Starting phenix.real_space_refine on Sat Feb 7 07:23:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gdo_51273/02_2026/9gdo_51273.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gdo_51273/02_2026/9gdo_51273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gdo_51273/02_2026/9gdo_51273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gdo_51273/02_2026/9gdo_51273.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gdo_51273/02_2026/9gdo_51273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gdo_51273/02_2026/9gdo_51273.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 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 115 5.49 5 Mg 1 5.21 5 S 115 5.16 5 C 18895 2.51 5 N 5440 2.21 5 O 6127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30695 Number of models: 1 Model: "" Number of chains: 10 Chain: "T" Number of atoms: 1180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1180 Classifications: {'DNA': 58} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 57} Chain: "N" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1197 Classifications: {'DNA': 58} Link IDs: {'rna3p': 57} Chain: "G" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 536 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "C" Number of atoms: 10421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1328, 10410 Classifications: {'peptide': 1328} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1272} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1328, 10410 Classifications: {'peptide': 1328} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1272} Chain breaks: 2 bond proxies already assigned to first conformer: 10562 Chain: "D" Number of atoms: 9435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1205, 9435 Classifications: {'peptide': 1205} Link IDs: {'PCIS': 2, 'PTRANS': 46, 'TRANS': 1156} Chain breaks: 4 Chain: "E" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 630 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "A" Number of atoms: 1786 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 231, 1776 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 231, 1776 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain breaks: 1 bond proxies already assigned to first conformer: 1786 Chain: "B" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1697 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 213} Chain breaks: 1 Chain: "F" Number of atoms: 3810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3810 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 16, 'TRANS': 451} Chain breaks: 2 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 13782 SG CYS D 70 98.057 120.537 120.932 1.00 75.54 S ATOM 13796 SG CYS D 72 95.927 120.161 124.254 1.00 80.34 S ATOM 13904 SG CYS D 85 99.717 121.031 124.364 1.00 77.93 S ATOM 13928 SG CYS D 88 98.433 117.703 123.450 1.00 79.46 S ATOM 19638 SG CYS D 814 133.491 74.911 86.286 1.00 76.38 S ATOM 20198 SG CYS D 888 129.795 75.470 86.825 1.00 63.22 S ATOM 20247 SG CYS D 895 131.610 77.335 84.018 1.00 59.26 S ATOM 20267 SG CYS D 898 130.965 73.684 83.671 1.00 68.91 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG C 97 " occ=0.52 ... (20 atoms not shown) pdb=" NH2BARG C 97 " occ=0.48 residue: pdb=" N AHIS A 37 " occ=0.40 ... (18 atoms not shown) pdb=" NE2BHIS A 37 " occ=0.60 Time building chain proxies: 8.90, per 1000 atoms: 0.29 Number of scatterers: 30695 At special positions: 0 Unit cell: (153.714, 188.238, 196.458, 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 115 16.00 P 115 15.00 Mg 1 11.99 O 6127 8.00 N 5440 7.00 C 18895 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " Number of angles added : 12 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6700 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 44 sheets defined 46.6% alpha, 16.0% beta 38 base pairs and 93 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'G' and resid 258 through 262 Processing helix chain 'G' and resid 264 through 272 Processing helix chain 'G' and resid 278 through 283 Processing helix chain 'G' and resid 285 through 291 removed outlier: 3.535A pdb=" N GLU G 289 " --> pdb=" O ARG G 285 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 311 Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.871A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.554A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 212 removed outlier: 3.667A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.913A pdb=" N LEU C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG C 247 " --> pdb=" O PRO C 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 242 through 247' Processing helix chain 'C' and resid 257 through 261 removed outlier: 3.719A pdb=" N VAL C 261 " --> pdb=" O ASP C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 279 Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.762A pdb=" N GLY C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 391 removed outlier: 3.891A pdb=" N SER C 391 " --> pdb=" O SER C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 410 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 481 removed outlier: 3.865A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 494 through 509 removed outlier: 4.669A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.675A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.774A pdb=" N TYR C 555 " --> pdb=" O VAL C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 614 removed outlier: 4.220A pdb=" N GLN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 686 removed outlier: 3.530A pdb=" N MET C 681 " --> pdb=" O ASN C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 713 removed outlier: 4.165A pdb=" N GLY C 713 " --> pdb=" O ALA C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 741 removed outlier: 4.285A pdb=" N LEU C 741 " --> pdb=" O GLU C 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 738 through 741' Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 942 through 981 Processing helix chain 'C' and resid 986 through 992 removed outlier: 3.774A pdb=" N ILE C 992 " --> pdb=" O LYS C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 994 through 1000 Processing helix chain 'C' and resid 1004 through 1019 removed outlier: 3.653A pdb=" N GLN C1010 " --> pdb=" O GLU C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1038 removed outlier: 4.007A pdb=" N ALA C1023 " --> pdb=" O ASP C1019 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP C1024 " --> pdb=" O GLU C1020 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE C1025 " --> pdb=" O LEU C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.702A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1164 through 1175 Processing helix chain 'C' and resid 1190 through 1201 Processing helix chain 'C' and resid 1237 through 1242 Processing helix chain 'C' and resid 1270 through 1281 Processing helix chain 'C' and resid 1282 through 1291 Processing helix chain 'C' and resid 1296 through 1309 removed outlier: 3.641A pdb=" N THR C1301 " --> pdb=" O VAL C1297 " (cutoff:3.500A) Processing helix chain 'C' and resid 1319 through 1332 removed outlier: 3.529A pdb=" N ASN C1323 " --> pdb=" O PRO C1319 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 77 through 81 removed outlier: 3.721A pdb=" N HIS D 80 " --> pdb=" O ARG D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.753A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.544A pdb=" N SER D 119 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 181 through 190 Processing helix chain 'D' and resid 193 through 207 Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.903A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 416 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 581 Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.691A pdb=" N LEU D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.734A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 670 removed outlier: 4.373A pdb=" N THR D 652 " --> pdb=" O ALA D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 702 Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.648A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS D 781 " --> pdb=" O HIS D 777 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.592A pdb=" N LEU D 838 " --> pdb=" O ALA D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 Processing helix chain 'D' and resid 926 through 928 No H-bonds generated for 'chain 'D' and resid 926 through 928' Processing helix chain 'D' and resid 1137 through 1146 Processing helix chain 'D' and resid 1215 through 1223 Processing helix chain 'D' and resid 1224 through 1243 removed outlier: 3.875A pdb=" N GLN D1243 " --> pdb=" O VAL D1239 " (cutoff:3.500A) Processing helix chain 'D' and resid 1248 through 1260 removed outlier: 4.179A pdb=" N ILE D1252 " --> pdb=" O ASN D1248 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN D1258 " --> pdb=" O THR D1254 " (cutoff:3.500A) Processing helix chain 'D' and resid 1281 through 1294 Processing helix chain 'D' and resid 1307 through 1314 Processing helix chain 'D' and resid 1317 through 1325 removed outlier: 3.691A pdb=" N ALA D1321 " --> pdb=" O SER D1317 " (cutoff:3.500A) Processing helix chain 'D' and resid 1326 through 1338 Processing helix chain 'D' and resid 1345 through 1352 removed outlier: 3.645A pdb=" N ASN D1349 " --> pdb=" O GLY D1345 " (cutoff:3.500A) Processing helix chain 'D' and resid 1358 through 1360 No H-bonds generated for 'chain 'D' and resid 1358 through 1360' Processing helix chain 'D' and resid 1361 through 1377 Processing helix chain 'E' and resid 7 through 14 Processing helix chain 'E' and resid 15 through 32 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 82 Processing helix chain 'A' and resid 34 through 48 Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.822A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 234 removed outlier: 4.449A pdb=" N ALA A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.539A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.536A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 160 Processing helix chain 'B' and resid 213 through 229 removed outlier: 3.569A pdb=" N LEU B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 109 removed outlier: 3.590A pdb=" N THR F 109 " --> pdb=" O ARG F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 138 Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.782A pdb=" N TYR F 145 " --> pdb=" O GLY F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 163 removed outlier: 3.653A pdb=" N LEU F 163 " --> pdb=" O ARG F 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 159 through 163' Processing helix chain 'F' and resid 224 through 243 Processing helix chain 'F' and resid 250 through 266 removed outlier: 3.779A pdb=" N GLU F 266 " --> pdb=" O ASP F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 300 Processing helix chain 'F' and resid 308 through 313 Processing helix chain 'F' and resid 313 through 318 removed outlier: 3.647A pdb=" N GLU F 318 " --> pdb=" O PHE F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 330 removed outlier: 4.154A pdb=" N LEU F 324 " --> pdb=" O ASN F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 360 removed outlier: 3.947A pdb=" N LYS F 351 " --> pdb=" O ARG F 347 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU F 352 " --> pdb=" O SER F 348 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN F 353 " --> pdb=" O ILE F 349 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N MET F 354 " --> pdb=" O GLN F 350 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE F 355 " --> pdb=" O LYS F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 400 removed outlier: 4.967A pdb=" N ARG F 393 " --> pdb=" O GLU F 389 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LEU F 394 " --> pdb=" O ALA F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 403 No H-bonds generated for 'chain 'F' and resid 401 through 403' Processing helix chain 'F' and resid 408 through 426 Processing helix chain 'F' and resid 428 through 432 removed outlier: 3.637A pdb=" N ARG F 431 " --> pdb=" O GLU F 428 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 455 removed outlier: 3.968A pdb=" N TYR F 438 " --> pdb=" O LYS F 434 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TRP F 441 " --> pdb=" O THR F 437 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TRP F 442 " --> pdb=" O TYR F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 483 Processing helix chain 'F' and resid 487 through 496 Processing helix chain 'F' and resid 498 through 507 Processing helix chain 'F' and resid 526 through 531 removed outlier: 3.816A pdb=" N ILE F 531 " --> pdb=" O GLY F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 557 Processing helix chain 'F' and resid 560 through 572 Processing helix chain 'F' and resid 580 through 589 removed outlier: 3.578A pdb=" N GLN F 587 " --> pdb=" O GLU F 583 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE F 588 " --> pdb=" O VAL F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 591 through 607 removed outlier: 3.619A pdb=" N ILE F 595 " --> pdb=" O THR F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 617 removed outlier: 3.796A pdb=" N SER F 617 " --> pdb=" O GLU F 613 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.478A pdb=" N LYS C 13 " --> pdb=" O ALA C1182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.981A pdb=" N SER C 66 " --> pdb=" O PHE C 105 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE C 104 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.981A pdb=" N SER C 66 " --> pdb=" O PHE C 105 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LYS C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLU C 126 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AA5, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.471A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 154 through 159 removed outlier: 5.289A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 236 through 239 Processing sheet with id=AA8, first strand: chain 'C' and resid 301 through 302 removed outlier: 4.182A pdb=" N ILE C 311 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.479A pdb=" N GLU C 602 " --> pdb=" O ARG C 593 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N THR C 600 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AB2, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.537A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.636A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AB5, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AB6, first strand: chain 'C' and resid 1208 through 1209 removed outlier: 7.493A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N THR C1225 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.801A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AB9, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.815A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 1243 through 1245 Processing sheet with id=AC2, first strand: chain 'C' and resid 1268 through 1269 Processing sheet with id=AC3, first strand: chain 'C' and resid 1334 through 1339 Processing sheet with id=AC4, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.574A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.229A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 9.891A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 159 through 160 removed outlier: 6.807A pdb=" N THR D 177 " --> pdb=" O THR D 147 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 253 through 254 removed outlier: 6.392A pdb=" N PHE D 260 " --> pdb=" O ILE F 513 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AC8, first strand: chain 'D' and resid 703 through 707 Processing sheet with id=AC9, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AD1, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AD2, first strand: chain 'D' and resid 825 through 826 removed outlier: 7.085A pdb=" N HIS D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 848 through 849 removed outlier: 3.542A pdb=" N ILE D 858 " --> pdb=" O ILE D 848 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 991 through 995 Processing sheet with id=AD5, first strand: chain 'D' and resid 1184 through 1189 Processing sheet with id=AD6, first strand: chain 'D' and resid 1278 through 1280 removed outlier: 4.389A pdb=" N LYS D1262 " --> pdb=" O GLU D1304 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ARG D1300 " --> pdb=" O THR D1266 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 12 through 20 removed outlier: 4.904A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N HIS A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N HIS A 23 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N THR A 208 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LYS A 25 " --> pdb=" O MET A 206 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N MET A 206 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N THR A 27 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ILE A 204 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N GLU A 29 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU A 202 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 116 through 117 removed outlier: 3.676A pdb=" N GLU A 58 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLU A 148 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N VAL A 56 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLY A 150 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N CYS A 54 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AE1, first strand: chain 'A' and resid 109 through 112 removed outlier: 3.601A pdb=" N CYS A 132 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 153 through 154 Processing sheet with id=AE3, first strand: chain 'B' and resid 13 through 20 removed outlier: 6.384A pdb=" N HIS B 23 " --> pdb=" O ILE B 19 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N HIS B 23 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N THR B 208 " --> pdb=" O HIS B 23 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LYS B 25 " --> pdb=" O MET B 206 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N MET B 206 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N THR B 27 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE B 204 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N GLU B 29 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU B 202 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N THR B 197 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL B 193 " --> pdb=" O THR B 197 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 116 through 117 removed outlier: 7.265A pdb=" N ALA B 142 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE B 61 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ARG B 144 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL B 59 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS B 146 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU B 148 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AE6, first strand: chain 'B' and resid 109 through 112 removed outlier: 3.655A pdb=" N CYS B 132 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AE8, first strand: chain 'F' and resid 164 through 166 removed outlier: 6.906A pdb=" N ARG F 268 " --> pdb=" O SER F 165 " (cutoff:3.500A) 1384 hydrogen bonds defined for protein. 3935 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 93 hydrogen bonds 186 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 93 stacking parallelities Total time for adding SS restraints: 9.29 Time building geometry restraints manager: 3.44 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: 9774 1.34 - 1.46: 4665 1.46 - 1.58: 16518 1.58 - 1.70: 229 1.70 - 1.82: 205 Bond restraints: 31391 Sorted by residual: bond pdb=" C ALA C 381 " pdb=" O ALA C 381 " ideal model delta sigma weight residual 1.236 1.277 -0.040 1.15e-02 7.56e+03 1.23e+01 bond pdb=" C GLU C 382 " pdb=" O GLU C 382 " ideal model delta sigma weight residual 1.236 1.276 -0.040 1.15e-02 7.56e+03 1.19e+01 bond pdb=" CA SER C 387 " pdb=" CB SER C 387 " ideal model delta sigma weight residual 1.530 1.486 0.044 1.63e-02 3.76e+03 7.17e+00 bond pdb=" CA SER C 383 " pdb=" CB SER C 383 " ideal model delta sigma weight residual 1.530 1.489 0.040 1.56e-02 4.11e+03 6.73e+00 bond pdb=" C ARG C 211 " pdb=" N VAL C 212 " ideal model delta sigma weight residual 1.336 1.309 0.027 1.17e-02 7.31e+03 5.42e+00 ... (remaining 31386 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 41989 1.77 - 3.54: 749 3.54 - 5.32: 94 5.32 - 7.09: 21 7.09 - 8.86: 9 Bond angle restraints: 42862 Sorted by residual: angle pdb=" CA LEU C 388 " pdb=" C LEU C 388 " pdb=" O LEU C 388 " ideal model delta sigma weight residual 120.90 116.44 4.46 1.07e+00 8.73e-01 1.74e+01 angle pdb=" CA GLU D 660 " pdb=" CB GLU D 660 " pdb=" CG GLU D 660 " ideal model delta sigma weight residual 114.10 121.93 -7.83 2.00e+00 2.50e-01 1.53e+01 angle pdb=" CA GLU E 79 " pdb=" CB GLU E 79 " pdb=" CG GLU E 79 " ideal model delta sigma weight residual 114.10 121.29 -7.19 2.00e+00 2.50e-01 1.29e+01 angle pdb=" CA LEU C 388 " pdb=" C LEU C 388 " pdb=" N PHE C 389 " ideal model delta sigma weight residual 116.97 121.23 -4.26 1.20e+00 6.94e-01 1.26e+01 angle pdb=" CB GLU E 79 " pdb=" CG GLU E 79 " pdb=" CD GLU E 79 " ideal model delta sigma weight residual 112.60 118.46 -5.86 1.70e+00 3.46e-01 1.19e+01 ... (remaining 42857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 17999 35.74 - 71.49: 1017 71.49 - 107.23: 34 107.23 - 142.98: 0 142.98 - 178.72: 6 Dihedral angle restraints: 19056 sinusoidal: 8681 harmonic: 10375 Sorted by residual: dihedral pdb=" C4' DA T -9 " pdb=" C3' DA T -9 " pdb=" O3' DA T -9 " pdb=" P DT T -8 " ideal model delta sinusoidal sigma weight residual -140.00 38.72 -178.72 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA N -8 " pdb=" C3' DA N -8 " pdb=" O3' DA N -8 " pdb=" P DA N -7 " ideal model delta sinusoidal sigma weight residual 220.00 53.34 166.66 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DA T 10 " pdb=" C3' DA T 10 " pdb=" O3' DA T 10 " pdb=" P DA T 11 " ideal model delta sinusoidal sigma weight residual -140.00 26.62 -166.62 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 19053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 4629 0.090 - 0.181: 259 0.181 - 0.271: 3 0.271 - 0.361: 0 0.361 - 0.451: 1 Chirality restraints: 4892 Sorted by residual: chirality pdb=" CB VAL C 212 " pdb=" CA VAL C 212 " pdb=" CG1 VAL C 212 " pdb=" CG2 VAL C 212 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" CA VAL E 6 " pdb=" N VAL E 6 " pdb=" C VAL E 6 " pdb=" CB VAL E 6 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB VAL E 6 " pdb=" CA VAL E 6 " pdb=" CG1 VAL E 6 " pdb=" CG2 VAL E 6 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 4889 not shown) Planarity restraints: 5190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 487 " -0.068 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO F 488 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO F 488 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO F 488 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 772 " 0.053 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO C 773 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO C 773 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 773 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET F 497 " -0.045 5.00e-02 4.00e+02 6.89e-02 7.59e+00 pdb=" N PRO F 498 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO F 498 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 498 " -0.038 5.00e-02 4.00e+02 ... (remaining 5187 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 357 2.65 - 3.21: 26872 3.21 - 3.77: 47382 3.77 - 4.34: 66225 4.34 - 4.90: 107610 Nonbonded interactions: 248446 Sorted by model distance: nonbonded pdb=" OG1 THR C 312 " pdb=" OE1 GLN C 315 " model vdw 2.087 3.040 nonbonded pdb=" O ILE F 349 " pdb=" NE2 GLN F 353 " model vdw 2.156 3.120 nonbonded pdb=" O VAL F 327 " pdb=" OG SER F 330 " model vdw 2.185 3.040 nonbonded pdb=" OD1 ASP C 158 " pdb=" N SER C 159 " model vdw 2.189 3.120 nonbonded pdb=" OG SER C 759 " pdb=" OG1 THR C 763 " model vdw 2.231 3.040 ... (remaining 248441 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' and (resid 4 through 36 or resid 38 through 160 or resid 169 through \ 233)) selection = (chain 'B' and (resid 4 through 36 or resid 38 through 233)) } 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 40.140 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.080 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:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 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 : 0.003 0.064 31399 Z= 0.140 Angle : 0.572 8.862 42874 Z= 0.310 Chirality : 0.041 0.451 4892 Planarity : 0.005 0.102 5190 Dihedral : 19.085 178.721 12356 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.71 % Favored : 98.26 % Rotamer: Outliers : 1.30 % Allowed : 23.51 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.14), residues: 3576 helix: 1.58 (0.14), residues: 1479 sheet: 0.61 (0.24), residues: 445 loop : 0.10 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 368 TYR 0.020 0.001 TYR D 165 PHE 0.010 0.001 PHE C1025 TRP 0.012 0.001 TRP D 686 HIS 0.004 0.001 HIS D1365 Details of bonding type rmsd covalent geometry : bond 0.00294 (31391) covalent geometry : angle 0.56845 (42862) hydrogen bonds : bond 0.12646 ( 1468) hydrogen bonds : angle 5.70278 ( 4121) metal coordination : bond 0.00576 ( 8) metal coordination : angle 3.66409 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 713 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 271 LEU cc_start: 0.8533 (mt) cc_final: 0.8149 (mt) REVERT: C 37 LYS cc_start: 0.8421 (mtpp) cc_final: 0.8211 (mtpp) REVERT: C 315 GLN cc_start: 0.7534 (tt0) cc_final: 0.6908 (tt0) REVERT: C 472 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7385 (tm-30) REVERT: C 1030 GLU cc_start: 0.7111 (tp30) cc_final: 0.6604 (tp30) REVERT: D 143 MET cc_start: 0.8198 (ptp) cc_final: 0.7971 (ptp) REVERT: D 386 GLU cc_start: 0.7688 (mp0) cc_final: 0.7358 (mp0) REVERT: D 399 LYS cc_start: 0.8285 (mptp) cc_final: 0.7838 (mttp) REVERT: D 1159 HIS cc_start: 0.7003 (OUTLIER) cc_final: 0.6660 (m90) REVERT: D 1222 LEU cc_start: 0.8401 (mt) cc_final: 0.8130 (mt) REVERT: B 62 GLU cc_start: 0.7483 (tp30) cc_final: 0.6885 (tp30) REVERT: F 400 LYS cc_start: 0.8366 (ttpp) cc_final: 0.8097 (ptmm) outliers start: 40 outliers final: 27 residues processed: 742 average time/residue: 0.8461 time to fit residues: 721.2847 Evaluate side-chains 721 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 693 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 272 LYS Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 984 TYR Chi-restraints excluded: chain C residue 1000 GLN Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 865 ASP Chi-restraints excluded: chain D residue 1003 LEU Chi-restraints excluded: chain D residue 1159 HIS Chi-restraints excluded: chain D residue 1238 GLU Chi-restraints excluded: chain D residue 1323 SER Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain F residue 525 SER Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 599 GLU Chi-restraints excluded: chain F residue 610 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1092 GLN C1311 ASN D 489 ASN D 700 ASN D 825 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 GLN A 75 GLN B 23 HIS ** F 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 597 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.151105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.114183 restraints weight = 83595.621| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.91 r_work: 0.3170 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31399 Z= 0.162 Angle : 0.542 8.538 42874 Z= 0.290 Chirality : 0.041 0.181 4892 Planarity : 0.005 0.079 5190 Dihedral : 16.958 176.843 5282 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.19 % Allowed : 20.88 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.14), residues: 3576 helix: 1.73 (0.13), residues: 1533 sheet: 0.70 (0.24), residues: 442 loop : 0.06 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 368 TYR 0.019 0.001 TYR D 631 PHE 0.031 0.001 PHE C 385 TRP 0.009 0.001 TRP C 997 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00374 (31391) covalent geometry : angle 0.53841 (42862) hydrogen bonds : bond 0.04509 ( 1468) hydrogen bonds : angle 4.58797 ( 4121) metal coordination : bond 0.00665 ( 8) metal coordination : angle 3.63556 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 710 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 120 GLN cc_start: 0.8046 (tt0) cc_final: 0.7846 (tt0) REVERT: C 315 GLN cc_start: 0.7894 (tt0) cc_final: 0.7437 (tt0) REVERT: C 386 GLU cc_start: 0.7153 (tp30) cc_final: 0.6718 (tp30) REVERT: C 390 PHE cc_start: 0.8351 (m-80) cc_final: 0.7922 (m-80) REVERT: C 472 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7562 (tm-30) REVERT: C 805 MET cc_start: 0.8618 (ptm) cc_final: 0.8394 (ptp) REVERT: C 1030 GLU cc_start: 0.7220 (tp30) cc_final: 0.6750 (tp30) REVERT: C 1034 ARG cc_start: 0.7803 (ttm-80) cc_final: 0.7504 (ttm-80) REVERT: C 1339 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7383 (mt-10) REVERT: D 137 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7426 (mtp180) REVERT: D 143 MET cc_start: 0.8427 (ptp) cc_final: 0.7620 (ptm) REVERT: D 201 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7824 (mtm) REVERT: D 294 ASN cc_start: 0.8498 (t0) cc_final: 0.8161 (t0) REVERT: D 370 LYS cc_start: 0.8282 (mtmt) cc_final: 0.8068 (mtmm) REVERT: D 386 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7316 (mp0) REVERT: D 399 LYS cc_start: 0.8363 (mptp) cc_final: 0.8049 (mttp) REVERT: D 402 GLU cc_start: 0.7928 (tt0) cc_final: 0.7728 (mt-10) REVERT: D 1222 LEU cc_start: 0.8323 (mt) cc_final: 0.8090 (mt) REVERT: B 171 ARG cc_start: 0.6317 (OUTLIER) cc_final: 0.5849 (mmm-85) REVERT: F 274 PHE cc_start: 0.7240 (t80) cc_final: 0.6918 (t80) REVERT: F 372 ARG cc_start: 0.7852 (mtt90) cc_final: 0.7197 (mtm-85) REVERT: F 382 ARG cc_start: 0.7685 (mmm-85) cc_final: 0.7443 (mmm-85) REVERT: F 384 LYS cc_start: 0.8292 (mmtt) cc_final: 0.8065 (mmtp) REVERT: F 400 LYS cc_start: 0.8478 (ttpp) cc_final: 0.8259 (ptmm) outliers start: 98 outliers final: 49 residues processed: 760 average time/residue: 0.8305 time to fit residues: 724.3444 Evaluate side-chains 747 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 695 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 272 LYS Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain G residue 285 ARG Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 984 TYR Chi-restraints excluded: chain C residue 1000 GLN Chi-restraints excluded: chain C residue 1254 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 371 LYS Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 718 SER Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 836 THR Chi-restraints excluded: chain D residue 889 ASP Chi-restraints excluded: chain D residue 1003 LEU Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 587 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 248 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 282 optimal weight: 0.0050 chunk 298 optimal weight: 3.9990 chunk 330 optimal weight: 10.0000 chunk 324 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 20 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 ASN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 910 ASN D1237 GLN D1349 ASN F 477 GLN F 597 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.150416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.114708 restraints weight = 65165.341| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.42 r_work: 0.3212 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31399 Z= 0.167 Angle : 0.534 8.265 42874 Z= 0.285 Chirality : 0.041 0.204 4892 Planarity : 0.004 0.074 5190 Dihedral : 16.840 177.586 5254 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.67 % Allowed : 20.91 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.14), residues: 3576 helix: 1.74 (0.13), residues: 1541 sheet: 0.65 (0.24), residues: 447 loop : 0.06 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 368 TYR 0.021 0.001 TYR D 631 PHE 0.011 0.001 PHE D 461 TRP 0.008 0.001 TRP F 323 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00393 (31391) covalent geometry : angle 0.53007 (42862) hydrogen bonds : bond 0.04368 ( 1468) hydrogen bonds : angle 4.42570 ( 4121) metal coordination : bond 0.00677 ( 8) metal coordination : angle 3.75327 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 713 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 120 GLN cc_start: 0.8025 (tt0) cc_final: 0.7732 (tt0) REVERT: C 315 GLN cc_start: 0.7883 (tt0) cc_final: 0.7402 (tt0) REVERT: C 386 GLU cc_start: 0.7099 (tp30) cc_final: 0.6720 (tp30) REVERT: C 417 GLN cc_start: 0.7807 (tt0) cc_final: 0.7600 (tt0) REVERT: C 472 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7523 (tm-30) REVERT: C 488 MET cc_start: 0.7846 (mmt) cc_final: 0.7515 (mmt) REVERT: C 726 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8395 (p) REVERT: C 805 MET cc_start: 0.8635 (ptm) cc_final: 0.8417 (ptp) REVERT: C 915 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7381 (p0) REVERT: C 1030 GLU cc_start: 0.7222 (tp30) cc_final: 0.6240 (tp30) REVERT: C 1033 ARG cc_start: 0.8113 (mtp-110) cc_final: 0.7627 (ttp-110) REVERT: C 1034 ARG cc_start: 0.7744 (ttm-80) cc_final: 0.7500 (ttm-80) REVERT: C 1166 GLU cc_start: 0.7247 (pm20) cc_final: 0.7004 (pm20) REVERT: C 1339 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7362 (mt-10) REVERT: D 137 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7430 (mtp180) REVERT: D 143 MET cc_start: 0.8317 (ptp) cc_final: 0.7438 (ptm) REVERT: D 204 GLU cc_start: 0.7506 (tp30) cc_final: 0.7086 (tm-30) REVERT: D 221 LEU cc_start: 0.8354 (tp) cc_final: 0.7972 (tm) REVERT: D 259 ARG cc_start: 0.8192 (mmt180) cc_final: 0.7870 (mmt180) REVERT: D 294 ASN cc_start: 0.8475 (t0) cc_final: 0.8150 (t0) REVERT: D 312 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7568 (tpt-90) REVERT: D 370 LYS cc_start: 0.8251 (mtmt) cc_final: 0.8032 (mtmm) REVERT: D 399 LYS cc_start: 0.8329 (mptp) cc_final: 0.8008 (mttp) REVERT: D 1159 HIS cc_start: 0.7110 (OUTLIER) cc_final: 0.6762 (m90) REVERT: D 1222 LEU cc_start: 0.8297 (mt) cc_final: 0.8072 (mt) REVERT: D 1340 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7625 (ttt-90) REVERT: B 171 ARG cc_start: 0.6345 (OUTLIER) cc_final: 0.5861 (mmm-85) REVERT: F 274 PHE cc_start: 0.7170 (t80) cc_final: 0.6751 (t80) REVERT: F 296 MET cc_start: 0.5724 (tpp) cc_final: 0.5420 (tpp) REVERT: F 400 LYS cc_start: 0.8424 (ttpp) cc_final: 0.8207 (ptmm) REVERT: F 428 GLU cc_start: 0.7447 (tt0) cc_final: 0.7200 (tt0) REVERT: F 563 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6722 (mt-10) outliers start: 113 outliers final: 66 residues processed: 758 average time/residue: 0.8249 time to fit residues: 716.7120 Evaluate side-chains 774 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 701 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain G residue 285 ARG Chi-restraints excluded: chain G residue 289 GLU Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 726 SER Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 984 TYR Chi-restraints excluded: chain C residue 1000 GLN Chi-restraints excluded: chain C residue 1105 SER Chi-restraints excluded: chain C residue 1254 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 312 ARG Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 718 SER Chi-restraints excluded: chain D residue 781 LYS Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 836 THR Chi-restraints excluded: chain D residue 865 ASP Chi-restraints excluded: chain D residue 889 ASP Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1003 LEU Chi-restraints excluded: chain D residue 1159 HIS Chi-restraints excluded: chain D residue 1340 ARG Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 476 ARG Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 587 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 113 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 366 optimal weight: 4.9990 chunk 324 optimal weight: 0.9980 chunk 149 optimal weight: 0.5980 chunk 298 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 ASN D 158 GLN D 700 ASN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1237 GLN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.149350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.114348 restraints weight = 57290.898| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.24 r_work: 0.3208 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 31399 Z= 0.197 Angle : 0.550 8.738 42874 Z= 0.292 Chirality : 0.042 0.195 4892 Planarity : 0.005 0.071 5190 Dihedral : 16.837 176.593 5248 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.77 % Allowed : 21.40 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.14), residues: 3576 helix: 1.69 (0.13), residues: 1540 sheet: 0.58 (0.24), residues: 430 loop : 0.04 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 368 TYR 0.023 0.001 TYR D 631 PHE 0.014 0.001 PHE D 461 TRP 0.009 0.001 TRP D 868 HIS 0.005 0.001 HIS C1173 Details of bonding type rmsd covalent geometry : bond 0.00470 (31391) covalent geometry : angle 0.54642 (42862) hydrogen bonds : bond 0.04514 ( 1468) hydrogen bonds : angle 4.40283 ( 4121) metal coordination : bond 0.00788 ( 8) metal coordination : angle 4.01875 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 716 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 37 LYS cc_start: 0.8587 (mtpp) cc_final: 0.8377 (mtpp) REVERT: C 120 GLN cc_start: 0.8141 (tt0) cc_final: 0.7840 (tt0) REVERT: C 371 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7242 (mtt-85) REVERT: C 386 GLU cc_start: 0.7409 (tp30) cc_final: 0.7046 (tp30) REVERT: C 402 ARG cc_start: 0.8331 (tpp-160) cc_final: 0.8073 (tpm170) REVERT: C 417 GLN cc_start: 0.8029 (tt0) cc_final: 0.7646 (tt0) REVERT: C 472 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7736 (tm-30) REVERT: C 488 MET cc_start: 0.7935 (mmt) cc_final: 0.7557 (mmt) REVERT: C 726 SER cc_start: 0.8715 (OUTLIER) cc_final: 0.8495 (p) REVERT: C 805 MET cc_start: 0.8758 (ptm) cc_final: 0.8544 (ptp) REVERT: C 915 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7545 (p0) REVERT: C 1030 GLU cc_start: 0.7483 (tp30) cc_final: 0.6964 (tp30) REVERT: C 1034 ARG cc_start: 0.7984 (ttm-80) cc_final: 0.7737 (ttm-80) REVERT: C 1166 GLU cc_start: 0.7556 (pm20) cc_final: 0.7318 (pm20) REVERT: C 1339 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7625 (mt-10) REVERT: D 137 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7667 (mtp180) REVERT: D 143 MET cc_start: 0.8563 (ptp) cc_final: 0.7820 (ptm) REVERT: D 192 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8400 (ttm) REVERT: D 204 GLU cc_start: 0.7683 (tp30) cc_final: 0.7174 (tm-30) REVERT: D 294 ASN cc_start: 0.8655 (t0) cc_final: 0.8333 (t0) REVERT: D 312 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7743 (tpt-90) REVERT: D 399 LYS cc_start: 0.8434 (mptp) cc_final: 0.8140 (mttp) REVERT: D 1159 HIS cc_start: 0.7379 (OUTLIER) cc_final: 0.6987 (m90) REVERT: D 1222 LEU cc_start: 0.8406 (mt) cc_final: 0.8181 (mt) REVERT: D 1340 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7899 (ttt-90) REVERT: B 58 GLU cc_start: 0.8084 (tt0) cc_final: 0.7663 (tt0) REVERT: B 171 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.6138 (mmm-85) REVERT: F 274 PHE cc_start: 0.7277 (t80) cc_final: 0.6841 (t80) REVERT: F 296 MET cc_start: 0.5897 (tpp) cc_final: 0.5574 (tpp) REVERT: F 372 ARG cc_start: 0.7965 (mtm-85) cc_final: 0.7425 (mtt90) REVERT: F 396 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7664 (tt) REVERT: F 400 LYS cc_start: 0.8541 (ttpp) cc_final: 0.8322 (ptmm) REVERT: F 428 GLU cc_start: 0.7686 (tt0) cc_final: 0.7443 (tt0) REVERT: F 563 GLU cc_start: 0.7400 (mt-10) cc_final: 0.7000 (mt-10) outliers start: 116 outliers final: 65 residues processed: 770 average time/residue: 0.8158 time to fit residues: 720.3696 Evaluate side-chains 770 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 695 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain G residue 285 ARG Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 726 SER Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 984 TYR Chi-restraints excluded: chain C residue 1000 GLN Chi-restraints excluded: chain C residue 1105 SER Chi-restraints excluded: chain C residue 1247 THR Chi-restraints excluded: chain C residue 1254 THR Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 312 ARG Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 718 SER Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 836 THR Chi-restraints excluded: chain D residue 889 ASP Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1003 LEU Chi-restraints excluded: chain D residue 1159 HIS Chi-restraints excluded: chain D residue 1340 ARG Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 476 ARG Chi-restraints excluded: chain F residue 575 MET Chi-restraints excluded: chain F residue 587 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 228 optimal weight: 0.1980 chunk 99 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 143 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 324 optimal weight: 0.8980 chunk 277 optimal weight: 3.9990 chunk 222 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 ASN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 ASN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.150729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.114900 restraints weight = 72768.262| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.56 r_work: 0.3207 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31399 Z= 0.132 Angle : 0.516 11.318 42874 Z= 0.274 Chirality : 0.040 0.207 4892 Planarity : 0.004 0.065 5190 Dihedral : 16.775 179.019 5248 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.45 % Allowed : 22.05 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.14), residues: 3576 helix: 1.85 (0.13), residues: 1540 sheet: 0.49 (0.24), residues: 423 loop : 0.13 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 368 TYR 0.019 0.001 TYR D 631 PHE 0.010 0.001 PHE C 35 TRP 0.007 0.001 TRP F 323 HIS 0.004 0.001 HIS C1173 Details of bonding type rmsd covalent geometry : bond 0.00302 (31391) covalent geometry : angle 0.50909 (42862) hydrogen bonds : bond 0.03907 ( 1468) hydrogen bonds : angle 4.25714 ( 4121) metal coordination : bond 0.01207 ( 8) metal coordination : angle 5.09166 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 710 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 120 GLN cc_start: 0.8023 (tt0) cc_final: 0.7651 (tt0) REVERT: C 371 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7068 (mtp180) REVERT: C 386 GLU cc_start: 0.7088 (tp30) cc_final: 0.6731 (tp30) REVERT: C 390 PHE cc_start: 0.7986 (m-80) cc_final: 0.7553 (m-80) REVERT: C 402 ARG cc_start: 0.8166 (tpp-160) cc_final: 0.7910 (tpm170) REVERT: C 417 GLN cc_start: 0.7782 (tt0) cc_final: 0.7484 (tt0) REVERT: C 472 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7528 (tm-30) REVERT: C 488 MET cc_start: 0.7860 (mmt) cc_final: 0.7440 (mmt) REVERT: C 726 SER cc_start: 0.8579 (OUTLIER) cc_final: 0.8352 (p) REVERT: C 739 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7911 (mp0) REVERT: C 805 MET cc_start: 0.8639 (ptm) cc_final: 0.8420 (ptp) REVERT: C 841 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7755 (mtt-85) REVERT: C 915 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7355 (p0) REVERT: C 955 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7596 (tp30) REVERT: C 1030 GLU cc_start: 0.7269 (tp30) cc_final: 0.6246 (tp30) REVERT: C 1033 ARG cc_start: 0.8116 (mtp-110) cc_final: 0.7575 (ttp-110) REVERT: C 1034 ARG cc_start: 0.7759 (ttm-80) cc_final: 0.7510 (ttm-80) REVERT: C 1166 GLU cc_start: 0.7282 (pm20) cc_final: 0.6984 (mp0) REVERT: C 1337 GLU cc_start: 0.7993 (pt0) cc_final: 0.7722 (pt0) REVERT: C 1339 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7420 (mt-10) REVERT: D 204 GLU cc_start: 0.7538 (tp30) cc_final: 0.7038 (tm-30) REVERT: D 221 LEU cc_start: 0.8283 (tp) cc_final: 0.7888 (tm) REVERT: D 259 ARG cc_start: 0.8195 (mmt180) cc_final: 0.7993 (mmt180) REVERT: D 294 ASN cc_start: 0.8491 (t0) cc_final: 0.8148 (t0) REVERT: D 370 LYS cc_start: 0.8278 (mtmt) cc_final: 0.8073 (mtmm) REVERT: D 386 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: D 399 LYS cc_start: 0.8351 (mptp) cc_final: 0.8031 (mttp) REVERT: D 556 ILE cc_start: 0.8081 (mm) cc_final: 0.7740 (mm) REVERT: D 736 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7220 (mt0) REVERT: D 833 VAL cc_start: 0.8894 (m) cc_final: 0.8622 (p) REVERT: D 854 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7317 (m-30) REVERT: D 1159 HIS cc_start: 0.7144 (OUTLIER) cc_final: 0.6776 (m90) REVERT: D 1222 LEU cc_start: 0.8297 (mt) cc_final: 0.8077 (mt) REVERT: D 1366 GLN cc_start: 0.7774 (mm110) cc_final: 0.7556 (mm-40) REVERT: F 138 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7421 (pp20) REVERT: F 274 PHE cc_start: 0.7201 (t80) cc_final: 0.6824 (t80) REVERT: F 296 MET cc_start: 0.5819 (tpp) cc_final: 0.5537 (tpp) REVERT: F 356 GLU cc_start: 0.7570 (mt-10) cc_final: 0.6998 (mm-30) REVERT: F 372 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7054 (mtt90) REVERT: F 396 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7720 (mt) REVERT: F 400 LYS cc_start: 0.8453 (ttpp) cc_final: 0.8224 (ptmm) REVERT: F 405 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7505 (mtm180) REVERT: F 563 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6760 (mt-10) outliers start: 106 outliers final: 60 residues processed: 760 average time/residue: 0.7893 time to fit residues: 685.9184 Evaluate side-chains 773 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 703 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 272 LYS Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 726 SER Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 841 ARG Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 984 TYR Chi-restraints excluded: chain C residue 1000 GLN Chi-restraints excluded: chain C residue 1105 SER Chi-restraints excluded: chain C residue 1143 GLU Chi-restraints excluded: chain C residue 1247 THR Chi-restraints excluded: chain C residue 1254 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 807 VAL Chi-restraints excluded: chain D residue 836 THR Chi-restraints excluded: chain D residue 854 ASP Chi-restraints excluded: chain D residue 879 GLN Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1003 LEU Chi-restraints excluded: chain D residue 1159 HIS Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1304 GLU Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 405 ARG Chi-restraints excluded: chain F residue 476 ARG Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 587 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 141 optimal weight: 2.9990 chunk 327 optimal weight: 7.9990 chunk 62 optimal weight: 0.3980 chunk 306 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 174 optimal weight: 0.6980 chunk 285 optimal weight: 1.9990 chunk 289 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN C 737 ASN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 ASN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.149205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.113989 restraints weight = 60232.901| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.28 r_work: 0.3202 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 31399 Z= 0.209 Angle : 0.561 12.241 42874 Z= 0.296 Chirality : 0.042 0.224 4892 Planarity : 0.004 0.064 5190 Dihedral : 16.851 175.834 5248 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.41 % Allowed : 22.41 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.14), residues: 3576 helix: 1.73 (0.13), residues: 1538 sheet: 0.50 (0.24), residues: 421 loop : 0.05 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 285 TYR 0.024 0.001 TYR D 631 PHE 0.014 0.001 PHE D 461 TRP 0.007 0.001 TRP F 323 HIS 0.005 0.001 HIS C1173 Details of bonding type rmsd covalent geometry : bond 0.00501 (31391) covalent geometry : angle 0.55481 (42862) hydrogen bonds : bond 0.04541 ( 1468) hydrogen bonds : angle 4.37264 ( 4121) metal coordination : bond 0.01103 ( 8) metal coordination : angle 5.16851 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 711 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7723 (mtpt) REVERT: C 120 GLN cc_start: 0.8035 (tt0) cc_final: 0.7661 (tt0) REVERT: C 371 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7286 (mtt-85) REVERT: C 386 GLU cc_start: 0.7178 (tp30) cc_final: 0.6807 (tp30) REVERT: C 390 PHE cc_start: 0.8181 (m-80) cc_final: 0.7862 (m-80) REVERT: C 402 ARG cc_start: 0.8199 (tpp-160) cc_final: 0.7968 (tpm170) REVERT: C 417 GLN cc_start: 0.7833 (tt0) cc_final: 0.7512 (tt0) REVERT: C 472 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7548 (tm-30) REVERT: C 488 MET cc_start: 0.7905 (mmt) cc_final: 0.7485 (mmt) REVERT: C 726 SER cc_start: 0.8558 (OUTLIER) cc_final: 0.8311 (p) REVERT: C 915 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.7391 (p0) REVERT: C 1030 GLU cc_start: 0.7288 (tp30) cc_final: 0.6748 (tp30) REVERT: C 1034 ARG cc_start: 0.7752 (ttm-80) cc_final: 0.7458 (ttm-80) REVERT: C 1166 GLU cc_start: 0.7280 (pm20) cc_final: 0.7015 (pm20) REVERT: C 1288 GLU cc_start: 0.7917 (tt0) cc_final: 0.7717 (tt0) REVERT: C 1339 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7268 (mt-10) REVERT: D 137 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7418 (mtp180) REVERT: D 204 GLU cc_start: 0.7600 (tp30) cc_final: 0.7010 (tm-30) REVERT: D 294 ASN cc_start: 0.8466 (t0) cc_final: 0.8134 (t0) REVERT: D 304 ASP cc_start: 0.7669 (m-30) cc_final: 0.7424 (m-30) REVERT: D 399 LYS cc_start: 0.8318 (mptp) cc_final: 0.7969 (mttp) REVERT: D 556 ILE cc_start: 0.8144 (mm) cc_final: 0.7814 (mm) REVERT: D 699 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7342 (tm-30) REVERT: D 1003 LEU cc_start: 0.3501 (OUTLIER) cc_final: 0.3239 (pp) REVERT: D 1159 HIS cc_start: 0.7159 (OUTLIER) cc_final: 0.6769 (m90) REVERT: D 1222 LEU cc_start: 0.8294 (mt) cc_final: 0.8064 (mt) REVERT: D 1340 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7610 (ttt-90) REVERT: D 1366 GLN cc_start: 0.7761 (mm110) cc_final: 0.7537 (mm-40) REVERT: B 171 ARG cc_start: 0.6395 (OUTLIER) cc_final: 0.5898 (mmm-85) REVERT: F 272 LYS cc_start: 0.8195 (tmtt) cc_final: 0.7939 (tmtt) REVERT: F 274 PHE cc_start: 0.7211 (t80) cc_final: 0.6889 (t80) REVERT: F 296 MET cc_start: 0.5703 (tpp) cc_final: 0.5432 (tpp) REVERT: F 372 ARG cc_start: 0.7751 (mtm-85) cc_final: 0.7467 (mtm-85) REVERT: F 400 LYS cc_start: 0.8406 (ttpp) cc_final: 0.8193 (ptmm) REVERT: F 559 LEU cc_start: 0.8399 (mt) cc_final: 0.8179 (mt) REVERT: F 563 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6698 (mt-10) outliers start: 105 outliers final: 61 residues processed: 754 average time/residue: 0.7671 time to fit residues: 662.0549 Evaluate side-chains 773 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 703 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 272 LYS Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 726 SER Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 984 TYR Chi-restraints excluded: chain C residue 1105 SER Chi-restraints excluded: chain C residue 1247 THR Chi-restraints excluded: chain C residue 1254 THR Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 718 SER Chi-restraints excluded: chain D residue 781 LYS Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 836 THR Chi-restraints excluded: chain D residue 879 GLN Chi-restraints excluded: chain D residue 889 ASP Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1003 LEU Chi-restraints excluded: chain D residue 1159 HIS Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1340 ARG Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 354 MET Chi-restraints excluded: chain F residue 476 ARG Chi-restraints excluded: chain F residue 587 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 329 optimal weight: 10.0000 chunk 316 optimal weight: 0.9980 chunk 365 optimal weight: 0.6980 chunk 147 optimal weight: 0.8980 chunk 29 optimal weight: 0.4980 chunk 200 optimal weight: 0.9980 chunk 323 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 136 optimal weight: 0.0970 chunk 199 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 ASN C1136 GLN D 158 GLN D 680 ASN D 739 GLN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 ASN F 291 GLN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.150971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.115143 restraints weight = 70525.422| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.51 r_work: 0.3224 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31399 Z= 0.130 Angle : 0.524 9.257 42874 Z= 0.277 Chirality : 0.040 0.253 4892 Planarity : 0.004 0.061 5190 Dihedral : 16.711 179.328 5244 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.80 % Allowed : 23.22 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.14), residues: 3576 helix: 1.87 (0.13), residues: 1540 sheet: 0.49 (0.25), residues: 410 loop : 0.13 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1033 TYR 0.019 0.001 TYR D 631 PHE 0.011 0.001 PHE C 35 TRP 0.006 0.001 TRP D 33 HIS 0.004 0.000 HIS C1173 Details of bonding type rmsd covalent geometry : bond 0.00299 (31391) covalent geometry : angle 0.51966 (42862) hydrogen bonds : bond 0.03827 ( 1468) hydrogen bonds : angle 4.22554 ( 4121) metal coordination : bond 0.00705 ( 8) metal coordination : angle 4.21185 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 708 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7684 (mtpt) REVERT: C 120 GLN cc_start: 0.8011 (tt0) cc_final: 0.7623 (tt0) REVERT: C 371 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7109 (mtp180) REVERT: C 386 GLU cc_start: 0.7129 (tp30) cc_final: 0.6759 (tp30) REVERT: C 391 SER cc_start: 0.8404 (t) cc_final: 0.7858 (p) REVERT: C 402 ARG cc_start: 0.8182 (tpp-160) cc_final: 0.7936 (tpm170) REVERT: C 417 GLN cc_start: 0.7845 (tt0) cc_final: 0.7533 (tt0) REVERT: C 472 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7539 (tm-30) REVERT: C 488 MET cc_start: 0.7881 (mmt) cc_final: 0.7449 (mmt) REVERT: C 726 SER cc_start: 0.8549 (OUTLIER) cc_final: 0.8323 (p) REVERT: C 955 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7617 (tp30) REVERT: C 1030 GLU cc_start: 0.7276 (tp30) cc_final: 0.6717 (tp30) REVERT: C 1034 ARG cc_start: 0.7790 (ttm-80) cc_final: 0.7499 (ttm-80) REVERT: C 1166 GLU cc_start: 0.7314 (pm20) cc_final: 0.7005 (mp0) REVERT: C 1339 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7289 (mt-10) REVERT: D 91 GLU cc_start: 0.8109 (tt0) cc_final: 0.7876 (pt0) REVERT: D 137 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7441 (mtp180) REVERT: D 204 GLU cc_start: 0.7528 (tp30) cc_final: 0.7057 (tm-30) REVERT: D 259 ARG cc_start: 0.8199 (mmt180) cc_final: 0.7998 (mmt180) REVERT: D 294 ASN cc_start: 0.8465 (t0) cc_final: 0.8118 (t0) REVERT: D 304 ASP cc_start: 0.7734 (m-30) cc_final: 0.7442 (m-30) REVERT: D 370 LYS cc_start: 0.8227 (mtmt) cc_final: 0.8025 (mtmm) REVERT: D 386 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7292 (mp0) REVERT: D 388 ARG cc_start: 0.8216 (mmm-85) cc_final: 0.7970 (ptp-170) REVERT: D 399 LYS cc_start: 0.8352 (mptp) cc_final: 0.8023 (mttp) REVERT: D 699 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7374 (tm-30) REVERT: D 803 VAL cc_start: 0.8477 (OUTLIER) cc_final: 0.8191 (p) REVERT: D 833 VAL cc_start: 0.8820 (m) cc_final: 0.8585 (p) REVERT: D 1003 LEU cc_start: 0.3473 (OUTLIER) cc_final: 0.3263 (pp) REVERT: D 1159 HIS cc_start: 0.7121 (OUTLIER) cc_final: 0.6741 (m90) REVERT: D 1222 LEU cc_start: 0.8303 (mt) cc_final: 0.8073 (mt) REVERT: D 1366 GLN cc_start: 0.7779 (mm110) cc_final: 0.7567 (mm-40) REVERT: F 138 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7401 (pp20) REVERT: F 272 LYS cc_start: 0.8210 (tmtt) cc_final: 0.7948 (tmtt) REVERT: F 296 MET cc_start: 0.5673 (tpp) cc_final: 0.5387 (tpp) REVERT: F 356 GLU cc_start: 0.7382 (tp30) cc_final: 0.6937 (mm-30) REVERT: F 372 ARG cc_start: 0.7753 (mtm-85) cc_final: 0.7364 (mtm-85) REVERT: F 396 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7711 (mt) REVERT: F 400 LYS cc_start: 0.8451 (ttpp) cc_final: 0.8209 (ptmm) REVERT: F 563 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6718 (mt-10) outliers start: 86 outliers final: 56 residues processed: 743 average time/residue: 0.7804 time to fit residues: 663.1694 Evaluate side-chains 765 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 701 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 272 LYS Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 726 SER Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 984 TYR Chi-restraints excluded: chain C residue 1105 SER Chi-restraints excluded: chain C residue 1143 GLU Chi-restraints excluded: chain C residue 1247 THR Chi-restraints excluded: chain C residue 1254 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 718 SER Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 781 LYS Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 836 THR Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1003 LEU Chi-restraints excluded: chain D residue 1159 HIS Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1304 GLU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 476 ARG Chi-restraints excluded: chain F residue 587 GLN Chi-restraints excluded: chain F residue 592 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 217 optimal weight: 0.4980 chunk 281 optimal weight: 3.9990 chunk 297 optimal weight: 0.6980 chunk 163 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 338 optimal weight: 6.9990 chunk 310 optimal weight: 5.9990 chunk 164 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 ASN D 158 GLN D 680 ASN D 700 ASN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 ASN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.148675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.113264 restraints weight = 64576.852| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.37 r_work: 0.3192 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 31399 Z= 0.239 Angle : 0.587 10.523 42874 Z= 0.308 Chirality : 0.044 0.266 4892 Planarity : 0.005 0.063 5190 Dihedral : 16.792 174.873 5242 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.70 % Allowed : 23.15 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.14), residues: 3576 helix: 1.69 (0.13), residues: 1537 sheet: 0.47 (0.24), residues: 435 loop : 0.02 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C1033 TYR 0.026 0.002 TYR D 631 PHE 0.015 0.002 PHE D 461 TRP 0.007 0.001 TRP F 323 HIS 0.005 0.001 HIS C1173 Details of bonding type rmsd covalent geometry : bond 0.00577 (31391) covalent geometry : angle 0.58238 (42862) hydrogen bonds : bond 0.04714 ( 1468) hydrogen bonds : angle 4.40689 ( 4121) metal coordination : bond 0.01015 ( 8) metal coordination : angle 4.55850 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 699 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7728 (mtpt) REVERT: C 203 LYS cc_start: 0.8731 (pttm) cc_final: 0.8507 (pttp) REVERT: C 371 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7036 (mtp-110) REVERT: C 386 GLU cc_start: 0.7273 (tp30) cc_final: 0.6877 (tp30) REVERT: C 391 SER cc_start: 0.8502 (t) cc_final: 0.7953 (p) REVERT: C 402 ARG cc_start: 0.8204 (tpp-160) cc_final: 0.7970 (tpm170) REVERT: C 417 GLN cc_start: 0.7878 (tt0) cc_final: 0.7544 (tt0) REVERT: C 472 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7590 (tm-30) REVERT: C 514 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7474 (m-80) REVERT: C 726 SER cc_start: 0.8552 (OUTLIER) cc_final: 0.8313 (p) REVERT: C 915 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7407 (p0) REVERT: C 955 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7692 (tp30) REVERT: C 1030 GLU cc_start: 0.7339 (tp30) cc_final: 0.6800 (tp30) REVERT: C 1034 ARG cc_start: 0.7778 (ttm-80) cc_final: 0.7473 (ttm-80) REVERT: C 1166 GLU cc_start: 0.7317 (pm20) cc_final: 0.6994 (mp0) REVERT: C 1339 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7345 (mt-10) REVERT: D 91 GLU cc_start: 0.8133 (tt0) cc_final: 0.7862 (pt0) REVERT: D 137 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7380 (mtp180) REVERT: D 204 GLU cc_start: 0.7599 (tp30) cc_final: 0.7056 (tm-30) REVERT: D 294 ASN cc_start: 0.8474 (t0) cc_final: 0.8140 (t0) REVERT: D 304 ASP cc_start: 0.7691 (m-30) cc_final: 0.7443 (m-30) REVERT: D 399 LYS cc_start: 0.8375 (mptp) cc_final: 0.8045 (mttp) REVERT: D 1003 LEU cc_start: 0.3215 (OUTLIER) cc_final: 0.2999 (pp) REVERT: D 1159 HIS cc_start: 0.7173 (OUTLIER) cc_final: 0.6786 (m90) REVERT: D 1222 LEU cc_start: 0.8308 (mt) cc_final: 0.8086 (mt) REVERT: D 1366 GLN cc_start: 0.7787 (mm110) cc_final: 0.7580 (mm-40) REVERT: B 58 GLU cc_start: 0.7792 (tt0) cc_final: 0.7299 (tt0) REVERT: B 171 ARG cc_start: 0.6408 (OUTLIER) cc_final: 0.5961 (mmm-85) REVERT: F 272 LYS cc_start: 0.8223 (tmtt) cc_final: 0.7961 (tmtt) REVERT: F 296 MET cc_start: 0.5680 (tpp) cc_final: 0.5377 (tpp) REVERT: F 356 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.7108 (tp30) REVERT: F 385 LYS cc_start: 0.8176 (tttp) cc_final: 0.7964 (tttm) REVERT: F 396 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7563 (tt) REVERT: F 400 LYS cc_start: 0.8406 (ttpp) cc_final: 0.8199 (ptmm) REVERT: F 489 GLU cc_start: 0.7066 (mp0) cc_final: 0.6813 (mp0) REVERT: F 559 LEU cc_start: 0.8451 (mt) cc_final: 0.8247 (mt) REVERT: F 563 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6715 (mt-10) outliers start: 83 outliers final: 57 residues processed: 731 average time/residue: 0.7867 time to fit residues: 658.8853 Evaluate side-chains 763 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 695 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 272 LYS Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 726 SER Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 984 TYR Chi-restraints excluded: chain C residue 1032 LYS Chi-restraints excluded: chain C residue 1105 SER Chi-restraints excluded: chain C residue 1247 THR Chi-restraints excluded: chain C residue 1254 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 718 SER Chi-restraints excluded: chain D residue 781 LYS Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 836 THR Chi-restraints excluded: chain D residue 879 GLN Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1003 LEU Chi-restraints excluded: chain D residue 1159 HIS Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1304 GLU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 354 MET Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 587 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 345 optimal weight: 1.9990 chunk 219 optimal weight: 0.5980 chunk 183 optimal weight: 0.5980 chunk 242 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 335 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 364 optimal weight: 0.1980 chunk 210 optimal weight: 0.0040 chunk 206 optimal weight: 0.9990 chunk 269 optimal weight: 0.9980 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 ASN D 158 GLN D 277 ASN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 ASN B 84 ASN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.151083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.115602 restraints weight = 67425.637| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.45 r_work: 0.3230 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31399 Z= 0.118 Angle : 0.526 12.184 42874 Z= 0.277 Chirality : 0.040 0.288 4892 Planarity : 0.004 0.060 5190 Dihedral : 16.681 179.492 5242 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.21 % Allowed : 24.07 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.14), residues: 3576 helix: 1.87 (0.13), residues: 1546 sheet: 0.53 (0.25), residues: 409 loop : 0.11 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1033 TYR 0.018 0.001 TYR D 631 PHE 0.009 0.001 PHE C 35 TRP 0.006 0.001 TRP D 33 HIS 0.004 0.000 HIS C1173 Details of bonding type rmsd covalent geometry : bond 0.00266 (31391) covalent geometry : angle 0.52254 (42862) hydrogen bonds : bond 0.03654 ( 1468) hydrogen bonds : angle 4.19296 ( 4121) metal coordination : bond 0.00596 ( 8) metal coordination : angle 3.69765 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 710 time to evaluate : 1.324 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: C 37 LYS cc_start: 0.8498 (ttmm) cc_final: 0.8244 (mtpp) REVERT: C 120 GLN cc_start: 0.7930 (tt0) cc_final: 0.7722 (tt0) REVERT: C 203 LYS cc_start: 0.8637 (pttm) cc_final: 0.8411 (pttp) REVERT: C 224 PHE cc_start: 0.7809 (m-80) cc_final: 0.7561 (m-80) REVERT: C 238 MET cc_start: 0.3232 (OUTLIER) cc_final: 0.2850 (tpt) REVERT: C 295 LYS cc_start: 0.6000 (mmpt) cc_final: 0.5273 (mttp) REVERT: C 386 GLU cc_start: 0.7109 (tp30) cc_final: 0.6732 (tp30) REVERT: C 391 SER cc_start: 0.8396 (t) cc_final: 0.7836 (p) REVERT: C 402 ARG cc_start: 0.8178 (tpp-160) cc_final: 0.7942 (tpm170) REVERT: C 417 GLN cc_start: 0.7860 (tt0) cc_final: 0.7522 (tt0) REVERT: C 472 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7522 (tm-30) REVERT: C 685 MET cc_start: 0.8434 (ptp) cc_final: 0.8222 (mtt) REVERT: C 726 SER cc_start: 0.8541 (OUTLIER) cc_final: 0.8326 (p) REVERT: C 955 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7679 (tp30) REVERT: C 1030 GLU cc_start: 0.7257 (tp30) cc_final: 0.6670 (tp30) REVERT: C 1034 ARG cc_start: 0.7767 (ttm-80) cc_final: 0.7458 (ttm-80) REVERT: C 1166 GLU cc_start: 0.7294 (pm20) cc_final: 0.6987 (mp0) REVERT: C 1197 MET cc_start: 0.8627 (mmm) cc_final: 0.8372 (mmt) REVERT: C 1339 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7328 (mt-10) REVERT: D 204 GLU cc_start: 0.7511 (tp30) cc_final: 0.7025 (tm-30) REVERT: D 294 ASN cc_start: 0.8428 (t0) cc_final: 0.8082 (t0) REVERT: D 304 ASP cc_start: 0.7743 (m-30) cc_final: 0.7450 (m-30) REVERT: D 370 LYS cc_start: 0.8190 (mtmt) cc_final: 0.7979 (mtmm) REVERT: D 386 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7240 (mp0) REVERT: D 399 LYS cc_start: 0.8318 (mptp) cc_final: 0.7970 (mttp) REVERT: D 699 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7393 (tm-30) REVERT: D 803 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8150 (p) REVERT: D 833 VAL cc_start: 0.8811 (m) cc_final: 0.8593 (p) REVERT: D 1159 HIS cc_start: 0.7125 (OUTLIER) cc_final: 0.6741 (m90) REVERT: D 1222 LEU cc_start: 0.8285 (mt) cc_final: 0.8055 (mt) REVERT: D 1366 GLN cc_start: 0.7794 (mm110) cc_final: 0.7580 (mm-40) REVERT: F 272 LYS cc_start: 0.8212 (tmtt) cc_final: 0.7941 (tmtt) REVERT: F 296 MET cc_start: 0.5609 (tpp) cc_final: 0.5313 (tpp) REVERT: F 372 ARG cc_start: 0.7792 (mtm-85) cc_final: 0.7240 (mtt90) REVERT: F 396 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7612 (mt) REVERT: F 400 LYS cc_start: 0.8439 (ttpp) cc_final: 0.8193 (ptmm) REVERT: F 453 ASP cc_start: 0.7451 (m-30) cc_final: 0.7148 (m-30) REVERT: F 489 GLU cc_start: 0.7075 (mp0) cc_final: 0.6826 (mp0) REVERT: F 559 LEU cc_start: 0.8353 (mt) cc_final: 0.8150 (mt) REVERT: F 563 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6675 (mt-10) outliers start: 68 outliers final: 45 residues processed: 735 average time/residue: 0.8000 time to fit residues: 674.4781 Evaluate side-chains 753 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 703 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 272 LYS Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 726 SER Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 984 TYR Chi-restraints excluded: chain C residue 1247 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 781 LYS Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 836 THR Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1159 HIS Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 476 ARG Chi-restraints excluded: chain F residue 587 GLN Chi-restraints excluded: chain F residue 592 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 366 optimal weight: 0.9980 chunk 92 optimal weight: 0.4980 chunk 10 optimal weight: 0.0870 chunk 244 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 276 optimal weight: 0.0000 chunk 180 optimal weight: 0.6980 chunk 311 optimal weight: 0.0470 chunk 127 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 223 optimal weight: 0.8980 overall best weight: 0.2460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 ASN C1080 ASN C1136 GLN D 158 GLN D 680 ASN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN ** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.152970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.117881 restraints weight = 63741.752| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.37 r_work: 0.3264 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 31399 Z= 0.108 Angle : 0.516 10.842 42874 Z= 0.270 Chirality : 0.040 0.289 4892 Planarity : 0.004 0.059 5190 Dihedral : 16.558 178.864 5240 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.46 % Allowed : 25.04 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.14), residues: 3576 helix: 2.01 (0.13), residues: 1552 sheet: 0.51 (0.25), residues: 427 loop : 0.19 (0.16), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 88 TYR 0.017 0.001 TYR D 144 PHE 0.016 0.001 PHE F 274 TRP 0.006 0.001 TRP D 33 HIS 0.004 0.000 HIS C1173 Details of bonding type rmsd covalent geometry : bond 0.00241 (31391) covalent geometry : angle 0.51343 (42862) hydrogen bonds : bond 0.03349 ( 1468) hydrogen bonds : angle 4.07319 ( 4121) metal coordination : bond 0.00522 ( 8) metal coordination : angle 3.31171 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 716 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 TYR cc_start: 0.8207 (m-80) cc_final: 0.7870 (m-80) REVERT: C 37 LYS cc_start: 0.8460 (ttmm) cc_final: 0.8239 (mtpp) REVERT: C 80 PHE cc_start: 0.8659 (m-80) cc_final: 0.8276 (m-80) REVERT: C 119 GLU cc_start: 0.7371 (tt0) cc_final: 0.7148 (tt0) REVERT: C 224 PHE cc_start: 0.7694 (m-80) cc_final: 0.7406 (m-80) REVERT: C 371 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7379 (mtt-85) REVERT: C 386 GLU cc_start: 0.6994 (tp30) cc_final: 0.6584 (tp30) REVERT: C 391 SER cc_start: 0.8326 (t) cc_final: 0.7756 (p) REVERT: C 402 ARG cc_start: 0.8142 (tpp-160) cc_final: 0.7921 (tpm170) REVERT: C 417 GLN cc_start: 0.7789 (tt0) cc_final: 0.7433 (tt0) REVERT: C 514 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.7205 (m-80) REVERT: C 726 SER cc_start: 0.8545 (OUTLIER) cc_final: 0.8332 (p) REVERT: C 800 MET cc_start: 0.7985 (mmm) cc_final: 0.7262 (mtm) REVERT: C 955 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7683 (tp30) REVERT: C 1034 ARG cc_start: 0.7717 (ttm-80) cc_final: 0.7514 (ttm-80) REVERT: C 1231 MET cc_start: 0.8518 (mtp) cc_final: 0.8284 (mmt) REVERT: C 1288 GLU cc_start: 0.7858 (tt0) cc_final: 0.7627 (tt0) REVERT: C 1339 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7305 (mt-10) REVERT: D 137 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7473 (mtp180) REVERT: D 143 MET cc_start: 0.8135 (ptm) cc_final: 0.7310 (ptp) REVERT: D 204 GLU cc_start: 0.7482 (tp30) cc_final: 0.7019 (tm-30) REVERT: D 259 ARG cc_start: 0.8172 (mmt180) cc_final: 0.7914 (mmt180) REVERT: D 304 ASP cc_start: 0.7702 (m-30) cc_final: 0.7385 (m-30) REVERT: D 370 LYS cc_start: 0.8211 (mtmt) cc_final: 0.7990 (mtmm) REVERT: D 399 LYS cc_start: 0.8381 (mptp) cc_final: 0.8058 (mttp) REVERT: D 416 ILE cc_start: 0.7517 (pp) cc_final: 0.7291 (mt) REVERT: D 699 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7381 (tm-30) REVERT: D 803 VAL cc_start: 0.8284 (OUTLIER) cc_final: 0.8005 (p) REVERT: D 833 VAL cc_start: 0.8732 (m) cc_final: 0.8507 (p) REVERT: D 1222 LEU cc_start: 0.8315 (mt) cc_final: 0.8084 (mt) REVERT: D 1339 LYS cc_start: 0.8330 (mttp) cc_final: 0.8111 (mttm) REVERT: A 184 ILE cc_start: 0.8861 (mm) cc_final: 0.8593 (mt) REVERT: B 58 GLU cc_start: 0.7735 (tt0) cc_final: 0.7506 (tt0) REVERT: F 272 LYS cc_start: 0.8196 (tmtt) cc_final: 0.7916 (tmtt) REVERT: F 296 MET cc_start: 0.5558 (tpp) cc_final: 0.5258 (tpp) REVERT: F 372 ARG cc_start: 0.7786 (mtm-85) cc_final: 0.7017 (mtt90) REVERT: F 396 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7622 (mt) REVERT: F 400 LYS cc_start: 0.8411 (ttpp) cc_final: 0.8162 (ptmm) REVERT: F 453 ASP cc_start: 0.7330 (m-30) cc_final: 0.7007 (m-30) REVERT: F 563 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6666 (mt-10) outliers start: 45 outliers final: 30 residues processed: 733 average time/residue: 0.8126 time to fit residues: 681.2913 Evaluate side-chains 734 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 698 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 272 LYS Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 726 SER Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 984 TYR Chi-restraints excluded: chain C residue 1247 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 781 LYS Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 836 THR Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 476 ARG Chi-restraints excluded: chain F residue 587 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 224 optimal weight: 0.7980 chunk 276 optimal weight: 0.0980 chunk 73 optimal weight: 0.3980 chunk 64 optimal weight: 0.4980 chunk 251 optimal weight: 4.9990 chunk 115 optimal weight: 20.0000 chunk 364 optimal weight: 7.9990 chunk 271 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 282 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 ASN C1092 GLN D 158 GLN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.152145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.117015 restraints weight = 61638.843| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.31 r_work: 0.3252 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31399 Z= 0.124 Angle : 0.528 10.809 42874 Z= 0.278 Chirality : 0.040 0.292 4892 Planarity : 0.004 0.059 5190 Dihedral : 16.569 178.951 5240 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.43 % Allowed : 25.69 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.14), residues: 3576 helix: 2.00 (0.13), residues: 1549 sheet: 0.57 (0.25), residues: 410 loop : 0.20 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 88 TYR 0.017 0.001 TYR D 631 PHE 0.014 0.001 PHE F 274 TRP 0.008 0.001 TRP D 33 HIS 0.004 0.000 HIS C1173 Details of bonding type rmsd covalent geometry : bond 0.00286 (31391) covalent geometry : angle 0.52533 (42862) hydrogen bonds : bond 0.03531 ( 1468) hydrogen bonds : angle 4.06728 ( 4121) metal coordination : bond 0.00558 ( 8) metal coordination : angle 3.45584 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15390.80 seconds wall clock time: 261 minutes 16.70 seconds (15676.70 seconds total)