Starting phenix.real_space_refine on Sat Jul 4 02:45:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ffb_50353/07_2026/9ffb_50353.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ffb_50353/07_2026/9ffb_50353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ffb_50353/07_2026/9ffb_50353.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ffb_50353/07_2026/9ffb_50353.map" model { file = "/net/cci-nas-00/data/ceres_data/9ffb_50353/07_2026/9ffb_50353.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ffb_50353/07_2026/9ffb_50353.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 491 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 42 5.49 5 S 96 5.16 5 C 10940 2.51 5 N 2905 2.21 5 O 3272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17255 Number of models: 1 Model: "" Number of chains: 4 Chain: "S" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 453 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "T" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 407 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 8884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1118, 8884 Classifications: {'peptide': 1118} Link IDs: {'PTRANS': 46, 'TRANS': 1071} Chain breaks: 10 Chain: "B" Number of atoms: 7511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7511 Classifications: {'peptide': 948} Link IDs: {'PTRANS': 27, 'TRANS': 920} Chain breaks: 12 Residues with excluded nonbonded symmetry interactions: 70 residue: pdb=" N ARG A 55 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG A 55 " occ=0.00 residue: pdb=" N ILE A 60 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE A 60 " occ=0.19 residue: pdb=" N GLY A 64 " occ=0.48 ... (2 atoms not shown) pdb=" O GLY A 64 " occ=0.00 residue: pdb=" N GLU A 65 " occ=0.45 ... (7 atoms not shown) pdb=" OE2 GLU A 65 " occ=0.82 residue: pdb=" N GLU A 69 " occ=0.29 ... (7 atoms not shown) pdb=" OE2 GLU A 69 " occ=0.61 residue: pdb=" N ASP A 73 " occ=0.00 ... (6 atoms not shown) pdb=" OD2 ASP A 73 " occ=0.00 residue: pdb=" N SER A 90 " occ=0.09 ... (4 atoms not shown) pdb=" OG SER A 90 " occ=0.36 residue: pdb=" N PRO A 92 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO A 92 " occ=0.00 residue: pdb=" N GLY A 93 " occ=0.33 ... (2 atoms not shown) pdb=" O GLY A 93 " occ=0.00 residue: pdb=" N VAL A 94 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL A 94 " occ=0.71 residue: pdb=" N GLU A 97 " occ=0.97 ... (7 atoms not shown) pdb=" OE2 GLU A 97 " occ=0.60 residue: pdb=" N ASN A 114 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN A 114 " occ=0.35 ... (remaining 58 not shown) Time building chain proxies: 3.86, per 1000 atoms: 0.22 Number of scatterers: 17255 At special positions: 0 Unit cell: (109.692, 169.524, 133.791, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 42 15.00 O 3272 8.00 N 2905 7.00 C 10940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 716.9 milliseconds 4034 Ramachandran restraints generated. 2017 Oldfield, 0 Emsley, 2017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3968 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 2 sheets defined 76.7% alpha, 0.5% beta 8 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 48 through 57 Processing helix chain 'A' and resid 76 through 88 Processing helix chain 'A' and resid 91 through 107 Processing helix chain 'A' and resid 108 through 116 removed outlier: 3.669A pdb=" N LEU A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 145 through 147 No H-bonds generated for 'chain 'A' and resid 145 through 147' Processing helix chain 'A' and resid 148 through 160 removed outlier: 3.927A pdb=" N VAL A 153 " --> pdb=" O GLN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 191 through 204 removed outlier: 3.675A pdb=" N LYS A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 222 Proline residue: A 219 - end of helix removed outlier: 3.545A pdb=" N LEU A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 241 Processing helix chain 'A' and resid 244 through 255 removed outlier: 4.032A pdb=" N ILE A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 272 removed outlier: 3.687A pdb=" N LYS A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 291 removed outlier: 4.374A pdb=" N VAL A 284 " --> pdb=" O ASP A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 308 removed outlier: 4.143A pdb=" N SER A 302 " --> pdb=" O VAL A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 360 removed outlier: 4.121A pdb=" N GLN A 360 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 378 removed outlier: 3.735A pdb=" N ASN A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 394 Processing helix chain 'A' and resid 400 through 413 Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 428 through 431 Processing helix chain 'A' and resid 433 through 446 removed outlier: 4.382A pdb=" N ILE A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N THR A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 466 removed outlier: 4.265A pdb=" N VAL A 454 " --> pdb=" O HIS A 450 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 486 Processing helix chain 'A' and resid 488 through 506 removed outlier: 3.620A pdb=" N LEU A 492 " --> pdb=" O ASN A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 524 removed outlier: 4.363A pdb=" N LEU A 510 " --> pdb=" O HIS A 506 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N THR A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N PHE A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 540 removed outlier: 3.985A pdb=" N TYR A 537 " --> pdb=" O ARG A 533 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 540 " --> pdb=" O PHE A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 564 Processing helix chain 'A' and resid 570 through 588 removed outlier: 4.081A pdb=" N GLN A 574 " --> pdb=" O PRO A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 623 Processing helix chain 'A' and resid 626 through 644 removed outlier: 3.664A pdb=" N LEU A 630 " --> pdb=" O THR A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 657 Processing helix chain 'A' and resid 659 through 664 removed outlier: 3.874A pdb=" N PHE A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 747 removed outlier: 3.727A pdb=" N ARG A 737 " --> pdb=" O SER A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 758 removed outlier: 3.650A pdb=" N LEU A 758 " --> pdb=" O ASP A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 776 removed outlier: 3.546A pdb=" N VAL A 769 " --> pdb=" O ASP A 766 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU A 770 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP A 774 " --> pdb=" O GLY A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 803 removed outlier: 3.609A pdb=" N SER A 786 " --> pdb=" O GLU A 782 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS A 803 " --> pdb=" O VAL A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 835 removed outlier: 3.941A pdb=" N LYS A 830 " --> pdb=" O ASN A 826 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS A 831 " --> pdb=" O VAL A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 924 Processing helix chain 'A' and resid 931 through 935 Processing helix chain 'A' and resid 961 through 979 removed outlier: 3.886A pdb=" N TRP A 973 " --> pdb=" O ASP A 969 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS A 974 " --> pdb=" O ASP A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1018 Processing helix chain 'A' and resid 1019 through 1036 removed outlier: 3.889A pdb=" N VAL A1036 " --> pdb=" O TYR A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1072 removed outlier: 3.718A pdb=" N LEU A1055 " --> pdb=" O GLN A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1078 Processing helix chain 'A' and resid 1079 through 1080 No H-bonds generated for 'chain 'A' and resid 1079 through 1080' Processing helix chain 'A' and resid 1081 through 1097 Processing helix chain 'A' and resid 1105 through 1118 Processing helix chain 'A' and resid 1126 through 1141 Processing helix chain 'A' and resid 1146 through 1163 Processing helix chain 'A' and resid 1176 through 1193 Processing helix chain 'A' and resid 1195 through 1206 Processing helix chain 'A' and resid 1208 through 1214 Processing helix chain 'A' and resid 1230 through 1248 removed outlier: 3.873A pdb=" N PHE A1234 " --> pdb=" O THR A1230 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1285 removed outlier: 3.848A pdb=" N LEU A1266 " --> pdb=" O LEU A1262 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS A1267 " --> pdb=" O GLU A1263 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N TRP A1268 " --> pdb=" O LYS A1264 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS A1283 " --> pdb=" O ILE A1279 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL A1284 " --> pdb=" O ASN A1280 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE A1285 " --> pdb=" O LEU A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1320 removed outlier: 3.680A pdb=" N LYS A1296 " --> pdb=" O SER A1292 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N MET A1310 " --> pdb=" O LEU A1306 " (cutoff:3.500A) Proline residue: A1311 - end of helix removed outlier: 3.866A pdb=" N HIS A1315 " --> pdb=" O PRO A1311 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LYS A1318 " --> pdb=" O ASP A1314 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS A1319 " --> pdb=" O HIS A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1321 through 1348 removed outlier: 4.527A pdb=" N GLN A1337 " --> pdb=" O LEU A1333 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU A1338 " --> pdb=" O SER A1334 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N HIS A1339 " --> pdb=" O THR A1335 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N HIS A1340 " --> pdb=" O ARG A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1353 through 1355 No H-bonds generated for 'chain 'A' and resid 1353 through 1355' Processing helix chain 'A' and resid 1356 through 1378 removed outlier: 3.551A pdb=" N LEU A1360 " --> pdb=" O HIS A1356 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS A1372 " --> pdb=" O VAL A1368 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN A1378 " --> pdb=" O MET A1374 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 224 removed outlier: 3.743A pdb=" N LYS B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 245 Processing helix chain 'B' and resid 264 through 284 removed outlier: 3.751A pdb=" N VAL B 269 " --> pdb=" O GLN B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 290 removed outlier: 4.494A pdb=" N GLU B 289 " --> pdb=" O GLN B 285 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU B 290 " --> pdb=" O ASP B 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 285 through 290' Processing helix chain 'B' and resid 293 through 302 Processing helix chain 'B' and resid 308 through 319 Processing helix chain 'B' and resid 324 through 349 Processing helix chain 'B' and resid 349 through 356 removed outlier: 3.572A pdb=" N GLN B 353 " --> pdb=" O SER B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 373 removed outlier: 3.629A pdb=" N VAL B 365 " --> pdb=" O ASP B 361 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL B 370 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 396 removed outlier: 4.375A pdb=" N GLU B 396 " --> pdb=" O MET B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 435 Processing helix chain 'B' and resid 438 through 451 removed outlier: 4.088A pdb=" N LEU B 451 " --> pdb=" O LEU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 472 removed outlier: 3.990A pdb=" N ILE B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 479 Processing helix chain 'B' and resid 483 through 491 removed outlier: 3.577A pdb=" N ASP B 488 " --> pdb=" O GLU B 485 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 490 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER B 491 " --> pdb=" O ASP B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 Proline residue: B 507 - end of helix Processing helix chain 'B' and resid 512 through 528 removed outlier: 4.295A pdb=" N PHE B 528 " --> pdb=" O GLN B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 549 removed outlier: 3.555A pdb=" N LEU B 544 " --> pdb=" O ALA B 540 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 546 " --> pdb=" O PHE B 542 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ARG B 547 " --> pdb=" O LEU B 543 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 589 removed outlier: 3.748A pdb=" N ILE B 589 " --> pdb=" O PHE B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 597 removed outlier: 4.576A pdb=" N LEU B 593 " --> pdb=" O ILE B 589 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 616 removed outlier: 4.487A pdb=" N MET B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU B 607 " --> pdb=" O VAL B 603 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR B 608 " --> pdb=" O ARG B 604 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR B 612 " --> pdb=" O TYR B 608 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASP B 613 " --> pdb=" O GLU B 609 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL B 614 " --> pdb=" O GLY B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 634 removed outlier: 3.663A pdb=" N SER B 623 " --> pdb=" O SER B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 637 No H-bonds generated for 'chain 'B' and resid 635 through 637' Processing helix chain 'B' and resid 648 through 652 Processing helix chain 'B' and resid 665 through 684 removed outlier: 3.579A pdb=" N VAL B 684 " --> pdb=" O TYR B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 719 removed outlier: 3.624A pdb=" N LYS B 718 " --> pdb=" O ARG B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 764 removed outlier: 3.579A pdb=" N LEU B 756 " --> pdb=" O ILE B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 786 removed outlier: 3.638A pdb=" N ASP B 773 " --> pdb=" O ASN B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 821 Processing helix chain 'B' and resid 830 through 836 removed outlier: 3.816A pdb=" N VAL B 834 " --> pdb=" O GLU B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 838 through 859 removed outlier: 4.508A pdb=" N ALA B 849 " --> pdb=" O ALA B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 891 removed outlier: 3.633A pdb=" N MET B 873 " --> pdb=" O ASN B 869 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG B 882 " --> pdb=" O CYS B 878 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL B 883 " --> pdb=" O LYS B 879 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE B 891 " --> pdb=" O ARG B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 924 removed outlier: 3.552A pdb=" N CYS B 910 " --> pdb=" O ILE B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 936 removed outlier: 3.598A pdb=" N PHE B 932 " --> pdb=" O ARG B 928 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 936 " --> pdb=" O PHE B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 971 removed outlier: 3.827A pdb=" N LYS B 953 " --> pdb=" O ASN B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 976 removed outlier: 3.583A pdb=" N PHE B 976 " --> pdb=" O GLU B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 992 removed outlier: 3.654A pdb=" N THR B 981 " --> pdb=" O ASN B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 995 No H-bonds generated for 'chain 'B' and resid 993 through 995' Processing helix chain 'B' and resid 1000 through 1016 removed outlier: 3.506A pdb=" N GLN B1004 " --> pdb=" O GLN B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1020 through 1035 removed outlier: 3.601A pdb=" N CYS B1024 " --> pdb=" O ASP B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1056 Processing helix chain 'B' and resid 1080 through 1106 removed outlier: 4.211A pdb=" N LEU B1086 " --> pdb=" O THR B1082 " (cutoff:3.500A) Processing helix chain 'B' and resid 1122 through 1146 removed outlier: 3.518A pdb=" N GLY B1129 " --> pdb=" O ALA B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1167 removed outlier: 3.728A pdb=" N ASP B1156 " --> pdb=" O GLY B1152 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B1167 " --> pdb=" O SER B1163 " (cutoff:3.500A) Processing helix chain 'B' and resid 1170 through 1176 Processing helix chain 'B' and resid 1177 through 1179 No H-bonds generated for 'chain 'B' and resid 1177 through 1179' Processing helix chain 'B' and resid 1188 through 1202 Processing helix chain 'B' and resid 1202 through 1222 removed outlier: 3.643A pdb=" N SER B1208 " --> pdb=" O PRO B1204 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B1210 " --> pdb=" O CYS B1206 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASN B1215 " --> pdb=" O THR B1211 " (cutoff:3.500A) Processing helix chain 'B' and resid 1242 through 1247 Processing helix chain 'B' and resid 1251 through 1274 removed outlier: 3.844A pdb=" N ASN B1255 " --> pdb=" O LYS B1251 " (cutoff:3.500A) Processing helix chain 'B' and resid 1293 through 1297 Processing sheet with id=AA1, first strand: chain 'A' and resid 685 through 687 removed outlier: 3.507A pdb=" N LEU A 687 " --> pdb=" O LEU A 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1386 through 1389 removed outlier: 4.612A pdb=" N SER B1287 " --> pdb=" O LEU A1389 " (cutoff:3.500A) 1042 hydrogen bonds defined for protein. 3054 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 3.34 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.40: 6836 1.40 - 1.58: 10564 1.58 - 1.77: 88 1.77 - 1.95: 141 1.95 - 2.13: 5 Bond restraints: 17634 Sorted by residual: bond pdb=" C ASN A 174 " pdb=" N PHE A 175 " ideal model delta sigma weight residual 1.331 2.003 -0.672 2.07e-02 2.33e+03 1.06e+03 bond pdb=" CE2 PHE A 163 " pdb=" CZ PHE A 163 " ideal model delta sigma weight residual 1.382 2.134 -0.752 3.00e-02 1.11e+03 6.28e+02 bond pdb=" CD1 PHE A 163 " pdb=" CE1 PHE A 163 " ideal model delta sigma weight residual 1.382 2.125 -0.743 3.00e-02 1.11e+03 6.13e+02 bond pdb=" CD2 PHE A 163 " pdb=" CE2 PHE A 163 " ideal model delta sigma weight residual 1.382 2.120 -0.738 3.00e-02 1.11e+03 6.05e+02 bond pdb=" CE1 PHE A 163 " pdb=" CZ PHE A 163 " ideal model delta sigma weight residual 1.382 2.059 -0.677 3.00e-02 1.11e+03 5.09e+02 ... (remaining 17629 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.78: 23926 7.78 - 15.56: 69 15.56 - 23.34: 1 23.34 - 31.12: 0 31.12 - 38.90: 1 Bond angle restraints: 23997 Sorted by residual: angle pdb=" C ASN A 174 " pdb=" N PHE A 175 " pdb=" CA PHE A 175 " ideal model delta sigma weight residual 121.80 160.70 -38.90 2.44e+00 1.68e-01 2.54e+02 angle pdb=" CA ASN A 174 " pdb=" C ASN A 174 " pdb=" O ASN A 174 " ideal model delta sigma weight residual 120.80 105.50 15.30 1.70e+00 3.46e-01 8.10e+01 angle pdb=" CA PRO A 207 " pdb=" N PRO A 207 " pdb=" CD PRO A 207 " ideal model delta sigma weight residual 112.00 101.99 10.01 1.40e+00 5.10e-01 5.11e+01 angle pdb=" CA PRO A1105 " pdb=" N PRO A1105 " pdb=" CD PRO A1105 " ideal model delta sigma weight residual 112.00 103.51 8.49 1.40e+00 5.10e-01 3.68e+01 angle pdb=" CA ASN A 174 " pdb=" C ASN A 174 " pdb=" N PHE A 175 " ideal model delta sigma weight residual 116.20 128.31 -12.11 2.00e+00 2.50e-01 3.67e+01 ... (remaining 23992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 10079 35.78 - 71.55: 537 71.55 - 107.33: 35 107.33 - 143.10: 1 143.10 - 178.88: 3 Dihedral angle restraints: 10655 sinusoidal: 4601 harmonic: 6054 Sorted by residual: dihedral pdb=" C4' DT S 18 " pdb=" C3' DT S 18 " pdb=" O3' DT S 18 " pdb=" P DC S 19 " ideal model delta sinusoidal sigma weight residual 220.00 41.12 178.88 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC S 5 " pdb=" C3' DC S 5 " pdb=" O3' DC S 5 " pdb=" P DT S 6 " ideal model delta sinusoidal sigma weight residual -140.00 31.84 -171.84 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DA S 11 " pdb=" C3' DA S 11 " pdb=" O3' DA S 11 " pdb=" P DG S 12 " ideal model delta sinusoidal sigma weight residual 220.00 59.54 160.46 1 3.50e+01 8.16e-04 1.52e+01 ... (remaining 10652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 2781 0.123 - 0.246: 24 0.246 - 0.369: 3 0.369 - 0.492: 18 0.492 - 0.616: 5 Chirality restraints: 2831 Sorted by residual: chirality pdb=" P DA T 49 " pdb=" OP1 DA T 49 " pdb=" OP2 DA T 49 " pdb=" O5' DA T 49 " both_signs ideal model delta sigma weight residual True 2.34 -2.95 -0.62 2.00e-01 2.50e+01 9.47e+00 chirality pdb=" P DG S 12 " pdb=" OP1 DG S 12 " pdb=" OP2 DG S 12 " pdb=" O5' DG S 12 " both_signs ideal model delta sigma weight residual True 2.34 -2.94 -0.61 2.00e-01 2.50e+01 9.20e+00 chirality pdb=" P DG T 50 " pdb=" OP1 DG T 50 " pdb=" OP2 DG T 50 " pdb=" O5' DG T 50 " both_signs ideal model delta sigma weight residual True 2.34 -2.89 -0.56 2.00e-01 2.50e+01 7.74e+00 ... (remaining 2828 not shown) Planarity restraints: 2874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 206 " 0.107 5.00e-02 4.00e+02 1.55e-01 3.85e+01 pdb=" N PRO A 207 " -0.268 5.00e-02 4.00e+02 pdb=" CA PRO A 207 " 0.083 5.00e-02 4.00e+02 pdb=" CD PRO A 207 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1104 " -0.067 5.00e-02 4.00e+02 9.59e-02 1.47e+01 pdb=" N PRO A1105 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO A1105 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A1105 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 175 " 0.058 5.00e-02 4.00e+02 8.69e-02 1.21e+01 pdb=" N PRO A 176 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " 0.048 5.00e-02 4.00e+02 ... (remaining 2871 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 217 2.59 - 3.17: 15650 3.17 - 3.75: 30274 3.75 - 4.32: 37750 4.32 - 4.90: 59082 Nonbonded interactions: 142973 Sorted by model distance: nonbonded pdb=" CD1 PHE A 163 " pdb=" N PHE A 175 " model vdw 2.015 3.420 nonbonded pdb=" CD2 PHE A 163 " pdb=" N PHE A 175 " model vdw 2.036 3.420 nonbonded pdb=" CG PHE A 163 " pdb=" N PHE A 175 " model vdw 2.050 3.340 nonbonded pdb=" OD1 ASP B 361 " pdb=" OG1 THR B 363 " model vdw 2.071 3.040 nonbonded pdb=" CE1 PHE A 163 " pdb=" N PHE A 175 " model vdw 2.073 3.420 ... (remaining 142968 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.73 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 18.330 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 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 : 0.013 0.752 17634 Z= 0.536 Angle : 0.963 38.896 23997 Z= 0.487 Chirality : 0.058 0.616 2831 Planarity : 0.006 0.155 2874 Dihedral : 20.149 178.879 6687 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.45 % Favored : 93.51 % Rotamer: Outliers : 0.16 % Allowed : 31.82 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.48 (0.19), residues: 2017 helix: 0.51 (0.14), residues: 1431 sheet: None (None), residues: 0 loop : -2.34 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1370 TYR 0.018 0.001 TYR A 461 PHE 0.041 0.002 PHE A1067 TRP 0.023 0.001 TRP A 794 HIS 0.008 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.01333 / 0.54 (17634) covalent geometry : angle 0.96327 / 0.49 (23997) hydrogen bonds : bond 0.17537 / 17.29 ( 1063) hydrogen bonds : angle 6.25499 / 6.10 ( 3096) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4034 Ramachandran restraints generated. 2017 Oldfield, 0 Emsley, 2017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4034 Ramachandran restraints generated. 2017 Oldfield, 0 Emsley, 2017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 117 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.7503 (mpp) cc_final: 0.7279 (mpp) REVERT: A 1127 PHE cc_start: 0.8488 (t80) cc_final: 0.8186 (t80) REVERT: B 996 ASP cc_start: 0.8658 (p0) cc_final: 0.7869 (p0) outliers start: 3 outliers final: 3 residues processed: 118 average time/residue: 0.1269 time to fit residues: 24.4924 Evaluate side-chains 115 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 621 PHE Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 423 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.0370 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 overall best weight: 3.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 GLN A 531 GLN A1024 ASN ** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.056283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.042396 restraints weight = 110642.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.043285 restraints weight = 55763.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.043875 restraints weight = 36607.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.044192 restraints weight = 28276.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.044442 restraints weight = 24412.827| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3189 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3196 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.741 17634 Z= 0.530 Angle : 0.811 38.629 23997 Z= 0.409 Chirality : 0.044 0.297 2831 Planarity : 0.005 0.091 2874 Dihedral : 16.771 178.919 2624 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.59 % Favored : 93.36 % Rotamer: Outliers : 4.06 % Allowed : 29.36 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.45 (0.19), residues: 2018 helix: 0.54 (0.14), residues: 1456 sheet: None (None), residues: 0 loop : -2.50 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1160 TYR 0.018 0.002 TYR A1297 PHE 0.028 0.002 PHE A 163 TRP 0.010 0.001 TRP A 794 HIS 0.008 0.001 HIS A 572 Details of bonding type rmsd/Z covalent geometry : bond 0.01356 / 0.53 (17634) covalent geometry : angle 0.81114 / 0.41 (23997) hydrogen bonds : bond 0.05942 / 5.97 ( 1063) hydrogen bonds : angle 4.92445 / 5.14 ( 3096) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 120 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLN cc_start: 0.9439 (mm110) cc_final: 0.9173 (mm-40) REVERT: A 279 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7342 (pp20) REVERT: A 420 MET cc_start: 0.8394 (ppp) cc_final: 0.7979 (ptm) REVERT: A 461 TYR cc_start: 0.7443 (OUTLIER) cc_final: 0.7024 (m-80) REVERT: A 618 LEU cc_start: 0.6302 (OUTLIER) cc_final: 0.6090 (tp) REVERT: A 968 LEU cc_start: 0.7590 (mp) cc_final: 0.7264 (mp) REVERT: A 1063 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8499 (tp) REVERT: B 237 PHE cc_start: 0.8429 (OUTLIER) cc_final: 0.8082 (t80) REVERT: B 363 THR cc_start: 0.9172 (p) cc_final: 0.8967 (p) REVERT: B 440 SER cc_start: 0.8577 (OUTLIER) cc_final: 0.8010 (p) REVERT: B 488 ASP cc_start: 0.9386 (p0) cc_final: 0.8717 (p0) REVERT: B 528 PHE cc_start: 0.7837 (OUTLIER) cc_final: 0.7375 (m-10) REVERT: B 716 MET cc_start: 0.9563 (mmp) cc_final: 0.9153 (mmp) REVERT: B 817 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8680 (mm) REVERT: B 996 ASP cc_start: 0.8620 (p0) cc_final: 0.8057 (p0) REVERT: B 1009 THR cc_start: 0.9241 (OUTLIER) cc_final: 0.9012 (p) REVERT: B 1289 ASP cc_start: 0.3818 (p0) cc_final: 0.3523 (p0) outliers start: 76 outliers final: 27 residues processed: 191 average time/residue: 0.1243 time to fit residues: 38.2906 Evaluate side-chains 153 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 740 ARG Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 972 CYS Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1187 CYS Chi-restraints excluded: chain A residue 1219 CYS Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain A residue 1320 HIS Chi-restraints excluded: chain A residue 1334 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 528 PHE Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 987 ILE Chi-restraints excluded: chain B residue 991 LEU Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1170 THR Chi-restraints excluded: chain B residue 1171 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 74 optimal weight: 8.9990 chunk 145 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 chunk 204 optimal weight: 0.9990 chunk 139 optimal weight: 8.9990 chunk 159 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 450 HIS ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 GLN A 644 GLN A1005 GLN ** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1030 HIS B 668 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.054458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.040745 restraints weight = 112189.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.041756 restraints weight = 62241.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.041810 restraints weight = 34241.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.041919 restraints weight = 32054.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.042028 restraints weight = 30671.877| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3196 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3247 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.752 17634 Z= 0.569 Angle : 0.890 38.737 23997 Z= 0.450 Chirality : 0.048 0.591 2831 Planarity : 0.006 0.089 2874 Dihedral : 16.868 178.045 2617 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.88 % Favored : 92.07 % Rotamer: Outliers : 6.31 % Allowed : 28.56 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.90 (0.18), residues: 2018 helix: 0.22 (0.13), residues: 1462 sheet: None (None), residues: 0 loop : -2.72 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 916 TYR 0.025 0.002 TYR A1297 PHE 0.028 0.003 PHE A1231 TRP 0.010 0.002 TRP B 377 HIS 0.006 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.01428 / 0.57 (17634) covalent geometry : angle 0.89008 / 0.45 (23997) hydrogen bonds : bond 0.05934 / 6.13 ( 1063) hydrogen bonds : angle 5.09249 / 5.35 ( 3096) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 114 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.7496 (mpp) cc_final: 0.7236 (mpp) REVERT: A 270 MET cc_start: 0.6642 (mmm) cc_final: 0.5898 (mmm) REVERT: A 279 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7253 (pp20) REVERT: A 538 ILE cc_start: 0.8139 (mm) cc_final: 0.7771 (tt) REVERT: A 745 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8709 (tm-30) REVERT: A 920 TYR cc_start: 0.8837 (OUTLIER) cc_final: 0.8526 (t80) REVERT: A 1060 TYR cc_start: 0.7732 (OUTLIER) cc_final: 0.7444 (t80) REVERT: A 1092 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7034 (pp) REVERT: A 1268 TRP cc_start: 0.8295 (m100) cc_final: 0.7408 (m100) REVERT: B 440 SER cc_start: 0.8411 (OUTLIER) cc_final: 0.7830 (p) REVERT: B 528 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.7201 (m-10) REVERT: B 716 MET cc_start: 0.9631 (mmp) cc_final: 0.9295 (mmp) REVERT: B 817 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8716 (mm) REVERT: B 1009 THR cc_start: 0.9236 (OUTLIER) cc_final: 0.9032 (p) REVERT: B 1037 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8946 (mm) REVERT: B 1127 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8171 (pp20) outliers start: 118 outliers final: 73 residues processed: 224 average time/residue: 0.1155 time to fit residues: 42.4443 Evaluate side-chains 194 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 110 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 621 PHE Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 740 ARG Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 785 CYS Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 920 TYR Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 965 CYS Chi-restraints excluded: chain A residue 972 CYS Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1058 SER Chi-restraints excluded: chain A residue 1060 TYR Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1145 MET Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1187 CYS Chi-restraints excluded: chain A residue 1219 CYS Chi-restraints excluded: chain A residue 1245 SER Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain A residue 1320 HIS Chi-restraints excluded: chain A residue 1334 SER Chi-restraints excluded: chain A residue 1390 LYS Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 528 PHE Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 987 ILE Chi-restraints excluded: chain B residue 990 THR Chi-restraints excluded: chain B residue 991 LEU Chi-restraints excluded: chain B residue 1002 PHE Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1127 GLU Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1155 VAL Chi-restraints excluded: chain B residue 1170 THR Chi-restraints excluded: chain B residue 1171 SER Chi-restraints excluded: chain B residue 1195 VAL Chi-restraints excluded: chain B residue 1221 LEU Chi-restraints excluded: chain B residue 1241 THR Chi-restraints excluded: chain B residue 1267 LEU Chi-restraints excluded: chain B residue 1276 VAL Chi-restraints excluded: chain B residue 1278 LEU Chi-restraints excluded: chain B residue 1289 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 61 optimal weight: 9.9990 chunk 49 optimal weight: 0.4980 chunk 109 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 205 optimal weight: 0.0170 chunk 165 optimal weight: 9.9990 chunk 170 optimal weight: 0.6980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 531 GLN A 800 ASN ** A1025 HIS ** 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 = 0.3669 r_free = 0.3669 target = 0.056464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.041877 restraints weight = 108707.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.042754 restraints weight = 54136.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.043329 restraints weight = 35434.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.043651 restraints weight = 27478.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.043888 restraints weight = 23739.691| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3249 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3247 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3285 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.747 17634 Z= 0.506 Angle : 0.792 38.726 23997 Z= 0.391 Chirality : 0.043 0.316 2831 Planarity : 0.005 0.089 2874 Dihedral : 16.878 179.707 2617 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.10 % Favored : 93.86 % Rotamer: Outliers : 4.60 % Allowed : 30.80 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.46 (0.19), residues: 2018 helix: 0.56 (0.14), residues: 1451 sheet: None (None), residues: 0 loop : -2.53 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1006 TYR 0.019 0.001 TYR A1297 PHE 0.025 0.002 PHE B 812 TRP 0.018 0.002 TRP A 794 HIS 0.008 0.001 HIS A1002 Details of bonding type rmsd/Z covalent geometry : bond 0.01311 / 0.51 (17634) covalent geometry : angle 0.79206 / 0.39 (23997) hydrogen bonds : bond 0.04658 / 4.76 ( 1063) hydrogen bonds : angle 4.63236 / 4.87 ( 3096) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 129 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ILE cc_start: 0.6485 (OUTLIER) cc_final: 0.5684 (tt) REVERT: A 270 MET cc_start: 0.6782 (mmm) cc_final: 0.6052 (mmm) REVERT: A 538 ILE cc_start: 0.8065 (mm) cc_final: 0.7758 (tt) REVERT: A 745 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8520 (tm-30) REVERT: A 764 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6616 (tp) REVERT: A 920 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.8566 (t80) REVERT: B 237 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.8215 (t80) REVERT: B 363 THR cc_start: 0.9241 (p) cc_final: 0.8988 (t) REVERT: B 440 SER cc_start: 0.8596 (OUTLIER) cc_final: 0.8045 (p) REVERT: B 528 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.7150 (m-10) REVERT: B 716 MET cc_start: 0.9608 (mmp) cc_final: 0.9220 (mmp) REVERT: B 817 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8677 (mm) REVERT: B 996 ASP cc_start: 0.8625 (p0) cc_final: 0.8111 (p0) REVERT: B 1037 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8934 (mm) REVERT: B 1078 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8822 (t) REVERT: B 1127 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8139 (pp20) outliers start: 86 outliers final: 37 residues processed: 204 average time/residue: 0.1173 time to fit residues: 39.2879 Evaluate side-chains 170 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 122 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain A residue 621 PHE Chi-restraints excluded: chain A residue 740 ARG Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 920 TYR Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1030 HIS Chi-restraints excluded: chain A residue 1058 SER Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1219 CYS Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain A residue 1320 HIS Chi-restraints excluded: chain A residue 1390 LYS Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 528 PHE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 1002 PHE Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain B residue 1127 GLU Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1155 VAL Chi-restraints excluded: chain B residue 1171 SER Chi-restraints excluded: chain B residue 1221 LEU Chi-restraints excluded: chain B residue 1242 VAL Chi-restraints excluded: chain B residue 1267 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 15 optimal weight: 0.5980 chunk 64 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 195 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 chunk 105 optimal weight: 0.9990 chunk 200 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 ASN A 825 GLN ** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.055832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.040966 restraints weight = 108479.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.041810 restraints weight = 54938.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.042369 restraints weight = 36344.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.042709 restraints weight = 28288.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.042917 restraints weight = 24397.794| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3285 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3334 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.750 17634 Z= 0.515 Angle : 0.800 38.774 23997 Z= 0.395 Chirality : 0.044 0.327 2831 Planarity : 0.005 0.089 2874 Dihedral : 16.845 179.562 2617 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.69 % Favored : 93.26 % Rotamer: Outliers : 4.92 % Allowed : 30.48 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.42 (0.19), residues: 2018 helix: 0.57 (0.13), residues: 1456 sheet: None (None), residues: 0 loop : -2.52 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 916 TYR 0.020 0.002 TYR A 461 PHE 0.024 0.002 PHE B 812 TRP 0.010 0.001 TRP A1073 HIS 0.007 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.01330 / 0.51 (17634) covalent geometry : angle 0.80036 / 0.39 (23997) hydrogen bonds : bond 0.04653 / 4.79 ( 1063) hydrogen bonds : angle 4.63730 / 4.89 ( 3096) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 117 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.7749 (mpp) cc_final: 0.6811 (mpp) REVERT: A 210 ILE cc_start: 0.6479 (OUTLIER) cc_final: 0.5608 (tt) REVERT: A 270 MET cc_start: 0.7058 (mmm) cc_final: 0.6169 (mmm) REVERT: A 538 ILE cc_start: 0.8131 (mm) cc_final: 0.7812 (tt) REVERT: A 745 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8521 (tm-30) REVERT: A 764 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6641 (tp) REVERT: A 920 TYR cc_start: 0.8781 (OUTLIER) cc_final: 0.8539 (t80) REVERT: A 1005 GLN cc_start: 0.6755 (OUTLIER) cc_final: 0.6105 (pp30) REVERT: A 1056 MET cc_start: 0.6527 (OUTLIER) cc_final: 0.6039 (ttm) REVERT: B 237 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.8194 (t80) REVERT: B 363 THR cc_start: 0.9256 (p) cc_final: 0.8972 (t) REVERT: B 440 SER cc_start: 0.8654 (OUTLIER) cc_final: 0.8159 (p) REVERT: B 528 PHE cc_start: 0.7718 (OUTLIER) cc_final: 0.7040 (m-10) REVERT: B 590 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8770 (mt) REVERT: B 709 LEU cc_start: 0.9749 (OUTLIER) cc_final: 0.9405 (mt) REVERT: B 716 MET cc_start: 0.9580 (mmp) cc_final: 0.9248 (mmp) REVERT: B 817 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8666 (mm) REVERT: B 824 ASN cc_start: 0.8549 (OUTLIER) cc_final: 0.8273 (m-40) REVERT: B 1078 THR cc_start: 0.9194 (OUTLIER) cc_final: 0.8913 (t) REVERT: B 1127 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8134 (pp20) outliers start: 92 outliers final: 55 residues processed: 197 average time/residue: 0.1158 time to fit residues: 37.1624 Evaluate side-chains 184 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 114 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 621 PHE Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 740 ARG Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 920 TYR Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 972 CYS Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1030 HIS Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1058 SER Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain A residue 1320 HIS Chi-restraints excluded: chain A residue 1335 THR Chi-restraints excluded: chain A residue 1390 LYS Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 528 PHE Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 824 ASN Chi-restraints excluded: chain B residue 991 LEU Chi-restraints excluded: chain B residue 1002 PHE Chi-restraints excluded: chain B residue 1024 CYS Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1127 GLU Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1155 VAL Chi-restraints excluded: chain B residue 1170 THR Chi-restraints excluded: chain B residue 1195 VAL Chi-restraints excluded: chain B residue 1221 LEU Chi-restraints excluded: chain B residue 1242 VAL Chi-restraints excluded: chain B residue 1267 LEU Chi-restraints excluded: chain B residue 1289 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 103 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 531 GLN A 800 ASN ** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.056097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.041033 restraints weight = 108182.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.041880 restraints weight = 54497.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.042438 restraints weight = 35952.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.042763 restraints weight = 28019.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.042979 restraints weight = 24197.719| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3334 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3406 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.749 17634 Z= 0.508 Angle : 0.793 38.781 23997 Z= 0.389 Chirality : 0.043 0.347 2831 Planarity : 0.005 0.089 2874 Dihedral : 16.809 179.952 2617 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.10 % Favored : 93.86 % Rotamer: Outliers : 5.51 % Allowed : 30.32 % Favored : 64.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.19), residues: 2018 helix: 0.65 (0.14), residues: 1459 sheet: None (None), residues: 0 loop : -2.53 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 916 TYR 0.018 0.001 TYR A1297 PHE 0.023 0.002 PHE A 163 TRP 0.011 0.001 TRP B1008 HIS 0.004 0.001 HIS A1192 Details of bonding type rmsd/Z covalent geometry : bond 0.01318 / 0.51 (17634) covalent geometry : angle 0.79276 / 0.39 (23997) hydrogen bonds : bond 0.04400 / 4.52 ( 1063) hydrogen bonds : angle 4.55025 / 4.80 ( 3096) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 125 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.6993 (OUTLIER) cc_final: 0.6737 (tp40) REVERT: A 200 MET cc_start: 0.7674 (mpp) cc_final: 0.6926 (mpp) REVERT: A 210 ILE cc_start: 0.6353 (OUTLIER) cc_final: 0.5454 (tt) REVERT: A 270 MET cc_start: 0.7153 (mmm) cc_final: 0.6254 (mmm) REVERT: A 538 ILE cc_start: 0.8138 (mm) cc_final: 0.7851 (tt) REVERT: A 745 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8489 (tm-30) REVERT: A 764 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6684 (tp) REVERT: A 920 TYR cc_start: 0.8737 (OUTLIER) cc_final: 0.8516 (t80) REVERT: A 1029 MET cc_start: 0.8967 (ppp) cc_final: 0.8730 (ppp) REVERT: A 1056 MET cc_start: 0.6484 (OUTLIER) cc_final: 0.5920 (ttm) REVERT: A 1092 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.6934 (pp) REVERT: A 1127 PHE cc_start: 0.8492 (t80) cc_final: 0.8135 (t80) REVERT: B 237 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.8239 (t80) REVERT: B 363 THR cc_start: 0.9263 (p) cc_final: 0.8932 (t) REVERT: B 440 SER cc_start: 0.8746 (OUTLIER) cc_final: 0.8224 (p) REVERT: B 528 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.6897 (m-10) REVERT: B 590 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8772 (mt) REVERT: B 716 MET cc_start: 0.9583 (OUTLIER) cc_final: 0.9249 (mmp) REVERT: B 817 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8669 (mm) REVERT: B 824 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8277 (m-40) REVERT: B 996 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.7921 (p0) REVERT: B 1078 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8884 (t) REVERT: B 1127 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8213 (pp20) REVERT: B 1289 ASP cc_start: 0.3605 (p0) cc_final: 0.3318 (p0) outliers start: 103 outliers final: 58 residues processed: 217 average time/residue: 0.1043 time to fit residues: 37.8371 Evaluate side-chains 195 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 120 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 621 PHE Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 740 ARG Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 920 TYR Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 972 CYS Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1030 HIS Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1058 SER Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1126 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1187 CYS Chi-restraints excluded: chain A residue 1219 CYS Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain A residue 1320 HIS Chi-restraints excluded: chain A residue 1335 THR Chi-restraints excluded: chain A residue 1390 LYS Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 528 PHE Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 824 ASN Chi-restraints excluded: chain B residue 987 ILE Chi-restraints excluded: chain B residue 996 ASP Chi-restraints excluded: chain B residue 1002 PHE Chi-restraints excluded: chain B residue 1024 CYS Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1127 GLU Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1155 VAL Chi-restraints excluded: chain B residue 1170 THR Chi-restraints excluded: chain B residue 1221 LEU Chi-restraints excluded: chain B residue 1242 VAL Chi-restraints excluded: chain B residue 1260 ILE Chi-restraints excluded: chain B residue 1267 LEU Chi-restraints excluded: chain B residue 1276 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 64 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 199 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 531 GLN A1005 GLN ** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 HIS ** B1004 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 = 0.3672 r_free = 0.3672 target = 0.056258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.041196 restraints weight = 106600.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.042037 restraints weight = 53879.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.042598 restraints weight = 35495.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.042903 restraints weight = 27603.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.043138 restraints weight = 23906.385| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3406 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3468 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.749 17634 Z= 0.507 Angle : 0.800 38.787 23997 Z= 0.390 Chirality : 0.043 0.305 2831 Planarity : 0.005 0.089 2874 Dihedral : 16.760 179.361 2617 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.19 % Favored : 93.76 % Rotamer: Outliers : 5.56 % Allowed : 30.16 % Favored : 64.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.28 (0.19), residues: 2018 helix: 0.69 (0.14), residues: 1457 sheet: None (None), residues: 0 loop : -2.52 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 232 TYR 0.017 0.001 TYR A1297 PHE 0.023 0.002 PHE A 163 TRP 0.012 0.001 TRP A1073 HIS 0.007 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.01315 / 0.51 (17634) covalent geometry : angle 0.80007 / 0.39 (23997) hydrogen bonds : bond 0.04275 / 4.39 ( 1063) hydrogen bonds : angle 4.52008 / 4.78 ( 3096) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 119 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.7604 (mpp) cc_final: 0.6904 (mpp) REVERT: A 210 ILE cc_start: 0.6272 (OUTLIER) cc_final: 0.5344 (tt) REVERT: A 270 MET cc_start: 0.7049 (mmm) cc_final: 0.6192 (mmm) REVERT: A 279 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7347 (pp20) REVERT: A 538 ILE cc_start: 0.8121 (mm) cc_final: 0.7843 (tt) REVERT: A 745 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8418 (tm-30) REVERT: A 764 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6598 (tp) REVERT: A 1056 MET cc_start: 0.6456 (OUTLIER) cc_final: 0.5915 (ttm) REVERT: A 1060 TYR cc_start: 0.7564 (OUTLIER) cc_final: 0.6805 (t80) REVERT: A 1092 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.6959 (pp) REVERT: A 1127 PHE cc_start: 0.8495 (t80) cc_final: 0.8127 (t80) REVERT: A 1153 MET cc_start: 0.7048 (mmp) cc_final: 0.6833 (mmp) REVERT: B 237 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.8267 (t80) REVERT: B 363 THR cc_start: 0.9254 (p) cc_final: 0.8905 (t) REVERT: B 440 SER cc_start: 0.8742 (OUTLIER) cc_final: 0.8241 (p) REVERT: B 528 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.6842 (m-10) REVERT: B 590 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8763 (mt) REVERT: B 709 LEU cc_start: 0.9766 (OUTLIER) cc_final: 0.9462 (mt) REVERT: B 716 MET cc_start: 0.9573 (OUTLIER) cc_final: 0.9240 (mmp) REVERT: B 817 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8658 (mm) REVERT: B 824 ASN cc_start: 0.8538 (OUTLIER) cc_final: 0.8271 (m-40) REVERT: B 996 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.7821 (p0) REVERT: B 1078 THR cc_start: 0.9204 (OUTLIER) cc_final: 0.8890 (t) REVERT: B 1127 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8146 (pp20) REVERT: B 1289 ASP cc_start: 0.3482 (p0) cc_final: 0.3205 (p0) outliers start: 104 outliers final: 63 residues processed: 211 average time/residue: 0.1083 time to fit residues: 37.7393 Evaluate side-chains 198 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 117 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 740 ARG Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1030 HIS Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1058 SER Chi-restraints excluded: chain A residue 1060 TYR Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1126 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1187 CYS Chi-restraints excluded: chain A residue 1219 CYS Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain A residue 1320 HIS Chi-restraints excluded: chain A residue 1390 LYS Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 528 PHE Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 790 GLU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 824 ASN Chi-restraints excluded: chain B residue 987 ILE Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain B residue 991 LEU Chi-restraints excluded: chain B residue 996 ASP Chi-restraints excluded: chain B residue 1002 PHE Chi-restraints excluded: chain B residue 1024 CYS Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1127 GLU Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1170 THR Chi-restraints excluded: chain B residue 1171 SER Chi-restraints excluded: chain B residue 1195 VAL Chi-restraints excluded: chain B residue 1221 LEU Chi-restraints excluded: chain B residue 1242 VAL Chi-restraints excluded: chain B residue 1260 ILE Chi-restraints excluded: chain B residue 1267 LEU Chi-restraints excluded: chain B residue 1276 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 67 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 187 optimal weight: 4.9990 chunk 3 optimal weight: 40.0000 chunk 175 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 chunk 154 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 ASN ** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 HIS B 703 GLN ** B1004 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 = 0.3672 r_free = 0.3672 target = 0.056134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.041016 restraints weight = 107107.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.041847 restraints weight = 54008.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.042407 restraints weight = 35568.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.042707 restraints weight = 27636.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.042944 restraints weight = 23940.381| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3468 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3495 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.750 17634 Z= 0.510 Angle : 0.805 38.780 23997 Z= 0.393 Chirality : 0.044 0.305 2831 Planarity : 0.005 0.089 2874 Dihedral : 16.746 178.900 2617 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.39 % Favored : 93.56 % Rotamer: Outliers : 5.08 % Allowed : 30.53 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.30 (0.19), residues: 2018 helix: 0.67 (0.14), residues: 1456 sheet: None (None), residues: 0 loop : -2.49 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 243 TYR 0.017 0.001 TYR A1297 PHE 0.023 0.002 PHE A 163 TRP 0.012 0.001 TRP A1073 HIS 0.004 0.001 HIS A1061 Details of bonding type rmsd/Z covalent geometry : bond 0.01323 / 0.51 (17634) covalent geometry : angle 0.80544 / 0.39 (23997) hydrogen bonds : bond 0.04304 / 4.43 ( 1063) hydrogen bonds : angle 4.55529 / 4.85 ( 3096) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 121 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.7594 (mpp) cc_final: 0.6924 (mpp) REVERT: A 210 ILE cc_start: 0.6205 (OUTLIER) cc_final: 0.5282 (tt) REVERT: A 270 MET cc_start: 0.7177 (mmm) cc_final: 0.6280 (mmm) REVERT: A 279 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7427 (pp20) REVERT: A 538 ILE cc_start: 0.8084 (mm) cc_final: 0.7817 (tt) REVERT: A 745 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8419 (tm-30) REVERT: A 764 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6651 (tp) REVERT: A 1029 MET cc_start: 0.9035 (ppp) cc_final: 0.8713 (ppp) REVERT: A 1056 MET cc_start: 0.6536 (OUTLIER) cc_final: 0.5942 (ttm) REVERT: A 1060 TYR cc_start: 0.7442 (OUTLIER) cc_final: 0.6731 (t80) REVERT: A 1092 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6916 (pp) REVERT: A 1127 PHE cc_start: 0.8520 (t80) cc_final: 0.8159 (t80) REVERT: A 1153 MET cc_start: 0.6951 (mmp) cc_final: 0.6719 (mmp) REVERT: B 363 THR cc_start: 0.9254 (p) cc_final: 0.8907 (t) REVERT: B 440 SER cc_start: 0.8756 (OUTLIER) cc_final: 0.8262 (p) REVERT: B 528 PHE cc_start: 0.7570 (OUTLIER) cc_final: 0.6778 (m-10) REVERT: B 590 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8776 (mt) REVERT: B 709 LEU cc_start: 0.9772 (OUTLIER) cc_final: 0.9476 (mt) REVERT: B 716 MET cc_start: 0.9568 (OUTLIER) cc_final: 0.9246 (mmp) REVERT: B 817 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8659 (mm) REVERT: B 824 ASN cc_start: 0.8542 (OUTLIER) cc_final: 0.8279 (m-40) REVERT: B 996 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.7725 (p0) REVERT: B 1078 THR cc_start: 0.9230 (OUTLIER) cc_final: 0.8886 (t) REVERT: B 1127 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8174 (pp20) REVERT: B 1289 ASP cc_start: 0.3555 (p0) cc_final: 0.3279 (p0) outliers start: 95 outliers final: 67 residues processed: 206 average time/residue: 0.1010 time to fit residues: 34.8290 Evaluate side-chains 203 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 119 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 740 ARG Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 972 CYS Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1030 HIS Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1058 SER Chi-restraints excluded: chain A residue 1060 TYR Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1126 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1187 CYS Chi-restraints excluded: chain A residue 1219 CYS Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain A residue 1320 HIS Chi-restraints excluded: chain A residue 1335 THR Chi-restraints excluded: chain A residue 1390 LYS Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 528 PHE Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 790 GLU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 824 ASN Chi-restraints excluded: chain B residue 987 ILE Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain B residue 991 LEU Chi-restraints excluded: chain B residue 996 ASP Chi-restraints excluded: chain B residue 1002 PHE Chi-restraints excluded: chain B residue 1024 CYS Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1127 GLU Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1170 THR Chi-restraints excluded: chain B residue 1171 SER Chi-restraints excluded: chain B residue 1195 VAL Chi-restraints excluded: chain B residue 1221 LEU Chi-restraints excluded: chain B residue 1242 VAL Chi-restraints excluded: chain B residue 1260 ILE Chi-restraints excluded: chain B residue 1267 LEU Chi-restraints excluded: chain B residue 1278 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 199 optimal weight: 2.9990 chunk 146 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 chunk 116 optimal weight: 30.0000 chunk 48 optimal weight: 1.9990 chunk 138 optimal weight: 0.2980 chunk 154 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 153 optimal weight: 0.7980 chunk 195 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1034 GLN ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.056389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.041234 restraints weight = 106766.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.042080 restraints weight = 53666.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.042647 restraints weight = 35265.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.042971 restraints weight = 27341.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.043196 restraints weight = 23537.425| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3495 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3521 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.750 17634 Z= 0.506 Angle : 0.806 38.773 23997 Z= 0.391 Chirality : 0.043 0.304 2831 Planarity : 0.005 0.089 2874 Dihedral : 16.679 177.725 2617 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.29 % Favored : 93.66 % Rotamer: Outliers : 5.03 % Allowed : 30.59 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.24 (0.19), residues: 2018 helix: 0.72 (0.14), residues: 1455 sheet: None (None), residues: 0 loop : -2.46 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 232 TYR 0.016 0.001 TYR A1297 PHE 0.023 0.002 PHE A 163 TRP 0.014 0.001 TRP A1073 HIS 0.004 0.001 HIS A1192 Details of bonding type rmsd/Z covalent geometry : bond 0.01314 / 0.51 (17634) covalent geometry : angle 0.80564 / 0.39 (23997) hydrogen bonds : bond 0.04154 / 4.26 ( 1063) hydrogen bonds : angle 4.51122 / 4.79 ( 3096) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 122 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.6664 (mpp) REVERT: A 210 ILE cc_start: 0.6206 (OUTLIER) cc_final: 0.5257 (tt) REVERT: A 279 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7492 (pp20) REVERT: A 461 TYR cc_start: 0.7901 (OUTLIER) cc_final: 0.7013 (t80) REVERT: A 538 ILE cc_start: 0.8052 (mm) cc_final: 0.7789 (tt) REVERT: A 745 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8361 (tm-30) REVERT: A 764 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6701 (tp) REVERT: A 1029 MET cc_start: 0.9037 (ppp) cc_final: 0.8660 (ppp) REVERT: A 1056 MET cc_start: 0.6421 (OUTLIER) cc_final: 0.5835 (ttm) REVERT: A 1060 TYR cc_start: 0.7366 (OUTLIER) cc_final: 0.6663 (t80) REVERT: A 1069 LEU cc_start: 0.7999 (mt) cc_final: 0.7716 (mm) REVERT: A 1092 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6910 (pp) REVERT: A 1127 PHE cc_start: 0.8574 (t80) cc_final: 0.8223 (t80) REVERT: B 363 THR cc_start: 0.9279 (p) cc_final: 0.8990 (t) REVERT: B 528 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.6804 (m-10) REVERT: B 590 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8771 (mt) REVERT: B 709 LEU cc_start: 0.9778 (OUTLIER) cc_final: 0.9486 (mt) REVERT: B 716 MET cc_start: 0.9562 (OUTLIER) cc_final: 0.9238 (mmp) REVERT: B 817 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8648 (mm) REVERT: B 824 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.8276 (m-40) REVERT: B 996 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.7682 (p0) REVERT: B 1078 THR cc_start: 0.9211 (OUTLIER) cc_final: 0.8859 (t) REVERT: B 1127 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8236 (pp20) REVERT: B 1289 ASP cc_start: 0.3471 (p0) cc_final: 0.3191 (p0) outliers start: 94 outliers final: 62 residues processed: 203 average time/residue: 0.1122 time to fit residues: 37.6248 Evaluate side-chains 199 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 119 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 740 ARG Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 972 CYS Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1030 HIS Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1058 SER Chi-restraints excluded: chain A residue 1060 TYR Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1126 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1187 CYS Chi-restraints excluded: chain A residue 1219 CYS Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain A residue 1320 HIS Chi-restraints excluded: chain A residue 1335 THR Chi-restraints excluded: chain A residue 1390 LYS Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 528 PHE Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 790 GLU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 824 ASN Chi-restraints excluded: chain B residue 987 ILE Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain B residue 991 LEU Chi-restraints excluded: chain B residue 996 ASP Chi-restraints excluded: chain B residue 1002 PHE Chi-restraints excluded: chain B residue 1024 CYS Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain B residue 1084 CYS Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1127 GLU Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1171 SER Chi-restraints excluded: chain B residue 1195 VAL Chi-restraints excluded: chain B residue 1221 LEU Chi-restraints excluded: chain B residue 1242 VAL Chi-restraints excluded: chain B residue 1260 ILE Chi-restraints excluded: chain B residue 1267 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 111 optimal weight: 0.4980 chunk 58 optimal weight: 0.4980 chunk 175 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 180 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 115 optimal weight: 0.0050 chunk 159 optimal weight: 0.3980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1344 HIS ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.057358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.042514 restraints weight = 105936.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.043429 restraints weight = 59381.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.043488 restraints weight = 33798.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.043625 restraints weight = 32824.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.043665 restraints weight = 28252.785| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3521 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3533 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.749 17634 Z= 0.503 Angle : 0.825 38.768 23997 Z= 0.398 Chirality : 0.043 0.291 2831 Planarity : 0.005 0.089 2874 Dihedral : 16.563 175.329 2617 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.05 % Favored : 93.90 % Rotamer: Outliers : 3.74 % Allowed : 31.87 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.17 (0.19), residues: 2018 helix: 0.77 (0.14), residues: 1454 sheet: None (None), residues: 0 loop : -2.44 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 232 TYR 0.013 0.001 TYR A1297 PHE 0.025 0.002 PHE A1231 TRP 0.019 0.001 TRP A1165 HIS 0.004 0.001 HIS A1192 Details of bonding type rmsd/Z covalent geometry : bond 0.01307 / 0.50 (17634) covalent geometry : angle 0.82531 / 0.40 (23997) hydrogen bonds : bond 0.03968 / 4.08 ( 1063) hydrogen bonds : angle 4.39533 / 4.65 ( 3096) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 127 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.6829 (mpp) REVERT: A 279 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7509 (pp20) REVERT: A 461 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.7054 (t80) REVERT: A 538 ILE cc_start: 0.8058 (mm) cc_final: 0.7820 (tt) REVERT: A 745 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8482 (mm-30) REVERT: A 764 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7150 (tp) REVERT: A 1029 MET cc_start: 0.9077 (ppp) cc_final: 0.8688 (ppp) REVERT: A 1056 MET cc_start: 0.6530 (OUTLIER) cc_final: 0.5933 (ttm) REVERT: A 1060 TYR cc_start: 0.7285 (OUTLIER) cc_final: 0.6605 (t80) REVERT: A 1069 LEU cc_start: 0.7919 (mt) cc_final: 0.7408 (mm) REVERT: A 1092 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.6930 (pp) REVERT: A 1127 PHE cc_start: 0.8565 (t80) cc_final: 0.8237 (t80) REVERT: B 363 THR cc_start: 0.9374 (p) cc_final: 0.9018 (t) REVERT: B 528 PHE cc_start: 0.7600 (OUTLIER) cc_final: 0.6823 (m-10) REVERT: B 590 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8765 (mt) REVERT: B 709 LEU cc_start: 0.9773 (OUTLIER) cc_final: 0.9493 (mt) REVERT: B 716 MET cc_start: 0.9634 (OUTLIER) cc_final: 0.9267 (mmp) REVERT: B 817 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8641 (mm) REVERT: B 824 ASN cc_start: 0.8563 (OUTLIER) cc_final: 0.8358 (m-40) REVERT: B 996 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.7650 (p0) REVERT: B 1127 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8125 (pp20) REVERT: B 1289 ASP cc_start: 0.3487 (p0) cc_final: 0.3193 (p0) outliers start: 70 outliers final: 43 residues processed: 187 average time/residue: 0.1123 time to fit residues: 34.1357 Evaluate side-chains 180 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 121 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 972 CYS Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1030 HIS Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1060 TYR Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1126 SER Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1219 CYS Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain A residue 1390 LYS Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 528 PHE Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 790 GLU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 824 ASN Chi-restraints excluded: chain B residue 987 ILE Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain B residue 996 ASP Chi-restraints excluded: chain B residue 1002 PHE Chi-restraints excluded: chain B residue 1024 CYS Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain B residue 1127 GLU Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain B residue 1171 SER Chi-restraints excluded: chain B residue 1221 LEU Chi-restraints excluded: chain B residue 1278 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 186 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 177 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 197 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 127 optimal weight: 8.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.057075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.042314 restraints weight = 106529.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.042892 restraints weight = 62285.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.043121 restraints weight = 38164.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.043242 restraints weight = 34547.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.043303 restraints weight = 30115.334| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3533 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3548 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.752 17634 Z= 0.504 Angle : 0.808 38.873 23997 Z= 0.392 Chirality : 0.042 0.284 2831 Planarity : 0.005 0.090 2874 Dihedral : 16.508 174.168 2617 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.10 % Favored : 93.86 % Rotamer: Outliers : 3.58 % Allowed : 31.82 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.11 (0.19), residues: 2018 helix: 0.83 (0.14), residues: 1451 sheet: None (None), residues: 0 loop : -2.44 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 243 TYR 0.014 0.001 TYR A1297 PHE 0.028 0.002 PHE A1231 TRP 0.017 0.001 TRP A1073 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.01312 / 0.50 (17634) covalent geometry : angle 0.80830 / 0.39 (23997) hydrogen bonds : bond 0.03995 / 4.13 ( 1063) hydrogen bonds : angle 4.39739 / 4.69 ( 3096) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3355.71 seconds wall clock time: 58 minutes 39.18 seconds (3519.18 seconds total)