Starting phenix.real_space_refine on Sat Jun 28 06:58:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fne_50591/06_2025/9fne_50591.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fne_50591/06_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_50591/06_2025/9fne_50591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fne_50591/06_2025/9fne_50591.map" model { file = "/net/cci-nas-00/data/ceres_data/9fne_50591/06_2025/9fne_50591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fne_50591/06_2025/9fne_50591.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 21.36, per 1000 atoms: 0.65 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: 8.67 Conformation dependent library (CDL) restraints added in 4.2 seconds 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: 12.63 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: 19.51 Time building geometry restraints manager: 9.89 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: 5.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 1.400 Check model and map are aligned: 0.250 Set scattering table: 0.340 Process input model: 95.690 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.470 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (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 TRP 0.008 0.001 TRP C 929 HIS 0.003 0.001 HIS D 505 PHE 0.009 0.001 PHE C 897 TYR 0.008 0.001 TYR C 335 ARG 0.002 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.15468 ( 1497) hydrogen bonds : angle 5.49610 ( 4243) metal coordination : bond 0.00436 ( 8) metal coordination : angle 2.20436 ( 12) covalent geometry : bond 0.00200 (33429) covalent geometry : angle 0.41677 (45666) *********************** 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 : 3.448 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: 0.5042 time to fit residues: 475.3925 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 : 3.269 ------------------------------------------------------------------------------- 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 339 optimal weight: 0.9980 chunk 304 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 205 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 315 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 234 optimal weight: 20.0000 chunk 365 optimal weight: 9.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 247 GLN ** 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 = 0.3986 r_free = 0.3986 target = 0.188923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.125292 restraints weight = 353464.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.126074 restraints weight = 213290.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.125619 restraints weight = 192283.585| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33437 Z= 0.166 Angle : 0.548 8.472 45678 Z= 0.286 Chirality : 0.042 0.215 5212 Planarity : 0.004 0.055 5715 Dihedral : 13.555 174.183 5347 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.17 % Allowed : 7.89 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.14), residues: 3968 helix: 2.25 (0.13), residues: 1589 sheet: 0.66 (0.24), residues: 541 loop : -0.45 (0.15), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D1221 HIS 0.017 0.001 HIS X 325 PHE 0.022 0.002 PHE D 226 TYR 0.028 0.001 TYR X 302 ARG 0.006 0.000 ARG C 778 Details of bonding type rmsd hydrogen bonds : bond 0.04296 ( 1497) hydrogen bonds : angle 4.39126 ( 4243) metal coordination : bond 0.01152 ( 8) metal coordination : angle 4.16752 ( 12) covalent geometry : bond 0.00405 (33429) covalent geometry : angle 0.54405 (45666) *********************** 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 433 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 361 time to evaluate : 4.232 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 45 SER cc_start: 0.9402 (m) cc_final: 0.8950 (t) REVERT: A 151 GLN cc_start: 0.6156 (pm20) cc_final: 0.5900 (mm-40) REVERT: B 123 MET cc_start: 0.9182 (ttp) cc_final: 0.8879 (ttm) REVERT: C 116 LYS cc_start: 0.8530 (mttm) cc_final: 0.8113 (tptp) REVERT: C 209 LYS cc_start: 0.7914 (mtmm) cc_final: 0.7516 (mtmm) REVERT: C 343 GLN cc_start: 0.8595 (mt0) cc_final: 0.7888 (tt0) REVERT: C 426 GLN cc_start: 0.8161 (tt0) cc_final: 0.7897 (tm-30) REVERT: C 474 MET cc_start: 0.8955 (ttp) cc_final: 0.8527 (mtp) REVERT: C 478 GLU cc_start: 0.8735 (tt0) cc_final: 0.8525 (tt0) REVERT: C 492 SER cc_start: 0.9650 (OUTLIER) cc_final: 0.9172 (p) REVERT: C 566 GLN cc_start: 0.8349 (tp40) cc_final: 0.7724 (tt0) REVERT: C 584 MET cc_start: 0.9042 (mtm) cc_final: 0.8754 (mtm) REVERT: C 590 HIS cc_start: 0.9269 (m-70) cc_final: 0.9043 (m-70) REVERT: C 602 MET cc_start: 0.7902 (mtm) cc_final: 0.7505 (mtt) REVERT: C 637 LYS cc_start: 0.9298 (mtmt) cc_final: 0.9043 (mtmm) REVERT: C 643 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7387 (mt-10) REVERT: C 652 MET cc_start: 0.8766 (tpt) cc_final: 0.7964 (tpt) REVERT: C 943 VAL cc_start: 0.8837 (t) cc_final: 0.8384 (m) REVERT: D 1 MET cc_start: 0.6980 (ptt) cc_final: 0.6584 (ptp) REVERT: D 84 ARG cc_start: 0.8271 (mtt90) cc_final: 0.7903 (mtm-85) REVERT: D 107 PHE cc_start: 0.8768 (t80) cc_final: 0.8565 (t80) REVERT: D 141 ASP cc_start: 0.7409 (p0) cc_final: 0.6947 (t0) REVERT: D 143 MET cc_start: 0.5016 (tpp) cc_final: 0.4645 (ttt) REVERT: D 147 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6702 (mp0) REVERT: D 250 GLU cc_start: 0.8044 (tp30) cc_final: 0.7566 (tp30) REVERT: D 373 MET cc_start: 0.8347 (mtm) cc_final: 0.8008 (mtt) REVERT: D 509 ILE cc_start: 0.9299 (mt) cc_final: 0.9076 (tt) REVERT: D 533 ASN cc_start: 0.9129 (t0) cc_final: 0.8918 (t0) REVERT: D 541 MET cc_start: 0.8911 (mtt) cc_final: 0.8537 (mtp) REVERT: D 570 SER cc_start: 0.9516 (p) cc_final: 0.9166 (t) REVERT: D 634 LYS cc_start: 0.9282 (mttt) cc_final: 0.8842 (mtpp) REVERT: D 803 LYS cc_start: 0.7071 (mmtt) cc_final: 0.6621 (mtmm) REVERT: D 980 ARG cc_start: 0.9016 (ttm-80) cc_final: 0.8599 (ttp80) REVERT: D 1011 MET cc_start: 0.6731 (ttp) cc_final: 0.6181 (ptp) REVERT: D 1113 MET cc_start: 0.7848 (mpp) cc_final: 0.7430 (mpp) REVERT: D 1150 ILE cc_start: 0.9088 (mt) cc_final: 0.8859 (tt) REVERT: E 66 ASN cc_start: 0.7881 (t0) cc_final: 0.7504 (t0) REVERT: F 156 ASP cc_start: 0.7638 (m-30) cc_final: 0.7257 (t70) REVERT: F 172 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7304 (mt0) REVERT: F 261 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8512 (mm-30) REVERT: F 336 GLU cc_start: 0.8109 (mp0) cc_final: 0.7813 (mp0) REVERT: F 449 MET cc_start: 0.7974 (mmm) cc_final: 0.7653 (mmm) REVERT: X 37 ASP cc_start: 0.8205 (m-30) cc_final: 0.7013 (t0) REVERT: X 105 TRP cc_start: 0.8442 (m100) cc_final: 0.8115 (m100) REVERT: X 106 GLN cc_start: 0.8486 (mm-40) cc_final: 0.8272 (mm110) outliers start: 72 outliers final: 45 residues processed: 420 average time/residue: 0.4913 time to fit residues: 341.2883 Evaluate side-chains 360 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 313 time to evaluate : 3.524 ------------------------------------------------------------------------------- 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 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 151 MET Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 196 ILE 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 617 VAL 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 644 THR Chi-restraints excluded: chain D residue 792 TYR 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 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 401 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 265 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 202 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 303 optimal weight: 0.9980 chunk 248 optimal weight: 0.0980 chunk 100 optimal weight: 0.5980 chunk 365 optimal weight: 40.0000 chunk 395 optimal weight: 9.9990 chunk 325 optimal weight: 9.9990 chunk 362 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 293 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.187488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.125089 restraints weight = 351734.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.126010 restraints weight = 211881.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.125447 restraints weight = 190335.576| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1998 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= 0.137 Angle : 0.505 13.325 45678 Z= 0.264 Chirality : 0.041 0.172 5212 Planarity : 0.004 0.053 5715 Dihedral : 13.623 173.308 5345 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.02 % Allowed : 9.49 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.14), residues: 3968 helix: 2.21 (0.13), residues: 1589 sheet: 0.45 (0.24), residues: 522 loop : -0.53 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D1221 HIS 0.008 0.001 HIS D 505 PHE 0.015 0.001 PHE D 512 TYR 0.016 0.001 TYR Y 254 ARG 0.005 0.000 ARG D 389 Details of bonding type rmsd hydrogen bonds : bond 0.03948 ( 1497) hydrogen bonds : angle 4.17208 ( 4243) metal coordination : bond 0.00892 ( 8) metal coordination : angle 3.31053 ( 12) covalent geometry : bond 0.00327 (33429) covalent geometry : angle 0.50218 (45666) *********************** 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 409 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 342 time to evaluate : 3.379 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: 0.9366 (m) cc_final: 0.9059 (t) REVERT: A 151 GLN cc_start: 0.6716 (pm20) cc_final: 0.6343 (mm-40) REVERT: B 123 MET cc_start: 0.9210 (ttp) cc_final: 0.8903 (ttm) REVERT: C 116 LYS cc_start: 0.8484 (mttm) cc_final: 0.8094 (tptp) REVERT: C 209 LYS cc_start: 0.7959 (mtmm) cc_final: 0.7724 (mtmm) REVERT: C 343 GLN cc_start: 0.8673 (mt0) cc_final: 0.7871 (tt0) REVERT: C 420 GLU cc_start: 0.7970 (tp30) cc_final: 0.7458 (tp30) REVERT: C 474 MET cc_start: 0.8955 (ttp) cc_final: 0.8550 (mtp) REVERT: C 492 SER cc_start: 0.9672 (OUTLIER) cc_final: 0.9254 (p) REVERT: C 563 SER cc_start: 0.8957 (p) cc_final: 0.8729 (t) REVERT: C 584 MET cc_start: 0.9004 (mtm) cc_final: 0.8802 (mtm) REVERT: C 602 MET cc_start: 0.7870 (mtm) cc_final: 0.7474 (mtt) REVERT: C 637 LYS cc_start: 0.9284 (mtmt) cc_final: 0.8927 (mttm) REVERT: C 652 MET cc_start: 0.8759 (tpt) cc_final: 0.7943 (tpt) REVERT: C 674 CYS cc_start: 0.8859 (t) cc_final: 0.8640 (p) REVERT: C 943 VAL cc_start: 0.8857 (t) cc_final: 0.8416 (m) REVERT: D 1 MET cc_start: 0.6961 (ptt) cc_final: 0.6567 (ptp) REVERT: D 84 ARG cc_start: 0.8322 (mtt90) cc_final: 0.7843 (mtm-85) REVERT: D 107 PHE cc_start: 0.8878 (t80) cc_final: 0.8636 (t80) REVERT: D 141 ASP cc_start: 0.7468 (p0) cc_final: 0.7024 (t0) REVERT: D 143 MET cc_start: 0.5001 (tpp) cc_final: 0.4713 (ttt) REVERT: D 250 GLU cc_start: 0.8026 (tp30) cc_final: 0.7678 (tp30) REVERT: D 373 MET cc_start: 0.8273 (mtm) cc_final: 0.7963 (mtt) REVERT: D 509 ILE cc_start: 0.9304 (mt) cc_final: 0.9072 (tt) REVERT: D 533 ASN cc_start: 0.9032 (t0) cc_final: 0.8832 (t0) REVERT: D 541 MET cc_start: 0.8896 (mtt) cc_final: 0.8558 (mtp) REVERT: D 570 SER cc_start: 0.9475 (p) cc_final: 0.9050 (t) REVERT: D 634 LYS cc_start: 0.9250 (mttt) cc_final: 0.8821 (mtpp) REVERT: D 803 LYS cc_start: 0.7106 (mmtt) cc_final: 0.6736 (mtmm) REVERT: D 938 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8095 (mm-30) REVERT: D 980 ARG cc_start: 0.9018 (ttm-80) cc_final: 0.8741 (ttp80) REVERT: E 66 ASN cc_start: 0.8149 (t0) cc_final: 0.7693 (t0) REVERT: F 156 ASP cc_start: 0.7471 (m-30) cc_final: 0.7185 (t70) REVERT: F 172 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7346 (mt0) REVERT: F 189 LYS cc_start: 0.8502 (mtmt) cc_final: 0.7984 (mtmm) REVERT: F 235 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7225 (mm-30) REVERT: F 336 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7920 (mt-10) REVERT: F 443 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7530 (pt0) REVERT: F 449 MET cc_start: 0.8027 (mmm) cc_final: 0.7678 (mmm) REVERT: Y 71 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7603 (tp30) REVERT: Y 272 MET cc_start: 0.5523 (tpp) cc_final: 0.5319 (tpt) REVERT: X 37 ASP cc_start: 0.8182 (m-30) cc_final: 0.6994 (t0) outliers start: 67 outliers final: 46 residues processed: 397 average time/residue: 0.4167 time to fit residues: 273.9134 Evaluate side-chains 365 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 314 time to evaluate : 3.331 ------------------------------------------------------------------------------- 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 136 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 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 408 LEU 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 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 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 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 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 325 LEU Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 401 VAL 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 Chi-restraints excluded: chain Y residue 60 LEU Chi-restraints excluded: chain Y residue 71 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 361 optimal weight: 0.8980 chunk 274 optimal weight: 2.9990 chunk 189 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 174 optimal weight: 30.0000 chunk 245 optimal weight: 2.9990 chunk 367 optimal weight: 9.9990 chunk 388 optimal weight: 7.9990 chunk 191 optimal weight: 1.9990 chunk 347 optimal weight: 9.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 314 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.186264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.123799 restraints weight = 353742.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.124800 restraints weight = 211680.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.124236 restraints weight = 185319.101| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2241 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= 0.143 Angle : 0.504 10.132 45678 Z= 0.263 Chirality : 0.041 0.212 5212 Planarity : 0.004 0.054 5715 Dihedral : 13.681 172.552 5345 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.38 % Allowed : 10.54 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.14), residues: 3968 helix: 2.15 (0.13), residues: 1590 sheet: 0.31 (0.24), residues: 523 loop : -0.61 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 935 HIS 0.009 0.001 HIS D 505 PHE 0.018 0.001 PHE X 48 TYR 0.014 0.001 TYR D 248 ARG 0.005 0.000 ARG D 389 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 1497) hydrogen bonds : angle 4.10309 ( 4243) metal coordination : bond 0.00854 ( 8) metal coordination : angle 3.18511 ( 12) covalent geometry : bond 0.00347 (33429) covalent geometry : angle 0.50120 (45666) *********************** 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 411 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 332 time to evaluate : 4.136 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: 0.9434 (m) cc_final: 0.9046 (t) REVERT: A 151 GLN cc_start: 0.6265 (pm20) cc_final: 0.5981 (mm-40) REVERT: C 116 LYS cc_start: 0.8495 (mttm) cc_final: 0.8171 (tptp) REVERT: C 145 MET cc_start: 0.8723 (mmt) cc_final: 0.8129 (mmt) REVERT: C 150 MET cc_start: 0.8136 (mmm) cc_final: 0.7187 (mtt) REVERT: C 209 LYS cc_start: 0.7955 (mtmm) cc_final: 0.7736 (mtmm) REVERT: C 343 GLN cc_start: 0.8679 (mt0) cc_final: 0.7874 (tt0) REVERT: C 420 GLU cc_start: 0.8090 (tp30) cc_final: 0.7463 (tp30) REVERT: C 426 GLN cc_start: 0.8319 (tm-30) cc_final: 0.7719 (tm-30) REVERT: C 474 MET cc_start: 0.8992 (ttp) cc_final: 0.8636 (mtp) REVERT: C 492 SER cc_start: 0.9693 (OUTLIER) cc_final: 0.9259 (p) REVERT: C 563 SER cc_start: 0.8903 (p) cc_final: 0.8599 (t) REVERT: C 602 MET cc_start: 0.7988 (mtm) cc_final: 0.7624 (mtt) REVERT: C 637 LYS cc_start: 0.9318 (mtmt) cc_final: 0.9013 (mttp) REVERT: C 652 MET cc_start: 0.8845 (tpt) cc_final: 0.8074 (tpt) REVERT: C 674 CYS cc_start: 0.8992 (t) cc_final: 0.8781 (p) REVERT: C 755 LEU cc_start: 0.5285 (mp) cc_final: 0.4737 (tt) REVERT: C 895 MET cc_start: 0.9188 (mmm) cc_final: 0.8896 (mmm) REVERT: C 943 VAL cc_start: 0.8876 (t) cc_final: 0.8446 (m) REVERT: D 84 ARG cc_start: 0.8394 (mtt90) cc_final: 0.7925 (mtm-85) REVERT: D 107 PHE cc_start: 0.8938 (t80) cc_final: 0.8632 (t80) REVERT: D 141 ASP cc_start: 0.7627 (p0) cc_final: 0.7179 (t0) REVERT: D 143 MET cc_start: 0.5417 (tpp) cc_final: 0.4900 (ttt) REVERT: D 250 GLU cc_start: 0.8112 (tp30) cc_final: 0.7810 (tp30) REVERT: D 339 ASP cc_start: 0.8596 (m-30) cc_final: 0.8251 (m-30) REVERT: D 373 MET cc_start: 0.8335 (mtm) cc_final: 0.7956 (mtt) REVERT: D 509 ILE cc_start: 0.9333 (mt) cc_final: 0.9122 (tt) REVERT: D 541 MET cc_start: 0.8749 (mtt) cc_final: 0.8463 (mtm) REVERT: D 570 SER cc_start: 0.9466 (p) cc_final: 0.9022 (t) REVERT: D 803 LYS cc_start: 0.7110 (mmtt) cc_final: 0.6736 (mtmm) REVERT: D 956 ILE cc_start: 0.8874 (mt) cc_final: 0.8560 (tp) REVERT: D 1113 MET cc_start: 0.7909 (mpp) cc_final: 0.7416 (mpp) REVERT: E 66 ASN cc_start: 0.8304 (t0) cc_final: 0.7788 (t0) REVERT: E 99 ASP cc_start: 0.8224 (m-30) cc_final: 0.8006 (m-30) REVERT: F 156 ASP cc_start: 0.7489 (m-30) cc_final: 0.7196 (t70) REVERT: F 172 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7287 (mt0) REVERT: F 261 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8297 (mm-30) REVERT: F 336 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7868 (mt-10) REVERT: X 37 ASP cc_start: 0.8113 (m-30) cc_final: 0.6957 (t0) outliers start: 79 outliers final: 57 residues processed: 391 average time/residue: 0.5130 time to fit residues: 333.3156 Evaluate side-chains 373 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 314 time to evaluate : 3.441 ------------------------------------------------------------------------------- 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 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 B residue 232 ILE Chi-restraints excluded: chain C residue 58 SER 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 408 LEU 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 910 THR 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 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 1007 THR 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 336 GLU Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 419 LEU 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 Chi-restraints excluded: chain Y residue 145 THR Chi-restraints excluded: chain X residue 30 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 323 optimal weight: 3.9990 chunk 220 optimal weight: 0.0170 chunk 5 optimal weight: 0.0970 chunk 289 optimal weight: 0.1980 chunk 160 optimal weight: 2.9990 chunk 331 optimal weight: 3.9990 chunk 268 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 348 optimal weight: 8.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.189525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.127200 restraints weight = 348474.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.128237 restraints weight = 204714.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.127817 restraints weight = 183139.508| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 33437 Z= 0.100 Angle : 0.463 11.144 45678 Z= 0.242 Chirality : 0.039 0.172 5212 Planarity : 0.004 0.053 5715 Dihedral : 13.612 173.103 5345 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.20 % Allowed : 11.17 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.14), residues: 3968 helix: 2.29 (0.13), residues: 1591 sheet: 0.39 (0.23), residues: 516 loop : -0.57 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP X 292 HIS 0.004 0.001 HIS D 505 PHE 0.011 0.001 PHE D 226 TYR 0.017 0.001 TYR C1020 ARG 0.006 0.000 ARG D 389 Details of bonding type rmsd hydrogen bonds : bond 0.03269 ( 1497) hydrogen bonds : angle 3.91905 ( 4243) metal coordination : bond 0.00518 ( 8) metal coordination : angle 2.54001 ( 12) covalent geometry : bond 0.00228 (33429) covalent geometry : angle 0.46121 (45666) *********************** 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 398 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 325 time to evaluate : 4.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.9381 (m) cc_final: 0.9031 (t) REVERT: A 151 GLN cc_start: 0.6143 (pm20) cc_final: 0.5919 (mm-40) REVERT: B 122 ASP cc_start: 0.8225 (p0) cc_final: 0.7938 (p0) REVERT: C 84 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6841 (tt) REVERT: C 112 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7604 (tm-30) REVERT: C 116 LYS cc_start: 0.8404 (mttm) cc_final: 0.7966 (tptp) REVERT: C 145 MET cc_start: 0.8673 (mmt) cc_final: 0.8015 (mmt) REVERT: C 343 GLN cc_start: 0.8756 (mt0) cc_final: 0.7810 (tt0) REVERT: C 420 GLU cc_start: 0.8047 (tp30) cc_final: 0.7714 (tp30) REVERT: C 426 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7563 (tm-30) REVERT: C 474 MET cc_start: 0.8878 (ttp) cc_final: 0.8585 (mtp) REVERT: C 602 MET cc_start: 0.7756 (mtm) cc_final: 0.7403 (mtt) REVERT: C 637 LYS cc_start: 0.9269 (mtmt) cc_final: 0.8872 (mttm) REVERT: C 652 MET cc_start: 0.8745 (tpt) cc_final: 0.7979 (tpt) REVERT: C 755 LEU cc_start: 0.5497 (mp) cc_final: 0.4856 (tt) REVERT: C 895 MET cc_start: 0.9195 (mmm) cc_final: 0.8890 (mmm) REVERT: C 943 VAL cc_start: 0.8942 (t) cc_final: 0.8503 (m) REVERT: D 84 ARG cc_start: 0.8339 (mtt90) cc_final: 0.7899 (mtm-85) REVERT: D 107 PHE cc_start: 0.8846 (t80) cc_final: 0.8491 (t80) REVERT: D 141 ASP cc_start: 0.7788 (p0) cc_final: 0.7247 (t0) REVERT: D 143 MET cc_start: 0.5109 (tpp) cc_final: 0.4764 (ttt) REVERT: D 250 GLU cc_start: 0.8253 (tp30) cc_final: 0.7900 (tp30) REVERT: D 327 MET cc_start: 0.9304 (tpp) cc_final: 0.9050 (tpt) REVERT: D 373 MET cc_start: 0.8186 (mtm) cc_final: 0.7883 (mtt) REVERT: D 509 ILE cc_start: 0.9255 (mt) cc_final: 0.9040 (tt) REVERT: D 541 MET cc_start: 0.8731 (mtt) cc_final: 0.8443 (mtm) REVERT: D 570 SER cc_start: 0.9469 (p) cc_final: 0.8956 (t) REVERT: D 673 ASN cc_start: 0.8633 (m-40) cc_final: 0.8259 (m110) REVERT: D 803 LYS cc_start: 0.7165 (mmtt) cc_final: 0.6758 (mtmm) REVERT: D 938 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8011 (mm-30) REVERT: D 956 ILE cc_start: 0.8868 (mt) cc_final: 0.8571 (tp) REVERT: D 1113 MET cc_start: 0.8064 (mpp) cc_final: 0.7599 (mpp) REVERT: E 66 ASN cc_start: 0.8362 (t0) cc_final: 0.7775 (t0) REVERT: F 156 ASP cc_start: 0.7426 (m-30) cc_final: 0.7130 (t70) REVERT: F 172 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7525 (mt0) REVERT: Y 55 TYR cc_start: 0.6740 (m-10) cc_final: 0.6312 (m-10) REVERT: Y 71 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7846 (tp30) REVERT: X 37 ASP cc_start: 0.8307 (m-30) cc_final: 0.7216 (t0) REVERT: X 90 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7154 (mp) outliers start: 73 outliers final: 49 residues processed: 387 average time/residue: 0.5245 time to fit residues: 347.7675 Evaluate side-chains 351 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 299 time to evaluate : 3.169 ------------------------------------------------------------------------------- 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 140 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 156 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 408 LEU 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 910 THR 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 644 THR Chi-restraints excluded: chain D residue 792 TYR Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 1090 ILE Chi-restraints excluded: chain D residue 1148 VAL 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 235 GLU Chi-restraints excluded: chain F residue 253 MET 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 24 VAL Chi-restraints excluded: chain Y residue 56 SER Chi-restraints excluded: chain Y residue 71 GLU Chi-restraints excluded: chain X residue 90 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 130 optimal weight: 0.8980 chunk 349 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 228 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 388 optimal weight: 9.9990 chunk 322 optimal weight: 2.9990 chunk 180 optimal weight: 0.3980 chunk 32 optimal weight: 7.9990 chunk 128 optimal weight: 8.9990 chunk 204 optimal weight: 0.6980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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** ** D 853 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 = 0.3931 r_free = 0.3931 target = 0.182835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.120369 restraints weight = 355252.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.121263 restraints weight = 212747.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.120842 restraints weight = 190473.560| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 33437 Z= 0.185 Angle : 0.551 9.731 45678 Z= 0.286 Chirality : 0.043 0.294 5212 Planarity : 0.004 0.059 5715 Dihedral : 13.757 171.038 5345 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.50 % Allowed : 11.68 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.14), residues: 3968 helix: 2.01 (0.13), residues: 1585 sheet: 0.24 (0.23), residues: 527 loop : -0.72 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 195 HIS 0.011 0.001 HIS D 505 PHE 0.021 0.002 PHE D 512 TYR 0.017 0.001 TYR A 168 ARG 0.006 0.000 ARG D 389 Details of bonding type rmsd hydrogen bonds : bond 0.04446 ( 1497) hydrogen bonds : angle 4.10603 ( 4243) metal coordination : bond 0.01113 ( 8) metal coordination : angle 3.48722 ( 12) covalent geometry : bond 0.00461 (33429) covalent geometry : angle 0.54815 (45666) *********************** 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 411 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 328 time to evaluate : 4.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.9488 (m) cc_final: 0.9092 (t) REVERT: B 122 ASP cc_start: 0.8338 (p0) cc_final: 0.8091 (p0) REVERT: C 84 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6549 (tt) REVERT: C 112 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7600 (tm-30) REVERT: C 116 LYS cc_start: 0.8503 (mttm) cc_final: 0.8121 (tptp) REVERT: C 150 MET cc_start: 0.8275 (mmm) cc_final: 0.7307 (mtt) REVERT: C 343 GLN cc_start: 0.8829 (mt0) cc_final: 0.7900 (tt0) REVERT: C 420 GLU cc_start: 0.8088 (tp30) cc_final: 0.7723 (tp30) REVERT: C 426 GLN cc_start: 0.8408 (tm-30) cc_final: 0.7707 (tm-30) REVERT: C 474 MET cc_start: 0.8911 (ttp) cc_final: 0.8596 (mtp) REVERT: C 492 SER cc_start: 0.9717 (m) cc_final: 0.9313 (p) REVERT: C 563 SER cc_start: 0.8708 (p) cc_final: 0.8409 (t) REVERT: C 602 MET cc_start: 0.7810 (mtm) cc_final: 0.7480 (mtt) REVERT: C 637 LYS cc_start: 0.9350 (mtmt) cc_final: 0.9031 (mttp) REVERT: C 652 MET cc_start: 0.8602 (tpt) cc_final: 0.7873 (tpt) REVERT: C 755 LEU cc_start: 0.5085 (mp) cc_final: 0.4578 (tt) REVERT: C 943 VAL cc_start: 0.8960 (t) cc_final: 0.8506 (m) REVERT: D 84 ARG cc_start: 0.8418 (mtt90) cc_final: 0.7906 (mtm-85) REVERT: D 141 ASP cc_start: 0.7696 (p0) cc_final: 0.7235 (t0) REVERT: D 143 MET cc_start: 0.5340 (tpp) cc_final: 0.4949 (ttt) REVERT: D 250 GLU cc_start: 0.8169 (tp30) cc_final: 0.7896 (tp30) REVERT: D 360 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8241 (mp) REVERT: D 509 ILE cc_start: 0.9356 (mt) cc_final: 0.9083 (tt) REVERT: D 530 GLU cc_start: 0.8285 (tp30) cc_final: 0.8067 (tp30) REVERT: D 541 MET cc_start: 0.8845 (mtt) cc_final: 0.8579 (mtm) REVERT: D 570 SER cc_start: 0.9487 (p) cc_final: 0.8967 (t) REVERT: D 740 GLN cc_start: 0.6621 (OUTLIER) cc_final: 0.5844 (pt0) REVERT: D 803 LYS cc_start: 0.7011 (mmtt) cc_final: 0.6621 (mtmm) REVERT: D 938 GLU cc_start: 0.8530 (mm-30) cc_final: 0.7963 (mm-30) REVERT: D 956 ILE cc_start: 0.8870 (mt) cc_final: 0.8600 (tp) REVERT: D 1113 MET cc_start: 0.8149 (mpp) cc_final: 0.7802 (mpp) REVERT: E 66 ASN cc_start: 0.8363 (t0) cc_final: 0.7770 (t0) REVERT: F 172 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7477 (mt0) REVERT: F 219 MET cc_start: 0.6739 (mmt) cc_final: 0.6484 (mmp) REVERT: F 445 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7256 (tt0) REVERT: Y 71 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7873 (tp30) REVERT: X 37 ASP cc_start: 0.8169 (m-30) cc_final: 0.7065 (t0) REVERT: X 156 LEU cc_start: 0.9281 (mm) cc_final: 0.9064 (mp) outliers start: 83 outliers final: 61 residues processed: 396 average time/residue: 0.4235 time to fit residues: 282.2171 Evaluate side-chains 377 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 312 time to evaluate : 3.382 ------------------------------------------------------------------------------- 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 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 910 THR 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 360 LEU 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 915 VAL Chi-restraints excluded: chain D residue 1007 THR 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 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 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 Chi-restraints excluded: chain Y residue 71 GLU Chi-restraints excluded: chain X residue 30 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 374 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 221 optimal weight: 0.7980 chunk 284 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 chunk 327 optimal weight: 0.0010 chunk 217 optimal weight: 0.8980 chunk 387 optimal weight: 9.9990 chunk 242 optimal weight: 0.7980 chunk 236 optimal weight: 0.9990 chunk 178 optimal weight: 9.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.186364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.124083 restraints weight = 354606.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.125072 restraints weight = 209044.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.124532 restraints weight = 187059.878| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33437 Z= 0.114 Angle : 0.487 9.180 45678 Z= 0.253 Chirality : 0.040 0.256 5212 Planarity : 0.004 0.057 5715 Dihedral : 13.680 172.358 5344 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.17 % Allowed : 12.53 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.14), residues: 3968 helix: 2.17 (0.13), residues: 1588 sheet: 0.28 (0.23), residues: 523 loop : -0.66 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP X 195 HIS 0.006 0.001 HIS D 505 PHE 0.016 0.001 PHE D 226 TYR 0.018 0.001 TYR D 248 ARG 0.006 0.000 ARG D 389 Details of bonding type rmsd hydrogen bonds : bond 0.03572 ( 1497) hydrogen bonds : angle 3.94672 ( 4243) metal coordination : bond 0.00632 ( 8) metal coordination : angle 2.75147 ( 12) covalent geometry : bond 0.00264 (33429) covalent geometry : angle 0.48461 (45666) *********************** 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 383 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 311 time to evaluate : 3.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.9433 (m) cc_final: 0.9052 (t) REVERT: B 122 ASP cc_start: 0.8399 (p0) cc_final: 0.8096 (p0) REVERT: C 84 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6951 (tt) REVERT: C 112 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7663 (tm-30) REVERT: C 116 LYS cc_start: 0.8473 (mttm) cc_final: 0.8025 (tptp) REVERT: C 343 GLN cc_start: 0.8832 (mt0) cc_final: 0.7928 (tt0) REVERT: C 420 GLU cc_start: 0.8085 (tp30) cc_final: 0.7714 (tp30) REVERT: C 426 GLN cc_start: 0.8362 (tm-30) cc_final: 0.7626 (tm-30) REVERT: C 474 MET cc_start: 0.8998 (ttp) cc_final: 0.8714 (mtp) REVERT: C 492 SER cc_start: 0.9677 (m) cc_final: 0.9209 (p) REVERT: C 602 MET cc_start: 0.7766 (mtm) cc_final: 0.7469 (mtt) REVERT: C 637 LYS cc_start: 0.9338 (mtmt) cc_final: 0.9015 (mttp) REVERT: C 652 MET cc_start: 0.8741 (tpt) cc_final: 0.7935 (tpt) REVERT: C 755 LEU cc_start: 0.4878 (mp) cc_final: 0.4479 (tt) REVERT: C 943 VAL cc_start: 0.8890 (t) cc_final: 0.8528 (m) REVERT: D 1 MET cc_start: 0.6971 (ptt) cc_final: 0.5796 (tpt) REVERT: D 84 ARG cc_start: 0.8380 (mtt90) cc_final: 0.7873 (mtm-85) REVERT: D 141 ASP cc_start: 0.7680 (p0) cc_final: 0.7243 (t0) REVERT: D 143 MET cc_start: 0.5467 (tpp) cc_final: 0.5143 (ttt) REVERT: D 250 GLU cc_start: 0.8115 (tp30) cc_final: 0.7869 (tp30) REVERT: D 360 LEU cc_start: 0.8489 (mt) cc_final: 0.8231 (mp) REVERT: D 541 MET cc_start: 0.8726 (mtt) cc_final: 0.8419 (mtm) REVERT: D 570 SER cc_start: 0.9447 (p) cc_final: 0.8902 (t) REVERT: D 740 GLN cc_start: 0.6431 (OUTLIER) cc_final: 0.5737 (pt0) REVERT: D 803 LYS cc_start: 0.7118 (mmtt) cc_final: 0.6715 (mtmm) REVERT: D 938 GLU cc_start: 0.8469 (mm-30) cc_final: 0.7911 (mm-30) REVERT: D 956 ILE cc_start: 0.8835 (mt) cc_final: 0.8560 (tp) REVERT: D 1113 MET cc_start: 0.8024 (mpp) cc_final: 0.7678 (mpp) REVERT: D 1251 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8025 (mt-10) REVERT: E 66 ASN cc_start: 0.8337 (t0) cc_final: 0.7685 (t0) REVERT: F 172 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7493 (mt0) REVERT: F 219 MET cc_start: 0.6735 (mmt) cc_final: 0.6472 (mmp) REVERT: F 261 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8193 (mm-30) REVERT: F 445 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7424 (tt0) REVERT: Y 71 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7745 (tp30) REVERT: X 37 ASP cc_start: 0.7931 (m-30) cc_final: 0.6895 (t0) REVERT: X 156 LEU cc_start: 0.9277 (mm) cc_final: 0.9027 (mp) outliers start: 72 outliers final: 59 residues processed: 371 average time/residue: 0.4185 time to fit residues: 261.0594 Evaluate side-chains 360 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 297 time to evaluate : 5.365 ------------------------------------------------------------------------------- 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 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 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 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 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 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 J residue 84 MET Chi-restraints excluded: chain Y residue 56 SER Chi-restraints excluded: chain Y residue 60 LEU Chi-restraints excluded: chain Y residue 71 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 239 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 231 optimal weight: 8.9990 chunk 116 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 263 optimal weight: 9.9990 chunk 191 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 304 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.182637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.119467 restraints weight = 358104.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.120098 restraints weight = 214299.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.119601 restraints weight = 194914.328| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 33437 Z= 0.213 Angle : 0.584 8.847 45678 Z= 0.306 Chirality : 0.044 0.239 5212 Planarity : 0.005 0.066 5715 Dihedral : 13.845 170.667 5344 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.44 % Allowed : 12.56 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.14), residues: 3968 helix: 1.85 (0.13), residues: 1580 sheet: 0.16 (0.23), residues: 527 loop : -0.91 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D1221 HIS 0.012 0.001 HIS D 505 PHE 0.021 0.002 PHE D 512 TYR 0.024 0.002 TYR Y 255 ARG 0.006 0.000 ARG D 389 Details of bonding type rmsd hydrogen bonds : bond 0.04810 ( 1497) hydrogen bonds : angle 4.21228 ( 4243) metal coordination : bond 0.01215 ( 8) metal coordination : angle 3.67796 ( 12) covalent geometry : bond 0.00531 (33429) covalent geometry : angle 0.58145 (45666) *********************** 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 384 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 303 time to evaluate : 3.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 84 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6513 (tt) REVERT: C 112 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7596 (tm-30) REVERT: C 116 LYS cc_start: 0.8542 (mttm) cc_final: 0.8093 (tptm) REVERT: C 145 MET cc_start: 0.8775 (mmt) cc_final: 0.8198 (mmt) REVERT: C 150 MET cc_start: 0.8287 (mmm) cc_final: 0.7399 (mtt) REVERT: C 209 LYS cc_start: 0.8293 (mtmt) cc_final: 0.7898 (ttmt) REVERT: C 343 GLN cc_start: 0.8983 (mt0) cc_final: 0.8090 (tt0) REVERT: C 420 GLU cc_start: 0.7965 (tp30) cc_final: 0.7560 (tp30) REVERT: C 426 GLN cc_start: 0.8660 (tm-30) cc_final: 0.7935 (tm-30) REVERT: C 474 MET cc_start: 0.8946 (ttp) cc_final: 0.8679 (mtp) REVERT: C 492 SER cc_start: 0.9721 (OUTLIER) cc_final: 0.9337 (p) REVERT: C 602 MET cc_start: 0.7881 (mtm) cc_final: 0.7611 (mtt) REVERT: C 637 LYS cc_start: 0.9330 (mtmt) cc_final: 0.9026 (mtmm) REVERT: C 652 MET cc_start: 0.8691 (tpt) cc_final: 0.8286 (tpt) REVERT: C 755 LEU cc_start: 0.4900 (mp) cc_final: 0.4476 (tt) REVERT: C 943 VAL cc_start: 0.8889 (t) cc_final: 0.8520 (m) REVERT: C 1026 HIS cc_start: 0.8770 (m-70) cc_final: 0.8486 (m170) REVERT: D 1 MET cc_start: 0.6877 (ptt) cc_final: 0.5738 (tpt) REVERT: D 84 ARG cc_start: 0.8480 (mtt90) cc_final: 0.8036 (mtm-85) REVERT: D 141 ASP cc_start: 0.7713 (p0) cc_final: 0.7308 (t0) REVERT: D 143 MET cc_start: 0.5363 (tpp) cc_final: 0.4946 (ttt) REVERT: D 339 ASP cc_start: 0.8604 (m-30) cc_final: 0.8205 (m-30) REVERT: D 360 LEU cc_start: 0.8616 (mt) cc_final: 0.8410 (mt) REVERT: D 541 MET cc_start: 0.8785 (mtt) cc_final: 0.8499 (mtm) REVERT: D 570 SER cc_start: 0.9482 (p) cc_final: 0.8963 (t) REVERT: D 740 GLN cc_start: 0.6458 (OUTLIER) cc_final: 0.5667 (pt0) REVERT: D 803 LYS cc_start: 0.7054 (mmtt) cc_final: 0.6649 (mtmm) REVERT: D 938 GLU cc_start: 0.8564 (mm-30) cc_final: 0.7993 (mm-30) REVERT: D 956 ILE cc_start: 0.8955 (mt) cc_final: 0.8604 (tp) REVERT: D 1113 MET cc_start: 0.7987 (mpp) cc_final: 0.7601 (mpp) REVERT: D 1150 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8672 (pt) REVERT: D 1251 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7957 (mt-10) REVERT: E 66 ASN cc_start: 0.8452 (t0) cc_final: 0.7794 (t0) REVERT: F 172 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7512 (mt0) REVERT: F 219 MET cc_start: 0.6711 (mmt) cc_final: 0.6448 (mmp) REVERT: F 261 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8351 (mm-30) REVERT: X 37 ASP cc_start: 0.7978 (m-30) cc_final: 0.6869 (t0) REVERT: X 156 LEU cc_start: 0.9310 (mm) cc_final: 0.9032 (mp) outliers start: 81 outliers final: 61 residues processed: 367 average time/residue: 0.4140 time to fit residues: 254.2034 Evaluate side-chains 358 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 292 time to evaluate : 3.327 ------------------------------------------------------------------------------- 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 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 551 MET 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 634 VAL Chi-restraints excluded: chain C residue 674 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 780 ILE 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 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 915 VAL Chi-restraints excluded: chain D residue 957 THR Chi-restraints excluded: chain D residue 1007 THR 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 1209 MET 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 343 ILE Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain Y residue 56 SER Chi-restraints excluded: chain Y residue 60 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 352 optimal weight: 6.9990 chunk 371 optimal weight: 4.9990 chunk 338 optimal weight: 6.9990 chunk 361 optimal weight: 0.0470 chunk 217 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 283 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 326 optimal weight: 10.0000 chunk 341 optimal weight: 0.9990 chunk 359 optimal weight: 5.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- 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 = 0.3919 r_free = 0.3919 target = 0.181967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.118943 restraints weight = 361077.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.119539 restraints weight = 215975.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.119080 restraints weight = 193894.038| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 33437 Z= 0.221 Angle : 0.594 8.465 45678 Z= 0.311 Chirality : 0.044 0.229 5212 Planarity : 0.005 0.065 5715 Dihedral : 13.928 171.126 5343 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.44 % Allowed : 12.95 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.13), residues: 3968 helix: 1.71 (0.13), residues: 1580 sheet: 0.06 (0.24), residues: 503 loop : -1.00 (0.14), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP Y 250 HIS 0.012 0.001 HIS D 505 PHE 0.024 0.002 PHE D 7 TYR 0.020 0.002 TYR C1020 ARG 0.007 0.000 ARG C 821 Details of bonding type rmsd hydrogen bonds : bond 0.04832 ( 1497) hydrogen bonds : angle 4.24445 ( 4243) metal coordination : bond 0.01338 ( 8) metal coordination : angle 3.82584 ( 12) covalent geometry : bond 0.00552 (33429) covalent geometry : angle 0.59053 (45666) *********************** 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 387 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 306 time to evaluate : 3.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.6641 (tt) REVERT: C 112 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7629 (tm-30) REVERT: C 116 LYS cc_start: 0.8548 (mttm) cc_final: 0.8132 (tptm) REVERT: C 145 MET cc_start: 0.8845 (mmt) cc_final: 0.8267 (mmt) REVERT: C 209 LYS cc_start: 0.8219 (mtmt) cc_final: 0.7836 (ttmt) REVERT: C 343 GLN cc_start: 0.9031 (mt0) cc_final: 0.8110 (tt0) REVERT: C 420 GLU cc_start: 0.8046 (tp30) cc_final: 0.7635 (tp30) REVERT: C 426 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8060 (tm-30) REVERT: C 430 PHE cc_start: 0.8316 (m-80) cc_final: 0.7937 (m-80) REVERT: C 474 MET cc_start: 0.8985 (ttp) cc_final: 0.8703 (mtp) REVERT: C 492 SER cc_start: 0.9757 (OUTLIER) cc_final: 0.9421 (p) REVERT: C 549 ARG cc_start: 0.8164 (mmm-85) cc_final: 0.7844 (mmm160) REVERT: C 602 MET cc_start: 0.7913 (mtm) cc_final: 0.7684 (mtt) REVERT: C 637 LYS cc_start: 0.9364 (mtmt) cc_final: 0.9046 (mtmm) REVERT: C 652 MET cc_start: 0.8713 (tpt) cc_final: 0.8342 (tpt) REVERT: C 755 LEU cc_start: 0.5225 (mp) cc_final: 0.4636 (tt) REVERT: C 943 VAL cc_start: 0.8865 (t) cc_final: 0.8505 (m) REVERT: C 1026 HIS cc_start: 0.8743 (m-70) cc_final: 0.8393 (m170) REVERT: D 1 MET cc_start: 0.6814 (ptt) cc_final: 0.5723 (tpt) REVERT: D 84 ARG cc_start: 0.8391 (mtt90) cc_final: 0.8007 (mtm-85) REVERT: D 96 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7845 (mm-30) REVERT: D 141 ASP cc_start: 0.7651 (p0) cc_final: 0.7304 (t0) REVERT: D 143 MET cc_start: 0.5577 (tpp) cc_final: 0.5187 (ttt) REVERT: D 250 GLU cc_start: 0.8085 (tp30) cc_final: 0.7606 (tp30) REVERT: D 339 ASP cc_start: 0.8640 (m-30) cc_final: 0.8272 (m-30) REVERT: D 360 LEU cc_start: 0.8743 (mt) cc_final: 0.8461 (mp) REVERT: D 435 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8512 (pt0) REVERT: D 541 MET cc_start: 0.8808 (mtt) cc_final: 0.8533 (mtm) REVERT: D 570 SER cc_start: 0.9463 (p) cc_final: 0.8969 (t) REVERT: D 687 MET cc_start: 0.8909 (mmt) cc_final: 0.8685 (mmt) REVERT: D 740 GLN cc_start: 0.6460 (OUTLIER) cc_final: 0.5653 (pt0) REVERT: D 803 LYS cc_start: 0.7171 (mmtt) cc_final: 0.6666 (mtmm) REVERT: D 929 VAL cc_start: 0.7889 (t) cc_final: 0.7659 (m) REVERT: D 938 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8066 (mm-30) REVERT: D 956 ILE cc_start: 0.8980 (mt) cc_final: 0.8598 (tp) REVERT: D 1113 MET cc_start: 0.8141 (mpp) cc_final: 0.7858 (mpp) REVERT: D 1150 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.8799 (pt) REVERT: D 1251 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7972 (mt-10) REVERT: E 66 ASN cc_start: 0.8613 (t0) cc_final: 0.7963 (t0) REVERT: F 172 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7511 (mt0) REVERT: F 219 MET cc_start: 0.6613 (mmt) cc_final: 0.6353 (mmp) REVERT: F 261 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8410 (mm-30) REVERT: F 428 ASP cc_start: 0.7800 (p0) cc_final: 0.7173 (t70) REVERT: Y 71 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7897 (tp30) REVERT: X 37 ASP cc_start: 0.7999 (m-30) cc_final: 0.6844 (t0) REVERT: X 156 LEU cc_start: 0.9320 (mm) cc_final: 0.9042 (mp) outliers start: 81 outliers final: 65 residues processed: 372 average time/residue: 0.4238 time to fit residues: 263.9137 Evaluate side-chains 366 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 294 time to evaluate : 5.114 ------------------------------------------------------------------------------- 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 551 MET 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 631 ASP Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 674 CYS Chi-restraints excluded: chain C residue 780 ILE 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 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 435 GLN 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 1090 ILE Chi-restraints excluded: chain D residue 1148 VAL Chi-restraints excluded: chain D residue 1150 ILE Chi-restraints excluded: chain D residue 1209 MET 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 343 ILE Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain Y residue 56 SER Chi-restraints excluded: chain Y residue 60 LEU Chi-restraints excluded: chain Y residue 71 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 237 optimal weight: 0.7980 chunk 381 optimal weight: 0.6980 chunk 233 optimal weight: 20.0000 chunk 181 optimal weight: 5.9990 chunk 265 optimal weight: 0.0030 chunk 400 optimal weight: 5.9990 chunk 368 optimal weight: 10.0000 chunk 318 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 195 optimal weight: 0.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 ASN D 329 GLN ** D 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 11 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.184046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.122528 restraints weight = 352410.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.123335 restraints weight = 208896.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.122910 restraints weight = 187714.490| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33437 Z= 0.123 Angle : 0.517 8.486 45678 Z= 0.270 Chirality : 0.041 0.227 5212 Planarity : 0.004 0.064 5715 Dihedral : 13.802 172.676 5343 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.20 % Allowed : 13.34 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3968 helix: 1.95 (0.13), residues: 1583 sheet: 0.11 (0.24), residues: 503 loop : -0.88 (0.14), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Y 250 HIS 0.008 0.001 HIS D 853 PHE 0.028 0.001 PHE D 226 TYR 0.024 0.001 TYR D 248 ARG 0.017 0.000 ARG F 438 Details of bonding type rmsd hydrogen bonds : bond 0.03803 ( 1497) hydrogen bonds : angle 4.02769 ( 4243) metal coordination : bond 0.00657 ( 8) metal coordination : angle 2.84309 ( 12) covalent geometry : bond 0.00287 (33429) covalent geometry : angle 0.51458 (45666) ********************** 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 378 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 305 time to evaluate : 3.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 84 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6586 (tt) REVERT: C 112 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7645 (tm-30) REVERT: C 116 LYS cc_start: 0.8546 (mttm) cc_final: 0.8100 (tptm) REVERT: C 209 LYS cc_start: 0.8252 (mtmt) cc_final: 0.7865 (ttmt) REVERT: C 343 GLN cc_start: 0.8979 (mt0) cc_final: 0.8074 (tt0) REVERT: C 420 GLU cc_start: 0.7902 (tp30) cc_final: 0.7506 (tp30) REVERT: C 426 GLN cc_start: 0.8703 (tm-30) cc_final: 0.8001 (tm-30) REVERT: C 474 MET cc_start: 0.8896 (ttp) cc_final: 0.8618 (mtp) REVERT: C 492 SER cc_start: 0.9711 (m) cc_final: 0.9298 (p) REVERT: C 602 MET cc_start: 0.7789 (mtm) cc_final: 0.7546 (mtt) REVERT: C 637 LYS cc_start: 0.9373 (mtmt) cc_final: 0.9055 (mtmm) REVERT: C 652 MET cc_start: 0.8689 (tpt) cc_final: 0.8301 (tpt) REVERT: C 943 VAL cc_start: 0.8867 (t) cc_final: 0.8512 (m) REVERT: D 84 ARG cc_start: 0.8415 (mtt90) cc_final: 0.7871 (mtm-85) REVERT: D 141 ASP cc_start: 0.7660 (p0) cc_final: 0.7187 (t0) REVERT: D 143 MET cc_start: 0.5672 (tpp) cc_final: 0.5233 (ttt) REVERT: D 250 GLU cc_start: 0.8023 (tp30) cc_final: 0.7545 (tp30) REVERT: D 360 LEU cc_start: 0.8618 (mt) cc_final: 0.8385 (mp) REVERT: D 435 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8396 (pt0) REVERT: D 541 MET cc_start: 0.8768 (mtt) cc_final: 0.8513 (mtm) REVERT: D 570 SER cc_start: 0.9512 (p) cc_final: 0.9002 (t) REVERT: D 740 GLN cc_start: 0.6244 (OUTLIER) cc_final: 0.5439 (pt0) REVERT: D 929 VAL cc_start: 0.7903 (t) cc_final: 0.7683 (m) REVERT: D 938 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8087 (mm-30) REVERT: D 956 ILE cc_start: 0.8991 (mt) cc_final: 0.8602 (tp) REVERT: D 1113 MET cc_start: 0.8075 (mpp) cc_final: 0.7795 (mpp) REVERT: D 1150 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8684 (pt) REVERT: D 1251 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7869 (mt-10) REVERT: E 66 ASN cc_start: 0.8526 (t0) cc_final: 0.7834 (t0) REVERT: F 172 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7500 (mt0) REVERT: F 219 MET cc_start: 0.6605 (mmt) cc_final: 0.6395 (mmp) REVERT: F 261 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8320 (mm-30) REVERT: F 428 ASP cc_start: 0.7582 (p0) cc_final: 0.7036 (t70) REVERT: Y 49 MET cc_start: 0.7972 (mtt) cc_final: 0.7673 (ttm) REVERT: Y 71 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7857 (tp30) REVERT: X 37 ASP cc_start: 0.8140 (m-30) cc_final: 0.7039 (t0) REVERT: X 106 GLN cc_start: 0.8330 (mm110) cc_final: 0.7982 (mm-40) outliers start: 73 outliers final: 60 residues processed: 368 average time/residue: 0.3981 time to fit residues: 246.1168 Evaluate side-chains 357 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 291 time to evaluate : 3.346 ------------------------------------------------------------------------------- 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 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 617 VAL Chi-restraints excluded: chain C residue 631 ASP Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 674 CYS Chi-restraints excluded: chain C residue 780 ILE 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 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 435 GLN Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 460 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 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 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 343 ILE Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain Y residue 56 SER Chi-restraints excluded: chain Y residue 60 LEU Chi-restraints excluded: chain Y residue 71 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 253 optimal weight: 0.5980 chunk 339 optimal weight: 0.7980 chunk 97 optimal weight: 0.0570 chunk 294 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 319 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 327 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.185149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.123633 restraints weight = 350389.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.124609 restraints weight = 206684.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.124103 restraints weight = 186097.503| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33437 Z= 0.114 Angle : 0.508 9.909 45678 Z= 0.265 Chirality : 0.040 0.226 5212 Planarity : 0.004 0.063 5715 Dihedral : 13.728 172.735 5343 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.90 % Allowed : 13.88 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.14), residues: 3968 helix: 2.03 (0.13), residues: 1584 sheet: 0.16 (0.24), residues: 523 loop : -0.82 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Y 250 HIS 0.007 0.001 HIS D 853 PHE 0.025 0.001 PHE D 226 TYR 0.024 0.001 TYR D 248 ARG 0.011 0.000 ARG D 56 Details of bonding type rmsd hydrogen bonds : bond 0.03552 ( 1497) hydrogen bonds : angle 3.95877 ( 4243) metal coordination : bond 0.00609 ( 8) metal coordination : angle 2.51980 ( 12) covalent geometry : bond 0.00264 (33429) covalent geometry : angle 0.50625 (45666) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10336.59 seconds wall clock time: 185 minutes 36.43 seconds (11136.43 seconds total)