " ideal model delta sigma weight residual 110.70 113.72 -3.02 1.22e+00 6.72e-01 6.13e+00 angle pdb=" CA GLY D 93 " pdb=" C GLY D 93 " pdb=" N HIS D 94 " ideal model delta sigma weight residual 114.56 117.49 -2.93 1.22e+00 6.72e-01 5.75e+00 angle pdb=" C LYS A 131 " pdb=" N GLY A 132 " pdb=" CA GLY A 132 " ideal model delta sigma weight residual 122.33 120.62 1.71 7.30e-01 1.88e+00 5.47e+00 ... (remaining 45661 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.43: 19895 34.43 - 68.86: 346 68.86 - 103.29: 5 103.29 - 137.73: 2 137.73 - 172.16: 1 Dihedral angle restraints: 20249 sinusoidal: 8812 harmonic: 11437 Sorted by residual: dihedral pdb=" C4' DA P 105 " pdb=" C3' DA P 105 " pdb=" O3' DA P 105 " pdb=" P DA P 106 " ideal model delta sinusoidal sigma weight residual -140.00 32.16 -172.16 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DA P 104 " pdb=" C3' DA P 104 " pdb=" O3' DA P 104 " pdb=" P DA P 105 " ideal model delta sinusoidal sigma weight residual 220.00 85.09 134.91 1 3.50e+01 8.16e-04 1.34e+01 dihedral pdb=" CA ALA E 49 " pdb=" C ALA E 49 " pdb=" N LEU E 50 " pdb=" CA LEU E 50 " ideal model delta harmonic sigma weight residual 180.00 161.72 18.28 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 20246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3231 0.027 - 0.054: 1256 0.054 - 0.080: 376 0.080 - 0.107: 255 0.107 - 0.134: 94 Chirality restraints: 5212 Sorted by residual: chirality pdb=" CA ILE A 193 " pdb=" N ILE A 193 " pdb=" C ILE A 193 " pdb=" CB ILE A 193 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ILE C 727 " pdb=" N ILE C 727 " pdb=" C ILE C 727 " pdb=" CB ILE C 727 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE C 585 " pdb=" N ILE C 585 " pdb=" C ILE C 585 " pdb=" CB ILE C 585 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 5209 not shown) Planarity restraints: 5715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 404 " 0.043 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO C 405 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 405 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 405 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO Y 219 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.09e+00 pdb=" N PRO Y 220 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO Y 220 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO Y 220 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO Y 217 " 0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO Y 218 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO Y 218 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO Y 218 " 0.021 5.00e-02 4.00e+02 ... (remaining 5712 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 619 2.70 - 3.25: 30314 3.25 - 3.80: 49083 3.80 - 4.35: 62709 4.35 - 4.90: 108410 Nonbonded interactions: 251135 Sorted by model distance: nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2002 " model vdw 2.145 2.170 nonbonded pdb=" O SER C 173 " pdb=" OH TYR C 177 " model vdw 2.207 3.040 nonbonded pdb=" OG1 THR F 333 " pdb=" OE1 GLU F 336 " model vdw 2.227 3.040 nonbonded pdb=" O PHE D 849 " pdb=" OG1 THR D 852 " model vdw 2.235 3.040 nonbonded pdb=" O LYS C 509 " pdb=" OG1 THR C 516 " model vdw 2.254 3.040 ... (remaining 251130 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 2 through 226) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 39.270 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.070 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 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 : 0.002 0.036 33437 Z= 0.095 Angle : 0.418 8.895 45678 Z= 0.226 Chirality : 0.038 0.134 5212 Planarity : 0.003 0.066 5715 Dihedral : 11.443 172.156 12883 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.99 % Allowed : 3.31 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1.56 (0.14), residues: 3968 helix: 2.61 (0.14), residues: 1567 sheet: 0.88 (0.25), residues: 511 loop : -0.28 (0.15), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 20 TYR 0.008 0.001 TYR C 335 PHE 0.009 0.001 PHE C 897 TRP 0.008 0.001 TRP C 929 HIS 0.003 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00200 (33429) covalent geometry : angle 0.41677 (45666) hydrogen bonds : bond 0.15468 ( 1497) hydrogen bonds : angle 5.49610 ( 4243) metal coordination : bond 0.00436 ( 8) metal coordination : angle 2.20436 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 582 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 VAL cc_start: 0.9204 (t) cc_final: 0.8881 (m) REVERT: A 45 SER cc_start: 0.9001 (m) cc_final: 0.8756 (t) REVERT: B 20 ARG cc_start: 0.8272 (ttm110) cc_final: 0.7377 (ttt90) REVERT: B 24 GLU cc_start: 0.8300 (pt0) cc_final: 0.8059 (pt0) REVERT: B 90 ASP cc_start: 0.7813 (m-30) cc_final: 0.7547 (t0) REVERT: B 122 ASP cc_start: 0.8685 (m-30) cc_final: 0.8437 (p0) REVERT: B 123 MET cc_start: 0.8100 (ttp) cc_final: 0.7865 (ttm) REVERT: C 116 LYS cc_start: 0.8143 (mttm) cc_final: 0.7306 (tptm) REVERT: C 118 MET cc_start: 0.7751 (mtm) cc_final: 0.7490 (mtp) REVERT: C 145 MET cc_start: 0.8551 (mmt) cc_final: 0.8140 (mmt) REVERT: C 180 GLU cc_start: 0.7851 (tt0) cc_final: 0.7602 (tt0) REVERT: C 209 LYS cc_start: 0.7503 (mtmm) cc_final: 0.7123 (mtmm) REVERT: C 343 GLN cc_start: 0.7538 (mt0) cc_final: 0.7039 (tt0) REVERT: C 426 GLN cc_start: 0.7295 (tt0) cc_final: 0.6770 (tm-30) REVERT: C 478 GLU cc_start: 0.8694 (tt0) cc_final: 0.8432 (tt0) REVERT: C 555 LYS cc_start: 0.6866 (tttp) cc_final: 0.6183 (ttmt) REVERT: C 566 GLN cc_start: 0.7361 (tp40) cc_final: 0.6826 (tt0) REVERT: C 584 MET cc_start: 0.9123 (mtm) cc_final: 0.8783 (mtm) REVERT: C 602 MET cc_start: 0.7590 (mtm) cc_final: 0.7030 (mtt) REVERT: C 637 LYS cc_start: 0.9144 (mtmt) cc_final: 0.8896 (mttm) REVERT: C 643 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7517 (mt-10) REVERT: C 648 TYR cc_start: 0.7992 (p90) cc_final: 0.7721 (p90) REVERT: C 652 MET cc_start: 0.8267 (tpt) cc_final: 0.7306 (tpt) REVERT: C 721 ASN cc_start: 0.9155 (p0) cc_final: 0.8944 (p0) REVERT: C 752 ASP cc_start: 0.6669 (t70) cc_final: 0.6347 (p0) REVERT: C 791 ASP cc_start: 0.7617 (m-30) cc_final: 0.7365 (t0) REVERT: C 917 MET cc_start: 0.7502 (mmm) cc_final: 0.7282 (mtm) REVERT: C 943 VAL cc_start: 0.8318 (t) cc_final: 0.8059 (m) REVERT: D 84 ARG cc_start: 0.7645 (mtt90) cc_final: 0.6630 (mtm-85) REVERT: D 141 ASP cc_start: 0.7003 (p0) cc_final: 0.6750 (t0) REVERT: D 237 ASP cc_start: 0.8049 (t0) cc_final: 0.7709 (m-30) REVERT: D 248 TYR cc_start: 0.7724 (m-80) cc_final: 0.7359 (m-80) REVERT: D 373 MET cc_start: 0.7417 (mtm) cc_final: 0.7206 (mtt) REVERT: D 509 ILE cc_start: 0.8980 (mt) cc_final: 0.8496 (tt) REVERT: D 530 GLU cc_start: 0.6987 (tt0) cc_final: 0.6330 (tp30) REVERT: D 533 ASN cc_start: 0.8455 (t0) cc_final: 0.8255 (t0) REVERT: D 541 MET cc_start: 0.9258 (mtt) cc_final: 0.8989 (mtp) REVERT: D 570 SER cc_start: 0.9258 (p) cc_final: 0.8857 (t) REVERT: D 634 LYS cc_start: 0.8729 (mttt) cc_final: 0.8499 (mtpt) REVERT: D 638 THR cc_start: 0.9328 (p) cc_final: 0.8801 (m) REVERT: D 730 VAL cc_start: 0.9138 (t) cc_final: 0.8921 (p) REVERT: D 894 ARG cc_start: 0.7925 (mtm180) cc_final: 0.6969 (mmp-170) REVERT: D 980 ARG cc_start: 0.8692 (ttm-80) cc_final: 0.8212 (ttp80) REVERT: D 1011 MET cc_start: 0.6041 (ttp) cc_final: 0.5435 (ptp) REVERT: D 1150 ILE cc_start: 0.8776 (mt) cc_final: 0.8461 (tt) REVERT: F 156 ASP cc_start: 0.7452 (m-30) cc_final: 0.7123 (t70) REVERT: F 172 GLN cc_start: 0.7546 (mm-40) cc_final: 0.6694 (mt0) REVERT: F 261 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8259 (mm-30) REVERT: F 290 ARG cc_start: 0.7196 (ttm-80) cc_final: 0.6723 (ttp80) REVERT: F 449 MET cc_start: 0.7466 (mmm) cc_final: 0.7229 (mmm) REVERT: F 463 ASP cc_start: 0.8167 (m-30) cc_final: 0.7781 (m-30) REVERT: Y 41 ASP cc_start: 0.7370 (t70) cc_final: 0.7138 (t0) REVERT: Y 71 GLU cc_start: 0.8422 (tt0) cc_final: 0.7877 (tp30) REVERT: Y 188 GLU cc_start: 0.8117 (tt0) cc_final: 0.7845 (tm-30) REVERT: Y 302 ARG cc_start: 0.9133 (ttt90) cc_final: 0.8718 (mtm110) REVERT: X 37 ASP cc_start: 0.8033 (m-30) cc_final: 0.6613 (t0) REVERT: X 105 TRP cc_start: 0.8350 (m100) cc_final: 0.7983 (m100) REVERT: X 106 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7810 (mm110) REVERT: X 115 GLN cc_start: 0.9077 (tp40) cc_final: 0.8785 (pt0) REVERT: X 298 GLU cc_start: 0.9493 (tt0) cc_final: 0.9221 (tt0) REVERT: X 302 TYR cc_start: 0.8697 (m-10) cc_final: 0.7640 (m-10) outliers start: 33 outliers final: 15 residues processed: 611 average time/residue: 0.2447 time to fit residues: 231.6494 Evaluate side-chains 359 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 344 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 1044 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain D residue 792 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS C 536 ASN C 880 HIS D 369 ASN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 ASN ** D 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1126 GLN F 232 HIS F 260 GLN Y 80 HIS X 11 ASN ** X 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.185058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.121405 restraints weight = 354859.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.122075 restraints weight = 218217.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.121653 restraints weight = 196250.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.121712 restraints weight = 189394.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.121567 restraints weight = 184350.104| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 33437 Z= 0.232 Angle : 0.614 9.204 45678 Z= 0.322 Chirality : 0.045 0.213 5212 Planarity : 0.005 0.060 5715 Dihedral : 13.699 173.455 5347 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.41 % Allowed : 8.01 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.92 (0.14), residues: 3968 helix: 2.01 (0.13), residues: 1585 sheet: 0.53 (0.23), residues: 551 loop : -0.61 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 440 TYR 0.030 0.002 TYR X 302 PHE 0.026 0.002 PHE D 512 TRP 0.013 0.001 TRP D1221 HIS 0.017 0.002 HIS X 325 Details of bonding type rmsd covalent geometry : bond 0.00569 (33429) covalent geometry : angle 0.60945 (45666) hydrogen bonds : bond 0.05072 ( 1497) hydrogen bonds : angle 4.50905 ( 4243) metal coordination : bond 0.01603 ( 8) metal coordination : angle 4.77570 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 361 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.9489 (m) cc_final: 0.9045 (t) REVERT: B 109 ASP cc_start: 0.8632 (m-30) cc_final: 0.8303 (m-30) REVERT: B 123 MET cc_start: 0.9252 (ttp) cc_final: 0.8944 (ttm) REVERT: C 116 LYS cc_start: 0.8585 (mttm) cc_final: 0.8182 (tptp) REVERT: C 209 LYS cc_start: 0.8005 (mtmm) cc_final: 0.7629 (mtmm) REVERT: C 343 GLN cc_start: 0.8638 (mt0) cc_final: 0.7898 (tt0) REVERT: C 420 GLU cc_start: 0.7946 (tp30) cc_final: 0.7441 (tp30) REVERT: C 426 GLN cc_start: 0.8237 (tt0) cc_final: 0.7943 (tm-30) REVERT: C 474 MET cc_start: 0.8985 (ttp) cc_final: 0.8596 (mtp) REVERT: C 478 GLU cc_start: 0.8806 (tt0) cc_final: 0.8594 (tt0) REVERT: C 492 SER cc_start: 0.9720 (OUTLIER) cc_final: 0.9281 (p) REVERT: C 566 GLN cc_start: 0.8274 (tp40) cc_final: 0.8044 (tt0) REVERT: C 584 MET cc_start: 0.8991 (mtm) cc_final: 0.8675 (mtm) REVERT: C 602 MET cc_start: 0.8018 (mtm) cc_final: 0.7652 (mtt) REVERT: C 637 LYS cc_start: 0.9287 (mtmt) cc_final: 0.9074 (mttp) REVERT: C 643 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7395 (mt-10) REVERT: C 652 MET cc_start: 0.8731 (tpt) cc_final: 0.7981 (tpt) REVERT: C 943 VAL cc_start: 0.8893 (t) cc_final: 0.8439 (m) REVERT: D 1 MET cc_start: 0.7002 (ptt) cc_final: 0.6560 (ptp) REVERT: D 84 ARG cc_start: 0.8378 (mtt90) cc_final: 0.7938 (mtm-85) REVERT: D 141 ASP cc_start: 0.7513 (p0) cc_final: 0.7101 (t0) REVERT: D 143 MET cc_start: 0.5245 (tpp) cc_final: 0.4850 (ttt) REVERT: D 147 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6786 (mp0) REVERT: D 250 GLU cc_start: 0.8076 (tp30) cc_final: 0.7611 (tp30) REVERT: D 327 MET cc_start: 0.9270 (tpp) cc_final: 0.9052 (tpt) REVERT: D 339 ASP cc_start: 0.8506 (m-30) cc_final: 0.8159 (m-30) REVERT: D 373 MET cc_start: 0.8362 (mtm) cc_final: 0.7972 (mtt) REVERT: D 509 ILE cc_start: 0.9379 (mt) cc_final: 0.9117 (tt) REVERT: D 533 ASN cc_start: 0.9173 (t0) cc_final: 0.8903 (t0) REVERT: D 541 MET cc_start: 0.8885 (mtt) cc_final: 0.8556 (mtp) REVERT: D 570 SER cc_start: 0.9521 (p) cc_final: 0.9131 (t) REVERT: D 634 LYS cc_start: 0.9308 (mttt) cc_final: 0.8938 (mtpt) REVERT: D 956 ILE cc_start: 0.8900 (mt) cc_final: 0.8584 (tp) REVERT: D 980 ARG cc_start: 0.9103 (ttm-80) cc_final: 0.8656 (ttp80) REVERT: D 1150 ILE cc_start: 0.9116 (mt) cc_final: 0.8892 (tt) REVERT: E 66 ASN cc_start: 0.8111 (t0) cc_final: 0.7751 (t0) REVERT: F 156 ASP cc_start: 0.7682 (m-30) cc_final: 0.7281 (t70) REVERT: F 172 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7342 (mt0) REVERT: F 189 LYS cc_start: 0.8483 (mtmt) cc_final: 0.7900 (mtmm) REVERT: F 336 GLU cc_start: 0.8143 (mp0) cc_final: 0.7820 (mp0) REVERT: F 449 MET cc_start: 0.8082 (mmm) cc_final: 0.7752 (mmm) REVERT: Y 188 GLU cc_start: 0.8013 (tt0) cc_final: 0.7685 (tp30) REVERT: X 12 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8400 (tt) REVERT: X 37 ASP cc_start: 0.8079 (m-30) cc_final: 0.6871 (t0) REVERT: X 106 GLN cc_start: 0.8505 (mm-40) cc_final: 0.8287 (mm110) REVERT: X 110 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7555 (mt) outliers start: 80 outliers final: 49 residues processed: 426 average time/residue: 0.2064 time to fit residues: 145.3215 Evaluate side-chains 373 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 320 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 492 SER Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 573 SER Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 619 THR Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 910 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 409 LYS Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain D residue 662 THR Chi-restraints excluded: chain D residue 792 TYR Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 957 THR Chi-restraints excluded: chain D residue 1007 THR Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1253 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 56 SER Chi-restraints excluded: chain Y residue 145 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 110 LEU Chi-restraints excluded: chain X residue 265 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 10.0000 chunk 111 optimal weight: 0.3980 chunk 258 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 386 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 316 optimal weight: 0.6980 chunk 128 optimal weight: 7.9990 chunk 272 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 HIS C 314 ASN C 512 ASN C 536 ASN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 GLN X 247 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.187199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.124482 restraints weight = 352359.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.125464 restraints weight = 211068.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.125016 restraints weight = 189258.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.124877 restraints weight = 186526.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.124936 restraints weight = 178185.433| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33437 Z= 0.125 Angle : 0.497 8.255 45678 Z= 0.261 Chirality : 0.040 0.160 5212 Planarity : 0.004 0.051 5715 Dihedral : 13.653 173.943 5345 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.90 % Allowed : 9.73 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.14), residues: 3968 helix: 2.13 (0.13), residues: 1590 sheet: 0.41 (0.24), residues: 523 loop : -0.58 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 389 TYR 0.014 0.001 TYR D 248 PHE 0.016 0.001 PHE X 48 TRP 0.009 0.001 TRP C 935 HIS 0.006 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00294 (33429) covalent geometry : angle 0.49398 (45666) hydrogen bonds : bond 0.03907 ( 1497) hydrogen bonds : angle 4.19671 ( 4243) metal coordination : bond 0.00850 ( 8) metal coordination : angle 3.37721 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 340 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.9375 (m) cc_final: 0.9024 (t) REVERT: B 123 MET cc_start: 0.9233 (ttp) cc_final: 0.8961 (ttm) REVERT: B 188 ASP cc_start: 0.8590 (p0) cc_final: 0.8366 (p0) REVERT: C 116 LYS cc_start: 0.8504 (mttm) cc_final: 0.8155 (tptp) REVERT: C 145 MET cc_start: 0.8861 (mmt) cc_final: 0.8196 (mmt) REVERT: C 209 LYS cc_start: 0.7911 (mtmm) cc_final: 0.7689 (mtmm) REVERT: C 343 GLN cc_start: 0.8686 (mt0) cc_final: 0.7913 (tt0) REVERT: C 420 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7336 (tp30) REVERT: C 426 GLN cc_start: 0.8171 (tt0) cc_final: 0.7884 (tm-30) REVERT: C 474 MET cc_start: 0.8945 (ttp) cc_final: 0.8539 (mtp) REVERT: C 478 GLU cc_start: 0.8818 (tt0) cc_final: 0.8599 (tt0) REVERT: C 492 SER cc_start: 0.9684 (m) cc_final: 0.9262 (p) REVERT: C 563 SER cc_start: 0.9005 (p) cc_final: 0.8740 (t) REVERT: C 602 MET cc_start: 0.7926 (mtm) cc_final: 0.7598 (mtt) REVERT: C 637 LYS cc_start: 0.9281 (mtmt) cc_final: 0.9061 (mttp) REVERT: C 652 MET cc_start: 0.8799 (tpt) cc_final: 0.8002 (tpt) REVERT: C 943 VAL cc_start: 0.8884 (t) cc_final: 0.8445 (m) REVERT: D 84 ARG cc_start: 0.8385 (mtt90) cc_final: 0.7901 (mtm-85) REVERT: D 107 PHE cc_start: 0.8903 (t80) cc_final: 0.8631 (t80) REVERT: D 141 ASP cc_start: 0.7524 (p0) cc_final: 0.7060 (t0) REVERT: D 143 MET cc_start: 0.5067 (tpp) cc_final: 0.4756 (ttt) REVERT: D 155 MET cc_start: 0.6655 (mmm) cc_final: 0.6326 (mmm) REVERT: D 250 GLU cc_start: 0.7977 (tp30) cc_final: 0.7602 (tp30) REVERT: D 373 MET cc_start: 0.8300 (mtm) cc_final: 0.7985 (mtt) REVERT: D 509 ILE cc_start: 0.9338 (mt) cc_final: 0.9092 (tt) REVERT: D 541 MET cc_start: 0.8860 (mtt) cc_final: 0.8497 (mtp) REVERT: D 570 SER cc_start: 0.9471 (p) cc_final: 0.9046 (t) REVERT: D 634 LYS cc_start: 0.9239 (mttt) cc_final: 0.8818 (mtpp) REVERT: D 803 LYS cc_start: 0.6993 (mmtt) cc_final: 0.6611 (mtmm) REVERT: D 980 ARG cc_start: 0.9043 (ttm-80) cc_final: 0.8778 (ttp80) REVERT: E 66 ASN cc_start: 0.8136 (t0) cc_final: 0.7683 (t0) REVERT: F 156 ASP cc_start: 0.7638 (m-30) cc_final: 0.7282 (t70) REVERT: F 172 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7320 (mt0) REVERT: F 189 LYS cc_start: 0.8512 (mtmt) cc_final: 0.7867 (mtmm) REVERT: F 235 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7242 (mm-30) REVERT: F 261 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8441 (mm-30) REVERT: F 443 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7520 (pt0) REVERT: F 449 MET cc_start: 0.8109 (mmm) cc_final: 0.7743 (mmm) REVERT: Y 188 GLU cc_start: 0.7946 (tt0) cc_final: 0.7549 (tp30) REVERT: Y 272 MET cc_start: 0.5439 (tpp) cc_final: 0.5224 (tpt) REVERT: X 37 ASP cc_start: 0.8099 (m-30) cc_final: 0.6906 (t0) outliers start: 63 outliers final: 43 residues processed: 393 average time/residue: 0.2104 time to fit residues: 135.7088 Evaluate side-chains 356 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 310 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 420 GLU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 674 CYS Chi-restraints excluded: chain C residue 952 GLU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain D residue 792 TYR Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 875 ARG Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1090 ILE Chi-restraints excluded: chain D residue 1253 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 235 GLU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain F residue 443 GLN Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 56 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 361 optimal weight: 4.9990 chunk 308 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 373 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 350 optimal weight: 20.0000 chunk 169 optimal weight: 0.8980 chunk 241 optimal weight: 3.9990 chunk 286 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 536 ASN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 673 ASN ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.186960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.125196 restraints weight = 353039.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.126056 restraints weight = 211912.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.125553 restraints weight = 185296.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.125511 restraints weight = 182086.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.125425 restraints weight = 174175.090| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 33437 Z= 0.123 Angle : 0.483 8.004 45678 Z= 0.253 Chirality : 0.040 0.142 5212 Planarity : 0.004 0.052 5715 Dihedral : 13.663 173.255 5345 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.20 % Allowed : 10.48 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.14), residues: 3968 helix: 2.18 (0.13), residues: 1588 sheet: 0.33 (0.24), residues: 515 loop : -0.59 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1242 TYR 0.015 0.001 TYR D 248 PHE 0.014 0.001 PHE F 417 TRP 0.008 0.001 TRP C 935 HIS 0.007 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00291 (33429) covalent geometry : angle 0.48067 (45666) hydrogen bonds : bond 0.03712 ( 1497) hydrogen bonds : angle 4.06312 ( 4243) metal coordination : bond 0.00740 ( 8) metal coordination : angle 3.08781 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 327 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.9395 (m) cc_final: 0.9001 (t) REVERT: B 123 MET cc_start: 0.9236 (ttp) cc_final: 0.8971 (ttm) REVERT: B 188 ASP cc_start: 0.8529 (p0) cc_final: 0.8266 (p0) REVERT: C 116 LYS cc_start: 0.8495 (mttm) cc_final: 0.8173 (tptp) REVERT: C 343 GLN cc_start: 0.8627 (mt0) cc_final: 0.7849 (tt0) REVERT: C 420 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7451 (tp30) REVERT: C 426 GLN cc_start: 0.8254 (tt0) cc_final: 0.8032 (tm-30) REVERT: C 474 MET cc_start: 0.8968 (ttp) cc_final: 0.8646 (mtp) REVERT: C 478 GLU cc_start: 0.8727 (tt0) cc_final: 0.8517 (tt0) REVERT: C 492 SER cc_start: 0.9696 (OUTLIER) cc_final: 0.9255 (p) REVERT: C 563 SER cc_start: 0.8898 (p) cc_final: 0.8572 (t) REVERT: C 602 MET cc_start: 0.7914 (mtm) cc_final: 0.7574 (mtt) REVERT: C 637 LYS cc_start: 0.9278 (mtmt) cc_final: 0.9066 (mttp) REVERT: C 652 MET cc_start: 0.8817 (tpt) cc_final: 0.8058 (tpt) REVERT: C 755 LEU cc_start: 0.5126 (mp) cc_final: 0.4626 (tt) REVERT: C 895 MET cc_start: 0.9199 (mmm) cc_final: 0.8913 (mmm) REVERT: C 943 VAL cc_start: 0.8901 (t) cc_final: 0.8474 (m) REVERT: D 1 MET cc_start: 0.6856 (ptt) cc_final: 0.6479 (ptp) REVERT: D 84 ARG cc_start: 0.8398 (mtt90) cc_final: 0.7925 (mtm-85) REVERT: D 107 PHE cc_start: 0.8937 (t80) cc_final: 0.8637 (t80) REVERT: D 141 ASP cc_start: 0.7561 (p0) cc_final: 0.7078 (t0) REVERT: D 143 MET cc_start: 0.5426 (tpp) cc_final: 0.5017 (ttt) REVERT: D 250 GLU cc_start: 0.8033 (tp30) cc_final: 0.7755 (tp30) REVERT: D 327 MET cc_start: 0.9385 (tpp) cc_final: 0.9150 (tpt) REVERT: D 339 ASP cc_start: 0.8611 (m-30) cc_final: 0.8229 (m-30) REVERT: D 360 LEU cc_start: 0.8691 (mt) cc_final: 0.8465 (mp) REVERT: D 373 MET cc_start: 0.8276 (mtm) cc_final: 0.7930 (mtt) REVERT: D 509 ILE cc_start: 0.9302 (mt) cc_final: 0.9100 (tt) REVERT: D 541 MET cc_start: 0.8740 (mtt) cc_final: 0.8449 (mtm) REVERT: D 570 SER cc_start: 0.9492 (p) cc_final: 0.9056 (t) REVERT: D 673 ASN cc_start: 0.8655 (m-40) cc_final: 0.7805 (m110) REVERT: D 803 LYS cc_start: 0.7048 (mmtt) cc_final: 0.6663 (mtmm) REVERT: D 938 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8097 (mm-30) REVERT: D 1113 MET cc_start: 0.7936 (mpp) cc_final: 0.7391 (mpp) REVERT: E 66 ASN cc_start: 0.8250 (t0) cc_final: 0.7745 (t0) REVERT: E 99 ASP cc_start: 0.8180 (m-30) cc_final: 0.7941 (m-30) REVERT: F 156 ASP cc_start: 0.7475 (m-30) cc_final: 0.7185 (t70) REVERT: F 172 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7325 (mt0) REVERT: F 189 LYS cc_start: 0.8473 (mtmt) cc_final: 0.7823 (mtmm) REVERT: F 261 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8394 (mm-30) REVERT: Y 49 MET cc_start: 0.7548 (mtt) cc_final: 0.7316 (mtt) REVERT: X 37 ASP cc_start: 0.8031 (m-30) cc_final: 0.6891 (t0) outliers start: 73 outliers final: 57 residues processed: 385 average time/residue: 0.2100 time to fit residues: 133.3242 Evaluate side-chains 372 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 313 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 420 GLU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 492 SER Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 674 CYS Chi-restraints excluded: chain C residue 910 THR Chi-restraints excluded: chain C residue 952 GLU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain D residue 792 TYR Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 957 THR Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1090 ILE Chi-restraints excluded: chain D residue 1150 ILE Chi-restraints excluded: chain D residue 1253 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 56 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 51 optimal weight: 0.2980 chunk 181 optimal weight: 5.9990 chunk 222 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 312 optimal weight: 4.9990 chunk 327 optimal weight: 0.0060 chunk 104 optimal weight: 2.9990 chunk 282 optimal weight: 0.0670 chunk 244 optimal weight: 1.9990 chunk 226 optimal weight: 0.5980 chunk 266 optimal weight: 0.6980 overall best weight: 0.3334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.189736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.127178 restraints weight = 348183.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.128284 restraints weight = 205407.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.127653 restraints weight = 183339.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.127861 restraints weight = 180851.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.127709 restraints weight = 170269.809| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 33437 Z= 0.095 Angle : 0.458 8.501 45678 Z= 0.240 Chirality : 0.039 0.170 5212 Planarity : 0.004 0.053 5715 Dihedral : 13.600 173.431 5345 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.05 % Allowed : 11.35 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1.13 (0.14), residues: 3968 helix: 2.30 (0.13), residues: 1591 sheet: 0.43 (0.24), residues: 508 loop : -0.53 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 389 TYR 0.016 0.001 TYR C1020 PHE 0.011 0.001 PHE C 897 TRP 0.016 0.001 TRP X 292 HIS 0.003 0.001 HIS D 853 Details of bonding type rmsd covalent geometry : bond 0.00210 (33429) covalent geometry : angle 0.45591 (45666) hydrogen bonds : bond 0.03198 ( 1497) hydrogen bonds : angle 3.92631 ( 4243) metal coordination : bond 0.00438 ( 8) metal coordination : angle 2.49434 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 320 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.9335 (m) cc_final: 0.8981 (t) REVERT: A 215 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8106 (mm) REVERT: B 188 ASP cc_start: 0.8485 (p0) cc_final: 0.8227 (p0) REVERT: C 84 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6841 (tt) REVERT: C 112 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7609 (tm-30) REVERT: C 116 LYS cc_start: 0.8406 (mttm) cc_final: 0.7962 (tptp) REVERT: C 145 MET cc_start: 0.8695 (mmt) cc_final: 0.8037 (mmt) REVERT: C 343 GLN cc_start: 0.8677 (mt0) cc_final: 0.7757 (tt0) REVERT: C 420 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7811 (tp30) REVERT: C 474 MET cc_start: 0.8865 (ttp) cc_final: 0.8568 (mtp) REVERT: C 478 GLU cc_start: 0.8726 (tt0) cc_final: 0.8515 (tt0) REVERT: C 602 MET cc_start: 0.7746 (mtm) cc_final: 0.7406 (mtt) REVERT: C 652 MET cc_start: 0.8687 (tpt) cc_final: 0.7915 (tpt) REVERT: C 755 LEU cc_start: 0.5430 (mp) cc_final: 0.4836 (tt) REVERT: C 895 MET cc_start: 0.9212 (mmm) cc_final: 0.8911 (mmm) REVERT: C 943 VAL cc_start: 0.8974 (t) cc_final: 0.8525 (m) REVERT: D 1 MET cc_start: 0.7096 (ptt) cc_final: 0.6729 (ptp) REVERT: D 84 ARG cc_start: 0.8350 (mtt90) cc_final: 0.7895 (mtm-85) REVERT: D 107 PHE cc_start: 0.8844 (t80) cc_final: 0.8530 (t80) REVERT: D 141 ASP cc_start: 0.7733 (p0) cc_final: 0.7171 (t0) REVERT: D 143 MET cc_start: 0.5153 (tpp) cc_final: 0.4796 (ttt) REVERT: D 250 GLU cc_start: 0.8162 (tp30) cc_final: 0.7829 (tp30) REVERT: D 327 MET cc_start: 0.9353 (tpp) cc_final: 0.9130 (tpt) REVERT: D 360 LEU cc_start: 0.8597 (mt) cc_final: 0.8331 (mp) REVERT: D 509 ILE cc_start: 0.9267 (mt) cc_final: 0.9036 (tt) REVERT: D 541 MET cc_start: 0.8753 (mtt) cc_final: 0.8474 (mtm) REVERT: D 570 SER cc_start: 0.9477 (p) cc_final: 0.8957 (t) REVERT: D 803 LYS cc_start: 0.7157 (mmtt) cc_final: 0.6761 (mtmm) REVERT: D 938 GLU cc_start: 0.8492 (mm-30) cc_final: 0.7952 (mm-30) REVERT: D 1113 MET cc_start: 0.8107 (mpp) cc_final: 0.7696 (mpp) REVERT: E 63 ASP cc_start: 0.7655 (m-30) cc_final: 0.7292 (m-30) REVERT: E 66 ASN cc_start: 0.8272 (t0) cc_final: 0.7708 (t0) REVERT: E 99 ASP cc_start: 0.8183 (m-30) cc_final: 0.7957 (m-30) REVERT: F 156 ASP cc_start: 0.7413 (m-30) cc_final: 0.7141 (t70) REVERT: F 172 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7512 (mt0) REVERT: F 445 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7353 (tt0) REVERT: X 37 ASP cc_start: 0.8119 (m-30) cc_final: 0.7012 (t0) outliers start: 68 outliers final: 50 residues processed: 377 average time/residue: 0.2045 time to fit residues: 129.6473 Evaluate side-chains 351 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 298 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 420 GLU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 910 THR Chi-restraints excluded: chain C residue 952 GLU Chi-restraints excluded: chain C residue 1078 GLU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain D residue 792 TYR Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 1007 THR Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1090 ILE Chi-restraints excluded: chain D residue 1211 ILE Chi-restraints excluded: chain D residue 1253 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 56 SER Chi-restraints excluded: chain Y residue 145 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 133 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 280 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 368 optimal weight: 20.0000 chunk 204 optimal weight: 3.9990 chunk 363 optimal weight: 7.9990 chunk 401 optimal weight: 0.0570 chunk 342 optimal weight: 5.9990 chunk 320 optimal weight: 0.8980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 673 ASN ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 11 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.187626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.125572 restraints weight = 352523.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.126414 restraints weight = 208557.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.126062 restraints weight = 188492.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.126127 restraints weight = 182584.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.125965 restraints weight = 179109.998| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 33437 Z= 0.116 Angle : 0.474 9.733 45678 Z= 0.247 Chirality : 0.040 0.183 5212 Planarity : 0.004 0.056 5715 Dihedral : 13.607 172.540 5344 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.53 % Allowed : 11.20 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1.11 (0.14), residues: 3968 helix: 2.28 (0.13), residues: 1589 sheet: 0.45 (0.24), residues: 520 loop : -0.55 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 389 TYR 0.016 0.001 TYR D 248 PHE 0.015 0.001 PHE D 226 TRP 0.009 0.001 TRP X 292 HIS 0.006 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00275 (33429) covalent geometry : angle 0.47174 (45666) hydrogen bonds : bond 0.03425 ( 1497) hydrogen bonds : angle 3.91303 ( 4243) metal coordination : bond 0.00653 ( 8) metal coordination : angle 2.69636 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 315 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.9358 (m) cc_final: 0.8979 (t) REVERT: B 188 ASP cc_start: 0.8527 (p0) cc_final: 0.8277 (p0) REVERT: C 84 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6888 (tt) REVERT: C 112 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7589 (tm-30) REVERT: C 116 LYS cc_start: 0.8405 (mttm) cc_final: 0.7967 (tptp) REVERT: C 145 MET cc_start: 0.8758 (mmt) cc_final: 0.8117 (mmt) REVERT: C 343 GLN cc_start: 0.8693 (mt0) cc_final: 0.7780 (tt0) REVERT: C 474 MET cc_start: 0.8864 (ttp) cc_final: 0.8560 (mtp) REVERT: C 478 GLU cc_start: 0.8716 (tt0) cc_final: 0.8494 (tt0) REVERT: C 602 MET cc_start: 0.7748 (mtm) cc_final: 0.7404 (mtt) REVERT: C 652 MET cc_start: 0.8706 (tpt) cc_final: 0.7970 (tpt) REVERT: C 755 LEU cc_start: 0.5329 (mp) cc_final: 0.4626 (tt) REVERT: C 895 MET cc_start: 0.9138 (mmm) cc_final: 0.8786 (mmm) REVERT: C 943 VAL cc_start: 0.8995 (t) cc_final: 0.8551 (m) REVERT: D 84 ARG cc_start: 0.8349 (mtt90) cc_final: 0.7883 (mtm-85) REVERT: D 107 PHE cc_start: 0.8864 (t80) cc_final: 0.8557 (t80) REVERT: D 141 ASP cc_start: 0.7710 (p0) cc_final: 0.7168 (t0) REVERT: D 143 MET cc_start: 0.5081 (tpp) cc_final: 0.4728 (ttt) REVERT: D 250 GLU cc_start: 0.8100 (tp30) cc_final: 0.7832 (tp30) REVERT: D 327 MET cc_start: 0.9332 (tpp) cc_final: 0.9066 (tpt) REVERT: D 339 ASP cc_start: 0.8568 (m-30) cc_final: 0.8133 (m-30) REVERT: D 360 LEU cc_start: 0.8607 (mt) cc_final: 0.8354 (mp) REVERT: D 509 ILE cc_start: 0.9302 (mt) cc_final: 0.9065 (tt) REVERT: D 541 MET cc_start: 0.8848 (mtt) cc_final: 0.8573 (mtm) REVERT: D 570 SER cc_start: 0.9418 (p) cc_final: 0.8876 (t) REVERT: D 740 GLN cc_start: 0.6398 (OUTLIER) cc_final: 0.5633 (pt0) REVERT: D 803 LYS cc_start: 0.6970 (mmtt) cc_final: 0.6600 (mtmm) REVERT: D 938 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8001 (mm-30) REVERT: D 1113 MET cc_start: 0.8080 (mpp) cc_final: 0.7723 (mpp) REVERT: E 63 ASP cc_start: 0.7748 (m-30) cc_final: 0.7345 (m-30) REVERT: E 66 ASN cc_start: 0.8324 (t0) cc_final: 0.7731 (t0) REVERT: E 99 ASP cc_start: 0.8193 (m-30) cc_final: 0.7979 (m-30) REVERT: F 156 ASP cc_start: 0.7404 (m-30) cc_final: 0.7184 (t70) REVERT: F 172 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7516 (mt0) REVERT: F 261 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8422 (mm-30) REVERT: X 37 ASP cc_start: 0.8187 (m-30) cc_final: 0.7104 (t0) outliers start: 84 outliers final: 65 residues processed: 383 average time/residue: 0.1917 time to fit residues: 124.2362 Evaluate side-chains 372 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 305 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 674 CYS Chi-restraints excluded: chain C residue 910 THR Chi-restraints excluded: chain C residue 1078 GLU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain D residue 740 GLN Chi-restraints excluded: chain D residue 792 TYR Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 957 THR Chi-restraints excluded: chain D residue 1007 THR Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1090 ILE Chi-restraints excluded: chain D residue 1150 ILE Chi-restraints excluded: chain D residue 1211 ILE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 56 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 0 optimal weight: 3.9990 chunk 313 optimal weight: 4.9990 chunk 252 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 373 optimal weight: 3.9990 chunk 166 optimal weight: 0.7980 chunk 360 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 97 optimal weight: 0.0270 chunk 290 optimal weight: 0.9980 overall best weight: 1.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 314 ASN ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.184981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.121249 restraints weight = 359593.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.122197 restraints weight = 212527.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.121789 restraints weight = 193181.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.121732 restraints weight = 187546.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.121639 restraints weight = 181170.418| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33437 Z= 0.176 Angle : 0.537 9.300 45678 Z= 0.281 Chirality : 0.042 0.283 5212 Planarity : 0.004 0.061 5715 Dihedral : 13.737 171.095 5344 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.53 % Allowed : 11.68 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.82 (0.14), residues: 3968 helix: 2.04 (0.13), residues: 1586 sheet: 0.27 (0.23), residues: 522 loop : -0.69 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 389 TYR 0.017 0.001 TYR C1020 PHE 0.020 0.002 PHE D 512 TRP 0.012 0.001 TRP X 105 HIS 0.011 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00436 (33429) covalent geometry : angle 0.53474 (45666) hydrogen bonds : bond 0.04303 ( 1497) hydrogen bonds : angle 4.08751 ( 4243) metal coordination : bond 0.01072 ( 8) metal coordination : angle 3.38798 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 315 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.9462 (m) cc_final: 0.9048 (t) REVERT: B 122 ASP cc_start: 0.8354 (p0) cc_final: 0.8148 (p0) REVERT: B 188 ASP cc_start: 0.8574 (p0) cc_final: 0.8298 (p0) REVERT: C 84 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6544 (tt) REVERT: C 112 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7666 (tm-30) REVERT: C 116 LYS cc_start: 0.8557 (mttm) cc_final: 0.8145 (tptp) REVERT: C 150 MET cc_start: 0.8315 (mmm) cc_final: 0.7359 (mtt) REVERT: C 343 GLN cc_start: 0.8765 (mt0) cc_final: 0.7859 (tt0) REVERT: C 420 GLU cc_start: 0.7974 (tp30) cc_final: 0.7260 (tp30) REVERT: C 474 MET cc_start: 0.9023 (ttp) cc_final: 0.8739 (mtp) REVERT: C 478 GLU cc_start: 0.8831 (tt0) cc_final: 0.8558 (tt0) REVERT: C 492 SER cc_start: 0.9696 (m) cc_final: 0.9250 (p) REVERT: C 563 SER cc_start: 0.8749 (p) cc_final: 0.8424 (t) REVERT: C 602 MET cc_start: 0.7839 (mtm) cc_final: 0.7504 (mtt) REVERT: C 652 MET cc_start: 0.8686 (tpt) cc_final: 0.8266 (tpt) REVERT: C 755 LEU cc_start: 0.4882 (mp) cc_final: 0.4467 (tt) REVERT: C 943 VAL cc_start: 0.8866 (t) cc_final: 0.8440 (m) REVERT: D 1 MET cc_start: 0.6965 (ptt) cc_final: 0.5721 (tpt) REVERT: D 84 ARG cc_start: 0.8405 (mtt90) cc_final: 0.7851 (mtm-85) REVERT: D 141 ASP cc_start: 0.7668 (p0) cc_final: 0.7262 (t0) REVERT: D 143 MET cc_start: 0.5446 (tpp) cc_final: 0.5123 (ttt) REVERT: D 250 GLU cc_start: 0.8129 (tp30) cc_final: 0.7839 (tp30) REVERT: D 327 MET cc_start: 0.9408 (tpp) cc_final: 0.9106 (tpt) REVERT: D 339 ASP cc_start: 0.8568 (m-30) cc_final: 0.8203 (m-30) REVERT: D 360 LEU cc_start: 0.8650 (mt) cc_final: 0.8407 (mp) REVERT: D 509 ILE cc_start: 0.9309 (mt) cc_final: 0.9075 (tt) REVERT: D 541 MET cc_start: 0.8813 (mtt) cc_final: 0.8480 (mtm) REVERT: D 570 SER cc_start: 0.9429 (p) cc_final: 0.8888 (t) REVERT: D 740 GLN cc_start: 0.6440 (OUTLIER) cc_final: 0.5726 (pt0) REVERT: D 803 LYS cc_start: 0.7044 (mmtt) cc_final: 0.6641 (mtmm) REVERT: D 938 GLU cc_start: 0.8485 (mm-30) cc_final: 0.7920 (mm-30) REVERT: D 956 ILE cc_start: 0.8861 (mt) cc_final: 0.8590 (tp) REVERT: D 1113 MET cc_start: 0.8009 (mpp) cc_final: 0.7681 (mpp) REVERT: E 66 ASN cc_start: 0.8377 (t0) cc_final: 0.7754 (t0) REVERT: E 99 ASP cc_start: 0.8352 (m-30) cc_final: 0.8066 (m-30) REVERT: F 156 ASP cc_start: 0.7491 (m-30) cc_final: 0.7238 (t70) REVERT: F 172 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7530 (mt0) REVERT: X 37 ASP cc_start: 0.7995 (m-30) cc_final: 0.6922 (t0) REVERT: X 156 LEU cc_start: 0.9254 (mp) cc_final: 0.9044 (mp) outliers start: 84 outliers final: 66 residues processed: 384 average time/residue: 0.2000 time to fit residues: 128.5350 Evaluate side-chains 376 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 308 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 674 CYS Chi-restraints excluded: chain C residue 910 THR Chi-restraints excluded: chain C residue 1078 GLU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 740 GLN Chi-restraints excluded: chain D residue 792 TYR Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 875 ARG Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 957 THR Chi-restraints excluded: chain D residue 1007 THR Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1090 ILE Chi-restraints excluded: chain D residue 1150 ILE Chi-restraints excluded: chain D residue 1211 ILE Chi-restraints excluded: chain D residue 1253 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain Y residue 56 SER Chi-restraints excluded: chain X residue 110 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 113 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 278 optimal weight: 0.8980 chunk 229 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 163 optimal weight: 0.8980 chunk 260 optimal weight: 7.9990 chunk 250 optimal weight: 0.0020 chunk 55 optimal weight: 0.9980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.186237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.124146 restraints weight = 350118.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.124947 restraints weight = 207764.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.124396 restraints weight = 188646.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.124435 restraints weight = 183789.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.124289 restraints weight = 178476.043| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 33437 Z= 0.112 Angle : 0.480 8.862 45678 Z= 0.251 Chirality : 0.040 0.262 5212 Planarity : 0.004 0.059 5715 Dihedral : 13.659 172.399 5343 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.20 % Allowed : 12.10 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.14), residues: 3968 helix: 2.20 (0.13), residues: 1587 sheet: 0.37 (0.24), residues: 524 loop : -0.64 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG C 821 TYR 0.019 0.001 TYR D 248 PHE 0.015 0.001 PHE D 226 TRP 0.019 0.001 TRP X 195 HIS 0.006 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00260 (33429) covalent geometry : angle 0.47810 (45666) hydrogen bonds : bond 0.03495 ( 1497) hydrogen bonds : angle 3.93363 ( 4243) metal coordination : bond 0.00608 ( 8) metal coordination : angle 2.70807 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 307 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.9382 (m) cc_final: 0.8999 (t) REVERT: B 122 ASP cc_start: 0.8215 (p0) cc_final: 0.7947 (p0) REVERT: B 188 ASP cc_start: 0.8524 (p0) cc_final: 0.8307 (p0) REVERT: C 84 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6870 (tt) REVERT: C 112 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7642 (tm-30) REVERT: C 116 LYS cc_start: 0.8473 (mttm) cc_final: 0.8005 (tptp) REVERT: C 420 GLU cc_start: 0.7876 (tp30) cc_final: 0.7116 (tp30) REVERT: C 474 MET cc_start: 0.8925 (ttp) cc_final: 0.8659 (mtp) REVERT: C 478 GLU cc_start: 0.8749 (tt0) cc_final: 0.8476 (tt0) REVERT: C 602 MET cc_start: 0.7867 (mtm) cc_final: 0.7549 (mtt) REVERT: C 652 MET cc_start: 0.8688 (tpt) cc_final: 0.8233 (tpt) REVERT: C 755 LEU cc_start: 0.4759 (mp) cc_final: 0.4430 (tt) REVERT: C 943 VAL cc_start: 0.8899 (t) cc_final: 0.8545 (m) REVERT: D 1 MET cc_start: 0.6945 (ptt) cc_final: 0.5796 (tpt) REVERT: D 84 ARG cc_start: 0.8382 (mtt90) cc_final: 0.7863 (mtm-85) REVERT: D 141 ASP cc_start: 0.7665 (p0) cc_final: 0.7209 (t0) REVERT: D 143 MET cc_start: 0.5406 (tpp) cc_final: 0.5087 (ttt) REVERT: D 327 MET cc_start: 0.9332 (tpp) cc_final: 0.9059 (tpt) REVERT: D 339 ASP cc_start: 0.8710 (m-30) cc_final: 0.8336 (m-30) REVERT: D 360 LEU cc_start: 0.8568 (mt) cc_final: 0.8286 (mp) REVERT: D 509 ILE cc_start: 0.9273 (mt) cc_final: 0.9059 (tt) REVERT: D 541 MET cc_start: 0.8773 (mtt) cc_final: 0.8471 (mtm) REVERT: D 570 SER cc_start: 0.9419 (p) cc_final: 0.8864 (t) REVERT: D 740 GLN cc_start: 0.6472 (OUTLIER) cc_final: 0.5704 (pt0) REVERT: D 803 LYS cc_start: 0.7067 (mmtt) cc_final: 0.6661 (mtmm) REVERT: D 938 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8210 (mm-30) REVERT: D 956 ILE cc_start: 0.8929 (mt) cc_final: 0.8611 (tp) REVERT: D 1113 MET cc_start: 0.8026 (mpp) cc_final: 0.7709 (mpp) REVERT: D 1251 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7819 (mt-10) REVERT: E 66 ASN cc_start: 0.8327 (t0) cc_final: 0.7625 (t0) REVERT: E 99 ASP cc_start: 0.8228 (m-30) cc_final: 0.8021 (m-30) REVERT: F 156 ASP cc_start: 0.7432 (m-30) cc_final: 0.7197 (t70) REVERT: F 172 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7513 (mt0) REVERT: F 261 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8061 (mm-30) REVERT: X 37 ASP cc_start: 0.7918 (m-30) cc_final: 0.6855 (t0) REVERT: X 156 LEU cc_start: 0.9279 (mp) cc_final: 0.9076 (mp) outliers start: 73 outliers final: 61 residues processed: 369 average time/residue: 0.1935 time to fit residues: 119.9456 Evaluate side-chains 364 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 300 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 674 CYS Chi-restraints excluded: chain C residue 910 THR Chi-restraints excluded: chain C residue 1078 GLU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 740 GLN Chi-restraints excluded: chain D residue 792 TYR Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 875 ARG Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 957 THR Chi-restraints excluded: chain D residue 1007 THR Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1090 ILE Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1150 ILE Chi-restraints excluded: chain D residue 1211 ILE Chi-restraints excluded: chain D residue 1251 GLU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain Y residue 56 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 154 optimal weight: 1.9990 chunk 282 optimal weight: 0.6980 chunk 149 optimal weight: 0.8980 chunk 361 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 280 optimal weight: 1.9990 chunk 170 optimal weight: 0.0980 chunk 276 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 308 optimal weight: 1.9990 chunk 300 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 ASN ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.184992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.123158 restraints weight = 352857.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.124234 restraints weight = 207117.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.123571 restraints weight = 186613.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.123494 restraints weight = 182220.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.123372 restraints weight = 176259.426| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33437 Z= 0.131 Angle : 0.499 9.885 45678 Z= 0.261 Chirality : 0.041 0.254 5212 Planarity : 0.004 0.089 5715 Dihedral : 13.664 172.014 5343 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.26 % Allowed : 12.41 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.92 (0.14), residues: 3968 helix: 2.16 (0.13), residues: 1587 sheet: 0.34 (0.23), residues: 529 loop : -0.68 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 821 TYR 0.026 0.001 TYR Y 255 PHE 0.022 0.002 PHE D 226 TRP 0.009 0.001 TRP C 935 HIS 0.007 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00314 (33429) covalent geometry : angle 0.49739 (45666) hydrogen bonds : bond 0.03687 ( 1497) hydrogen bonds : angle 3.94868 ( 4243) metal coordination : bond 0.00748 ( 8) metal coordination : angle 2.81026 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 311 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.9390 (m) cc_final: 0.9043 (t) REVERT: B 122 ASP cc_start: 0.8283 (p0) cc_final: 0.8048 (p0) REVERT: B 188 ASP cc_start: 0.8491 (p0) cc_final: 0.8231 (p0) REVERT: C 84 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6939 (tt) REVERT: C 112 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7657 (tm-30) REVERT: C 116 LYS cc_start: 0.8525 (mttm) cc_final: 0.8101 (tptp) REVERT: C 343 GLN cc_start: 0.8816 (mt0) cc_final: 0.7920 (tt0) REVERT: C 420 GLU cc_start: 0.7982 (tp30) cc_final: 0.7460 (tp30) REVERT: C 474 MET cc_start: 0.8997 (ttp) cc_final: 0.8723 (mtp) REVERT: C 478 GLU cc_start: 0.8714 (tt0) cc_final: 0.8465 (tt0) REVERT: C 492 SER cc_start: 0.9699 (OUTLIER) cc_final: 0.9306 (p) REVERT: C 602 MET cc_start: 0.7751 (mtm) cc_final: 0.7444 (mtt) REVERT: C 652 MET cc_start: 0.8678 (tpt) cc_final: 0.8266 (tpt) REVERT: C 755 LEU cc_start: 0.4794 (mp) cc_final: 0.4426 (tt) REVERT: C 943 VAL cc_start: 0.8855 (t) cc_final: 0.8480 (m) REVERT: D 1 MET cc_start: 0.6873 (ptt) cc_final: 0.5740 (tpt) REVERT: D 11 ARG cc_start: 0.8619 (ttp-170) cc_final: 0.8402 (ttp80) REVERT: D 84 ARG cc_start: 0.8357 (mtt90) cc_final: 0.7850 (mtm-85) REVERT: D 141 ASP cc_start: 0.7655 (p0) cc_final: 0.7200 (t0) REVERT: D 143 MET cc_start: 0.5602 (tpp) cc_final: 0.5228 (ttt) REVERT: D 250 GLU cc_start: 0.7988 (tp30) cc_final: 0.7478 (tp30) REVERT: D 339 ASP cc_start: 0.8639 (m-30) cc_final: 0.8280 (m-30) REVERT: D 360 LEU cc_start: 0.8636 (mt) cc_final: 0.8361 (mp) REVERT: D 509 ILE cc_start: 0.9320 (mt) cc_final: 0.9073 (tt) REVERT: D 541 MET cc_start: 0.8851 (mtt) cc_final: 0.8560 (mtm) REVERT: D 570 SER cc_start: 0.9407 (p) cc_final: 0.8851 (t) REVERT: D 740 GLN cc_start: 0.6533 (OUTLIER) cc_final: 0.5791 (pt0) REVERT: D 803 LYS cc_start: 0.7057 (mmtt) cc_final: 0.6704 (mtmm) REVERT: D 938 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8305 (mm-30) REVERT: D 956 ILE cc_start: 0.8957 (mt) cc_final: 0.8628 (tp) REVERT: D 1113 MET cc_start: 0.8095 (mpp) cc_final: 0.7825 (mpp) REVERT: D 1251 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7912 (mt-10) REVERT: E 66 ASN cc_start: 0.8354 (t0) cc_final: 0.7659 (t0) REVERT: F 156 ASP cc_start: 0.7461 (m-30) cc_final: 0.7209 (t70) REVERT: F 172 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7474 (mt0) REVERT: F 186 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7637 (tp30) REVERT: F 261 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8091 (mm-30) REVERT: X 37 ASP cc_start: 0.7922 (m-30) cc_final: 0.6821 (t0) REVERT: X 106 GLN cc_start: 0.8293 (mm110) cc_final: 0.7851 (mm-40) REVERT: X 156 LEU cc_start: 0.9290 (mp) cc_final: 0.9062 (mp) outliers start: 75 outliers final: 68 residues processed: 373 average time/residue: 0.1974 time to fit residues: 123.9971 Evaluate side-chains 374 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 302 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 492 SER Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 674 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 910 THR Chi-restraints excluded: chain C residue 1078 GLU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 740 GLN Chi-restraints excluded: chain D residue 792 TYR Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 875 ARG Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 957 THR Chi-restraints excluded: chain D residue 1007 THR Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1090 ILE Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1150 ILE Chi-restraints excluded: chain D residue 1211 ILE Chi-restraints excluded: chain D residue 1251 GLU Chi-restraints excluded: chain D residue 1253 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain Y residue 56 SER Chi-restraints excluded: chain Y residue 145 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 147 optimal weight: 0.6980 chunk 227 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 305 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 162 optimal weight: 0.6980 chunk 294 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 94 optimal weight: 0.0980 chunk 96 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 329 GLN ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.186797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.124797 restraints weight = 351773.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.125709 restraints weight = 207291.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.125178 restraints weight = 185379.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.125259 restraints weight = 181304.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.125133 restraints weight = 171453.641| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 33437 Z= 0.113 Angle : 0.488 11.409 45678 Z= 0.255 Chirality : 0.040 0.244 5212 Planarity : 0.004 0.063 5715 Dihedral : 13.627 172.280 5343 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.23 % Allowed : 12.56 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1.00 (0.14), residues: 3968 helix: 2.22 (0.13), residues: 1587 sheet: 0.37 (0.24), residues: 525 loop : -0.64 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 56 TYR 0.021 0.001 TYR D 248 PHE 0.020 0.001 PHE D 226 TRP 0.010 0.001 TRP C 935 HIS 0.006 0.001 HIS D 853 Details of bonding type rmsd covalent geometry : bond 0.00267 (33429) covalent geometry : angle 0.48658 (45666) hydrogen bonds : bond 0.03407 ( 1497) hydrogen bonds : angle 3.88481 ( 4243) metal coordination : bond 0.00580 ( 8) metal coordination : angle 2.51650 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 307 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.9400 (m) cc_final: 0.9061 (t) REVERT: A 215 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8038 (mm) REVERT: B 122 ASP cc_start: 0.8326 (p0) cc_final: 0.8119 (p0) REVERT: B 188 ASP cc_start: 0.8527 (p0) cc_final: 0.8258 (p0) REVERT: C 84 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6870 (tt) REVERT: C 112 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7648 (tm-30) REVERT: C 116 LYS cc_start: 0.8486 (mttm) cc_final: 0.8049 (tptp) REVERT: C 420 GLU cc_start: 0.7878 (tp30) cc_final: 0.7387 (tp30) REVERT: C 474 MET cc_start: 0.8919 (ttp) cc_final: 0.8659 (mtp) REVERT: C 478 GLU cc_start: 0.8721 (tt0) cc_final: 0.8488 (tt0) REVERT: C 602 MET cc_start: 0.7774 (mtm) cc_final: 0.7416 (mtt) REVERT: C 652 MET cc_start: 0.8668 (tpt) cc_final: 0.8273 (tpt) REVERT: C 755 LEU cc_start: 0.4795 (mp) cc_final: 0.4469 (tt) REVERT: C 895 MET cc_start: 0.9196 (mmm) cc_final: 0.8952 (mmm) REVERT: C 943 VAL cc_start: 0.8889 (t) cc_final: 0.8537 (m) REVERT: D 1 MET cc_start: 0.6885 (ptt) cc_final: 0.5911 (tpt) REVERT: D 84 ARG cc_start: 0.8323 (mtt90) cc_final: 0.7796 (mtm-85) REVERT: D 141 ASP cc_start: 0.7660 (p0) cc_final: 0.7117 (t0) REVERT: D 143 MET cc_start: 0.5436 (tpp) cc_final: 0.5125 (ttt) REVERT: D 250 GLU cc_start: 0.7946 (tp30) cc_final: 0.7477 (tp30) REVERT: D 327 MET cc_start: 0.9293 (tpp) cc_final: 0.9028 (tpt) REVERT: D 339 ASP cc_start: 0.8602 (m-30) cc_final: 0.8226 (m-30) REVERT: D 541 MET cc_start: 0.8837 (mtt) cc_final: 0.8542 (mtm) REVERT: D 570 SER cc_start: 0.9391 (p) cc_final: 0.8814 (t) REVERT: D 740 GLN cc_start: 0.6521 (OUTLIER) cc_final: 0.5771 (pt0) REVERT: D 803 LYS cc_start: 0.6991 (mmtt) cc_final: 0.6636 (mtmm) REVERT: D 938 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8316 (mm-30) REVERT: D 956 ILE cc_start: 0.8984 (mt) cc_final: 0.8653 (tp) REVERT: D 1113 MET cc_start: 0.8035 (mpp) cc_final: 0.7749 (mpp) REVERT: D 1251 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7888 (mt-10) REVERT: E 66 ASN cc_start: 0.8328 (t0) cc_final: 0.7639 (t0) REVERT: F 156 ASP cc_start: 0.7390 (m-30) cc_final: 0.7170 (t70) REVERT: F 172 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7496 (mt0) REVERT: F 261 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8091 (mm-30) REVERT: F 428 ASP cc_start: 0.7283 (p0) cc_final: 0.6803 (t70) REVERT: X 37 ASP cc_start: 0.8037 (m-30) cc_final: 0.6939 (t0) REVERT: X 52 LYS cc_start: 0.8344 (ttmt) cc_final: 0.8126 (tttt) REVERT: X 106 GLN cc_start: 0.8281 (mm110) cc_final: 0.7811 (mm-40) REVERT: X 156 LEU cc_start: 0.9306 (mp) cc_final: 0.9067 (mp) outliers start: 74 outliers final: 65 residues processed: 368 average time/residue: 0.1967 time to fit residues: 123.1282 Evaluate side-chains 368 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 299 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 492 SER Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 674 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 910 THR Chi-restraints excluded: chain C residue 1078 GLU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 740 GLN Chi-restraints excluded: chain D residue 792 TYR Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 957 THR Chi-restraints excluded: chain D residue 1007 THR Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1090 ILE Chi-restraints excluded: chain D residue 1150 ILE Chi-restraints excluded: chain D residue 1211 ILE Chi-restraints excluded: chain D residue 1251 GLU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain Y residue 56 SER Chi-restraints excluded: chain Y residue 145 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 95 optimal weight: 0.2980 chunk 16 optimal weight: 0.4980 chunk 313 optimal weight: 4.9990 chunk 336 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 243 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 347 optimal weight: 9.9990 chunk 387 optimal weight: 0.0010 chunk 66 optimal weight: 8.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.185629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.123749 restraints weight = 350086.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.124757 restraints weight = 207878.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.124139 restraints weight = 186610.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.124204 restraints weight = 182891.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.124041 restraints weight = 175652.255| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33437 Z= 0.121 Angle : 0.495 12.101 45678 Z= 0.258 Chirality : 0.040 0.234 5212 Planarity : 0.004 0.061 5715 Dihedral : 13.627 171.915 5343 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.14 % Allowed : 12.92 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.97 (0.14), residues: 3968 helix: 2.20 (0.13), residues: 1587 sheet: 0.38 (0.24), residues: 523 loop : -0.66 (0.14), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG C 821 TYR 0.020 0.001 TYR D 248 PHE 0.019 0.001 PHE D 226 TRP 0.014 0.001 TRP Y 250 HIS 0.006 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00289 (33429) covalent geometry : angle 0.49316 (45666) hydrogen bonds : bond 0.03516 ( 1497) hydrogen bonds : angle 3.88871 ( 4243) metal coordination : bond 0.00673 ( 8) metal coordination : angle 2.61228 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5100.59 seconds wall clock time: 89 minutes 11.71 seconds (5351.71 seconds total)