Starting phenix.real_space_refine on Sun Jun 15 22:06:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ffb_50353/06_2025/9ffb_50353.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ffb_50353/06_2025/9ffb_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_50353/06_2025/9ffb_50353.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ffb_50353/06_2025/9ffb_50353.map" model { file = "/net/cci-nas-00/data/ceres_data/9ffb_50353/06_2025/9ffb_50353.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ffb_50353/06_2025/9ffb_50353.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.78, per 1000 atoms: 0.62 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: 4.99 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 6.23 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: 7.29 Time building geometry restraints manager: 5.57 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 - 0.121: 2779 0.121 - 0.242: 26 0.242 - 0.363: 3 0.363 - 0.484: 18 0.484 - 0.605: 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 2.35 -2.95 -0.61 2.00e-01 2.50e+01 9.16e+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 2.35 -2.94 -0.60 2.00e-01 2.50e+01 8.89e+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 2.35 -2.89 -0.55 2.00e-01 2.50e+01 7.46e+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: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.760 Check model and map are aligned: 0.090 Set scattering table: 0.210 Process input model: 49.770 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 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= 0.510 Angle : 0.950 38.896 23997 Z= 0.442 Chirality : 0.056 0.605 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (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 TRP 0.023 0.001 TRP A 794 HIS 0.008 0.001 HIS A 290 PHE 0.041 0.002 PHE A1067 TYR 0.018 0.001 TYR A 461 ARG 0.007 0.000 ARG A1370 Details of bonding type rmsd hydrogen bonds : bond 0.17537 ( 1063) hydrogen bonds : angle 6.25499 ( 3096) covalent geometry : bond 0.01325 (17634) covalent geometry : angle 0.95037 (23997) *********************** 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 : 2.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.7502 (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: 0.2733 time to fit residues: 52.5988 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 : 2.052 ------------------------------------------------------------------------------- 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 176 optimal weight: 9.9990 chunk 158 optimal weight: 0.1980 chunk 87 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 121 optimal weight: 20.0000 chunk 189 optimal weight: 3.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN A 531 GLN A1024 ASN ** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN A1344 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.057575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.043757 restraints weight = 109693.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.044685 restraints weight = 54482.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.045296 restraints weight = 35394.380| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 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 = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3194 | |-----------------------------------------------------------------------------| r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.739 17634 Z= 0.508 Angle : 0.759 38.473 23997 Z= 0.378 Chirality : 0.040 0.165 2831 Planarity : 0.005 0.085 2874 Dihedral : 16.664 179.257 2624 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.95 % Favored : 94.00 % Rotamer: Outliers : 3.32 % Allowed : 29.04 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.19), residues: 2018 helix: 0.72 (0.14), residues: 1457 sheet: None (None), residues: 0 loop : -2.41 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1073 HIS 0.006 0.001 HIS A 290 PHE 0.029 0.002 PHE A 163 TYR 0.013 0.001 TYR A1297 ARG 0.008 0.001 ARG B1160 Details of bonding type rmsd hydrogen bonds : bond 0.05049 ( 1063) hydrogen bonds : angle 4.62726 ( 3096) covalent geometry : bond 0.01318 (17634) covalent geometry : angle 0.75889 (23997) *********************** 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 185 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 123 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 MET cc_start: 0.8396 (ppp) cc_final: 0.8177 (ptm) REVERT: A 461 TYR cc_start: 0.7470 (OUTLIER) cc_final: 0.7115 (m-80) REVERT: A 538 ILE cc_start: 0.7939 (mm) cc_final: 0.7665 (tt) REVERT: A 618 LEU cc_start: 0.6181 (OUTLIER) cc_final: 0.5957 (tp) REVERT: A 1127 PHE cc_start: 0.8608 (t80) cc_final: 0.8183 (t80) REVERT: B 237 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.8102 (t80) REVERT: B 330 ASP cc_start: 0.9221 (OUTLIER) cc_final: 0.9002 (p0) REVERT: B 363 THR cc_start: 0.9208 (p) cc_final: 0.9007 (p) REVERT: B 440 SER cc_start: 0.8592 (OUTLIER) cc_final: 0.8019 (p) REVERT: B 488 ASP cc_start: 0.9388 (p0) cc_final: 0.8763 (p0) REVERT: B 528 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7450 (m-10) REVERT: B 716 MET cc_start: 0.9548 (mmp) cc_final: 0.9127 (mmp) REVERT: B 817 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8662 (mm) REVERT: B 996 ASP cc_start: 0.8614 (p0) cc_final: 0.7896 (p0) outliers start: 62 outliers final: 15 residues processed: 181 average time/residue: 0.2926 time to fit residues: 86.5202 Evaluate side-chains 140 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 SER 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 787 LEU Chi-restraints excluded: chain A residue 825 GLN Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 972 CYS Chi-restraints excluded: chain A residue 1132 ILE 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 B residue 218 LEU Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 330 ASP 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 817 LEU Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 1145 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 181 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 119 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 182 optimal weight: 0.9980 chunk 97 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** B 668 HIS B 703 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.055175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.041020 restraints weight = 110172.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.041861 restraints weight = 56039.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.042429 restraints weight = 36978.407| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3194 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3245 | |-----------------------------------------------------------------------------| r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.750 17634 Z= 0.539 Angle : 0.818 38.705 23997 Z= 0.410 Chirality : 0.043 0.276 2831 Planarity : 0.005 0.090 2874 Dihedral : 16.647 176.634 2617 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.04 % Favored : 92.91 % Rotamer: Outliers : 5.08 % Allowed : 28.66 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.18), residues: 2018 helix: 0.55 (0.13), residues: 1446 sheet: None (None), residues: 0 loop : -2.50 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 886 HIS 0.005 0.001 HIS A1030 PHE 0.028 0.002 PHE A1231 TYR 0.022 0.002 TYR A1297 ARG 0.007 0.001 ARG B 916 Details of bonding type rmsd hydrogen bonds : bond 0.05181 ( 1063) hydrogen bonds : angle 4.76364 ( 3096) covalent geometry : bond 0.01378 (17634) covalent geometry : angle 0.81817 (23997) *********************** 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 210 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 115 time to evaluate : 1.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.7621 (mpp) cc_final: 0.7020 (mpp) REVERT: A 270 MET cc_start: 0.7096 (mmm) cc_final: 0.5976 (mmm) REVERT: A 279 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7252 (pp20) REVERT: A 538 ILE cc_start: 0.8079 (mm) cc_final: 0.7794 (tt) REVERT: A 745 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8518 (tm-30) REVERT: A 764 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6488 (tp) REVERT: A 920 TYR cc_start: 0.8830 (OUTLIER) cc_final: 0.8567 (t80) REVERT: A 1006 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7608 (mtm-85) REVERT: B 237 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.8184 (t80) REVERT: B 440 SER cc_start: 0.8647 (OUTLIER) cc_final: 0.8080 (p) REVERT: B 486 THR cc_start: 0.8337 (OUTLIER) cc_final: 0.8129 (m) REVERT: B 488 ASP cc_start: 0.9284 (p0) cc_final: 0.8721 (p0) REVERT: B 528 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.7211 (m-10) REVERT: B 716 MET cc_start: 0.9597 (mmp) cc_final: 0.9261 (mmp) REVERT: B 817 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8697 (mm) REVERT: B 996 ASP cc_start: 0.8525 (p0) cc_final: 0.7976 (p0) REVERT: B 1009 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.9010 (p) REVERT: B 1078 THR cc_start: 0.9286 (OUTLIER) cc_final: 0.8984 (t) REVERT: B 1127 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8118 (pp20) outliers start: 95 outliers final: 49 residues processed: 204 average time/residue: 0.2543 time to fit residues: 84.4842 Evaluate side-chains 173 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 111 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 530 CYS 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 785 CYS Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 788 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 972 CYS Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1006 ARG Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1058 SER Chi-restraints excluded: chain A residue 1063 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 1281 LEU Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain A residue 1295 LEU 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 237 PHE 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 486 THR Chi-restraints excluded: chain B residue 528 PHE Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 780 CYS 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 1002 PHE Chi-restraints excluded: chain B residue 1009 THR 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 1171 SER Chi-restraints excluded: chain B residue 1195 VAL Chi-restraints excluded: chain B residue 1221 LEU Chi-restraints excluded: chain B residue 1267 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 68 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 109 optimal weight: 0.0370 chunk 16 optimal weight: 30.0000 chunk 31 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 overall best weight: 1.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN A 531 GLN A 800 ASN A1005 GLN ** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.056189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.041587 restraints weight = 108649.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.042451 restraints weight = 54840.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.043027 restraints weight = 36136.317| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3245 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3292 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1626 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 : 0.759 38.790 23997 Z= 0.374 Chirality : 0.040 0.176 2831 Planarity : 0.005 0.089 2874 Dihedral : 16.652 178.430 2617 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.05 % Favored : 93.90 % Rotamer: Outliers : 4.60 % Allowed : 29.63 % Favored : 65.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.19), residues: 2018 helix: 0.72 (0.14), residues: 1449 sheet: None (None), residues: 0 loop : -2.45 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 794 HIS 0.004 0.001 HIS A1002 PHE 0.034 0.002 PHE B 812 TYR 0.018 0.001 TYR A1297 ARG 0.004 0.000 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.04353 ( 1063) hydrogen bonds : angle 4.48850 ( 3096) covalent geometry : bond 0.01319 (17634) covalent geometry : angle 0.75892 (23997) *********************** 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 208 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 122 time to evaluate : 2.131 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: 0.7525 (OUTLIER) cc_final: 0.7066 (mpp) REVERT: A 270 MET cc_start: 0.7070 (mmm) cc_final: 0.6048 (mmm) REVERT: A 538 ILE cc_start: 0.8048 (mm) cc_final: 0.7790 (tt) REVERT: A 745 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8501 (tm-30) REVERT: A 764 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.6403 (tp) REVERT: A 1092 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7041 (pp) REVERT: A 1127 PHE cc_start: 0.8511 (t80) cc_final: 0.8139 (t80) REVERT: B 237 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.8185 (t80) REVERT: B 330 ASP cc_start: 0.9195 (OUTLIER) cc_final: 0.8988 (p0) REVERT: B 363 THR cc_start: 0.9271 (p) cc_final: 0.8996 (t) REVERT: B 486 THR cc_start: 0.8284 (OUTLIER) cc_final: 0.8066 (m) REVERT: B 488 ASP cc_start: 0.9267 (p0) cc_final: 0.8769 (p0) REVERT: B 528 PHE cc_start: 0.7757 (OUTLIER) cc_final: 0.7175 (m-10) REVERT: B 716 MET cc_start: 0.9590 (mmp) cc_final: 0.9243 (mmp) REVERT: B 817 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8680 (mm) REVERT: B 996 ASP cc_start: 0.8511 (p0) cc_final: 0.7829 (p0) REVERT: B 1009 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.9001 (p) REVERT: B 1078 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8877 (t) REVERT: B 1127 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8161 (pp20) REVERT: B 1289 ASP cc_start: 0.3483 (p0) cc_final: 0.3208 (p0) outliers start: 86 outliers final: 42 residues processed: 196 average time/residue: 0.2508 time to fit residues: 80.2806 Evaluate side-chains 172 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 118 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 535 LEU 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 825 GLN Chi-restraints excluded: chain A residue 931 VAL 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 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 1185 LEU Chi-restraints excluded: chain A residue 1219 CYS Chi-restraints excluded: chain A residue 1266 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 237 PHE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 330 ASP 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 486 THR 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 987 ILE 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 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 1170 THR Chi-restraints excluded: chain B residue 1171 SER Chi-restraints excluded: chain B residue 1221 LEU 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 66 optimal weight: 10.0000 chunk 186 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 190 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 188 optimal weight: 0.6980 chunk 129 optimal weight: 20.0000 chunk 96 optimal weight: 0.0980 chunk 164 optimal weight: 0.0030 overall best weight: 1.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 ASN A1005 GLN ** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1081 ASN ** 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 = 0.056275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.041919 restraints weight = 109322.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.042713 restraints weight = 62354.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.042816 restraints weight = 37411.319| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3292 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3324 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1769 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= 0.509 Angle : 0.764 38.804 23997 Z= 0.374 Chirality : 0.040 0.169 2831 Planarity : 0.005 0.089 2874 Dihedral : 16.568 178.883 2617 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.29 % Favored : 93.66 % Rotamer: Outliers : 5.56 % Allowed : 28.93 % Favored : 65.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.19), residues: 2018 helix: 0.75 (0.14), residues: 1456 sheet: None (None), residues: 0 loop : -2.43 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1165 HIS 0.007 0.001 HIS A1192 PHE 0.022 0.002 PHE A 163 TYR 0.017 0.001 TYR A1297 ARG 0.005 0.000 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.04252 ( 1063) hydrogen bonds : angle 4.44415 ( 3096) covalent geometry : bond 0.01322 (17634) covalent geometry : angle 0.76387 (23997) *********************** 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 227 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 123 time to evaluate : 1.862 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: A 200 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.7046 (mpp) REVERT: A 270 MET cc_start: 0.7168 (mmm) cc_final: 0.6237 (mmm) REVERT: A 279 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7257 (pp20) REVERT: A 420 MET cc_start: 0.8527 (ptm) cc_final: 0.8087 (ppp) REVERT: A 538 ILE cc_start: 0.8142 (mm) cc_final: 0.7879 (tt) REVERT: A 745 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8605 (tm-30) REVERT: A 764 LEU cc_start: 0.7251 (mt) cc_final: 0.6826 (tp) REVERT: A 1056 MET cc_start: 0.6540 (OUTLIER) cc_final: 0.6010 (ttm) REVERT: A 1092 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.6907 (pp) REVERT: A 1127 PHE cc_start: 0.8521 (t80) cc_final: 0.8147 (t80) REVERT: B 237 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.8067 (t80) REVERT: B 330 ASP cc_start: 0.9196 (OUTLIER) cc_final: 0.8978 (p0) REVERT: B 363 THR cc_start: 0.9267 (p) cc_final: 0.8973 (t) REVERT: B 440 SER cc_start: 0.8480 (OUTLIER) cc_final: 0.7971 (p) REVERT: B 486 THR cc_start: 0.8295 (OUTLIER) cc_final: 0.8074 (m) REVERT: B 488 ASP cc_start: 0.9212 (p0) cc_final: 0.8767 (p0) REVERT: B 528 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.7004 (m-10) REVERT: B 590 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8753 (mt) REVERT: B 716 MET cc_start: 0.9636 (mmp) cc_final: 0.9293 (mmp) REVERT: B 817 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8689 (mm) REVERT: B 824 ASN cc_start: 0.8541 (OUTLIER) cc_final: 0.8306 (m-40) REVERT: B 996 ASP cc_start: 0.8472 (p0) cc_final: 0.7959 (p0) REVERT: B 1009 THR cc_start: 0.9261 (OUTLIER) cc_final: 0.9036 (p) REVERT: B 1078 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8874 (t) REVERT: B 1127 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8057 (pp20) outliers start: 104 outliers final: 56 residues processed: 215 average time/residue: 0.2711 time to fit residues: 93.3541 Evaluate side-chains 193 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 121 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 290 HIS 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 535 LEU 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 787 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 825 GLN 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 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 1132 ILE Chi-restraints excluded: chain A residue 1133 LEU 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 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 237 PHE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 330 ASP 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 486 THR 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 780 CYS 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 991 LEU Chi-restraints excluded: chain B residue 1002 PHE Chi-restraints excluded: chain B residue 1009 THR 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 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 1267 LEU Chi-restraints excluded: chain B residue 1276 VAL Chi-restraints excluded: chain B residue 1278 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 174 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 134 optimal weight: 20.0000 chunk 187 optimal weight: 0.1980 chunk 147 optimal weight: 7.9990 chunk 204 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 197 optimal weight: 0.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 ASN ** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1034 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.056605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.042099 restraints weight = 107227.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.042974 restraints weight = 61733.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.043086 restraints weight = 36474.467| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3324 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3406 | |-----------------------------------------------------------------------------| r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1893 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= 0.505 Angle : 0.767 38.723 23997 Z= 0.374 Chirality : 0.040 0.197 2831 Planarity : 0.005 0.091 2874 Dihedral : 16.498 179.995 2617 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.24 % Favored : 93.71 % Rotamer: Outliers : 5.08 % Allowed : 29.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.19), residues: 2018 helix: 0.84 (0.14), residues: 1453 sheet: None (None), residues: 0 loop : -2.43 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1165 HIS 0.005 0.001 HIS A1192 PHE 0.023 0.002 PHE A 163 TYR 0.016 0.001 TYR A1297 ARG 0.004 0.000 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.04068 ( 1063) hydrogen bonds : angle 4.35509 ( 3096) covalent geometry : bond 0.01313 (17634) covalent geometry : angle 0.76710 (23997) *********************** 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 220 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 125 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.7041 (mpp) REVERT: A 270 MET cc_start: 0.7274 (mmm) cc_final: 0.6320 (mmm) REVERT: A 279 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7345 (pp20) REVERT: A 420 MET cc_start: 0.8532 (ptm) cc_final: 0.8011 (ppp) REVERT: A 538 ILE cc_start: 0.8085 (mm) cc_final: 0.7838 (tt) REVERT: A 745 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8432 (tm-30) REVERT: A 764 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6951 (mt) REVERT: A 1029 MET cc_start: 0.9003 (ppp) cc_final: 0.8694 (ppp) REVERT: A 1056 MET cc_start: 0.6454 (OUTLIER) cc_final: 0.5922 (ttm) REVERT: A 1060 TYR cc_start: 0.7607 (OUTLIER) cc_final: 0.6911 (t80) REVERT: A 1092 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.6927 (pp) REVERT: A 1127 PHE cc_start: 0.8601 (t80) cc_final: 0.8220 (t80) REVERT: B 237 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.8049 (t80) REVERT: B 330 ASP cc_start: 0.9135 (OUTLIER) cc_final: 0.8931 (p0) REVERT: B 363 THR cc_start: 0.9242 (p) cc_final: 0.8909 (t) REVERT: B 440 SER cc_start: 0.8494 (OUTLIER) cc_final: 0.8022 (p) REVERT: B 486 THR cc_start: 0.8334 (OUTLIER) cc_final: 0.8112 (m) REVERT: B 488 ASP cc_start: 0.9193 (p0) cc_final: 0.8825 (p0) REVERT: B 528 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.6913 (m-10) REVERT: B 590 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8758 (mt) REVERT: B 716 MET cc_start: 0.9626 (mmp) cc_final: 0.9290 (mmp) REVERT: B 817 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8668 (mm) REVERT: B 824 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.8291 (m-40) REVERT: B 858 GLU cc_start: 0.9388 (OUTLIER) cc_final: 0.9168 (mp0) REVERT: B 996 ASP cc_start: 0.8391 (p0) cc_final: 0.7749 (p0) REVERT: B 1078 THR cc_start: 0.9169 (OUTLIER) cc_final: 0.8855 (t) REVERT: B 1127 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8166 (pp20) REVERT: B 1216 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7956 (tp) outliers start: 95 outliers final: 56 residues processed: 207 average time/residue: 0.2564 time to fit residues: 86.0638 Evaluate side-chains 197 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 122 time to evaluate : 1.878 ------------------------------------------------------------------------------- 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 495 SER Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 626 THR 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 972 CYS Chi-restraints excluded: chain A residue 1022 LEU 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 1132 ILE Chi-restraints excluded: chain A residue 1133 LEU 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 1334 SER 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 236 PHE Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 330 ASP 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 486 THR 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 817 LEU Chi-restraints excluded: chain B residue 824 ASN Chi-restraints excluded: chain B residue 858 GLU Chi-restraints excluded: chain B residue 987 ILE Chi-restraints excluded: chain B residue 991 LEU Chi-restraints excluded: chain B residue 1002 PHE 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 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 1216 ILE Chi-restraints excluded: chain B residue 1221 LEU Chi-restraints excluded: chain B residue 1267 LEU Chi-restraints excluded: chain B residue 1276 VAL Chi-restraints excluded: chain B residue 1278 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 32 optimal weight: 3.9990 chunk 46 optimal weight: 0.0170 chunk 166 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN A 558 HIS ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 GLN ** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.055678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.040880 restraints weight = 107900.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.041758 restraints weight = 62708.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.041823 restraints weight = 36747.072| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3406 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3447 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.751 17634 Z= 0.523 Angle : 0.800 39.023 23997 Z= 0.396 Chirality : 0.042 0.411 2831 Planarity : 0.005 0.087 2874 Dihedral : 16.491 179.567 2617 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.69 % Favored : 93.26 % Rotamer: Outliers : 5.72 % Allowed : 29.52 % Favored : 64.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.19), residues: 2018 helix: 0.69 (0.13), residues: 1459 sheet: None (None), residues: 0 loop : -2.46 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1073 HIS 0.007 0.001 HIS A 290 PHE 0.022 0.002 PHE A 163 TYR 0.019 0.002 TYR A1297 ARG 0.012 0.001 ARG A1006 Details of bonding type rmsd hydrogen bonds : bond 0.04439 ( 1063) hydrogen bonds : angle 4.51916 ( 3096) covalent geometry : bond 0.01349 (17634) covalent geometry : angle 0.79993 (23997) *********************** 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 226 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 119 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.6797 (mpp) REVERT: A 267 GLN cc_start: 0.9470 (mm110) cc_final: 0.9207 (mm-40) REVERT: A 270 MET cc_start: 0.7318 (mmm) cc_final: 0.6280 (mmm) REVERT: A 279 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7319 (pp20) REVERT: A 420 MET cc_start: 0.8601 (ptm) cc_final: 0.8036 (ppp) REVERT: A 538 ILE cc_start: 0.8233 (mm) cc_final: 0.7933 (tt) REVERT: A 745 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8546 (tm-30) REVERT: A 764 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.6389 (mp) REVERT: A 920 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.8227 (t80) REVERT: A 1056 MET cc_start: 0.6494 (OUTLIER) cc_final: 0.5933 (ttm) REVERT: A 1060 TYR cc_start: 0.7631 (OUTLIER) cc_final: 0.7020 (t80) REVERT: A 1092 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.6819 (pp) REVERT: A 1118 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8044 (mm) REVERT: B 237 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.8034 (t80) REVERT: B 363 THR cc_start: 0.9236 (p) cc_final: 0.8954 (t) REVERT: B 440 SER cc_start: 0.8553 (OUTLIER) cc_final: 0.8075 (p) REVERT: B 486 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8233 (m) REVERT: B 488 ASP cc_start: 0.9179 (p0) cc_final: 0.8830 (p0) REVERT: B 528 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.6879 (m-10) REVERT: B 709 LEU cc_start: 0.9787 (OUTLIER) cc_final: 0.9498 (mt) REVERT: B 716 MET cc_start: 0.9649 (mmp) cc_final: 0.9340 (mmp) REVERT: B 817 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8667 (mm) REVERT: B 824 ASN cc_start: 0.8579 (OUTLIER) cc_final: 0.8361 (m-40) REVERT: B 1009 THR cc_start: 0.9277 (OUTLIER) cc_final: 0.9038 (p) REVERT: B 1078 THR cc_start: 0.9295 (OUTLIER) cc_final: 0.8959 (t) outliers start: 107 outliers final: 63 residues processed: 213 average time/residue: 0.2410 time to fit residues: 83.4797 Evaluate side-chains 199 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 118 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 626 THR 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 767 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 788 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 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 1118 LEU Chi-restraints excluded: chain A residue 1133 LEU 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 1334 SER 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 230 LEU Chi-restraints excluded: chain B residue 236 PHE 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 434 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 486 THR 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 780 CYS 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 1002 PHE Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1028 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 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 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 1288 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 105 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 173 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 208 optimal weight: 7.9990 chunk 146 optimal weight: 0.0870 chunk 201 optimal weight: 1.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.056089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.040851 restraints weight = 106441.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.041701 restraints weight = 53902.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.042261 restraints weight = 35725.141| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3447 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3511 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.751 17634 Z= 0.511 Angle : 0.796 38.936 23997 Z= 0.390 Chirality : 0.042 0.270 2831 Planarity : 0.005 0.085 2874 Dihedral : 16.475 178.985 2617 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.34 % Favored : 93.61 % Rotamer: Outliers : 4.97 % Allowed : 30.16 % Favored : 64.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.19), residues: 2018 helix: 0.72 (0.14), residues: 1460 sheet: None (None), residues: 0 loop : -2.45 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1073 HIS 0.004 0.001 HIS A 212 PHE 0.027 0.002 PHE B 329 TYR 0.018 0.001 TYR A 461 ARG 0.005 0.000 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 1063) hydrogen bonds : angle 4.46361 ( 3096) covalent geometry : bond 0.01328 (17634) covalent geometry : angle 0.79603 (23997) *********************** 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 220 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 127 time to evaluate : 1.871 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: 0.7426 (OUTLIER) cc_final: 0.6958 (mpp) REVERT: A 267 GLN cc_start: 0.9465 (mm110) cc_final: 0.9178 (mm-40) REVERT: A 270 MET cc_start: 0.7528 (mmm) cc_final: 0.6469 (mmm) REVERT: A 279 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7401 (pp20) REVERT: A 420 MET cc_start: 0.8473 (ptm) cc_final: 0.8122 (ppp) REVERT: A 538 ILE cc_start: 0.8159 (mm) cc_final: 0.7841 (tt) REVERT: A 745 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8364 (tm-30) REVERT: A 764 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6580 (tp) REVERT: A 920 TYR cc_start: 0.8658 (OUTLIER) cc_final: 0.8282 (t80) REVERT: A 1029 MET cc_start: 0.9014 (ppp) cc_final: 0.8627 (ppp) REVERT: A 1056 MET cc_start: 0.6493 (OUTLIER) cc_final: 0.5886 (ttm) REVERT: A 1060 TYR cc_start: 0.7549 (OUTLIER) cc_final: 0.6995 (t80) REVERT: A 1092 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.6829 (pp) REVERT: A 1118 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7994 (mm) REVERT: A 1127 PHE cc_start: 0.8510 (t80) cc_final: 0.8138 (t80) REVERT: B 237 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.8172 (t80) REVERT: B 363 THR cc_start: 0.9273 (p) cc_final: 0.8920 (t) REVERT: B 440 SER cc_start: 0.8713 (OUTLIER) cc_final: 0.8231 (p) REVERT: B 486 THR cc_start: 0.8472 (OUTLIER) cc_final: 0.8245 (m) REVERT: B 488 ASP cc_start: 0.9211 (p0) cc_final: 0.8869 (p0) REVERT: B 528 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.6765 (m-10) REVERT: B 709 LEU cc_start: 0.9793 (OUTLIER) cc_final: 0.9495 (mt) REVERT: B 716 MET cc_start: 0.9597 (mmp) cc_final: 0.9293 (mmp) REVERT: B 817 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8665 (mm) REVERT: B 824 ASN cc_start: 0.8575 (OUTLIER) cc_final: 0.8328 (m-40) REVERT: B 1078 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.8927 (t) REVERT: B 1127 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8133 (pp20) outliers start: 93 outliers final: 63 residues processed: 207 average time/residue: 0.2613 time to fit residues: 88.5059 Evaluate side-chains 204 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 123 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 163 PHE 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 368 ILE Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 626 THR 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 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 1022 LEU 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 1118 LEU 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 1245 SER 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 1334 SER 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 236 PHE 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 372 ASN Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 486 THR 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 780 CYS Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 824 ASN Chi-restraints excluded: chain B residue 924 LEU 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 1002 PHE 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 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 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 34 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 141 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 124 optimal weight: 0.1980 chunk 103 optimal weight: 5.9990 chunk 132 optimal weight: 0.0070 chunk 17 optimal weight: 30.0000 chunk 147 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 overall best weight: 1.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.056543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.041330 restraints weight = 106664.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.042173 restraints weight = 54086.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.042741 restraints weight = 35660.775| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3511 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3545 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.751 17634 Z= 0.508 Angle : 0.800 38.957 23997 Z= 0.390 Chirality : 0.041 0.224 2831 Planarity : 0.005 0.085 2874 Dihedral : 16.407 178.291 2617 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.24 % Favored : 93.71 % Rotamer: Outliers : 5.13 % Allowed : 30.05 % Favored : 64.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.19), residues: 2018 helix: 0.75 (0.14), residues: 1459 sheet: None (None), residues: 0 loop : -2.45 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1073 HIS 0.004 0.001 HIS A 212 PHE 0.022 0.002 PHE A 163 TYR 0.019 0.001 TYR A 461 ARG 0.005 0.000 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.04096 ( 1063) hydrogen bonds : angle 4.44030 ( 3096) covalent geometry : bond 0.01321 (17634) covalent geometry : angle 0.80029 (23997) *********************** 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 221 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 125 time to evaluate : 1.905 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: A 74 GLN cc_start: 0.6644 (OUTLIER) cc_final: 0.5117 (mt0) REVERT: A 200 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.6994 (mpp) REVERT: A 270 MET cc_start: 0.7436 (mmm) cc_final: 0.6425 (mmm) REVERT: A 279 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7421 (pp20) REVERT: A 420 MET cc_start: 0.8475 (ptm) cc_final: 0.8124 (ppp) REVERT: A 538 ILE cc_start: 0.8108 (mm) cc_final: 0.7811 (tt) REVERT: A 745 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8361 (tm-30) REVERT: A 764 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6034 (mp) REVERT: A 920 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.8363 (t80) REVERT: A 1029 MET cc_start: 0.9039 (ppp) cc_final: 0.8628 (ppp) REVERT: A 1056 MET cc_start: 0.6546 (OUTLIER) cc_final: 0.5945 (ttm) REVERT: A 1060 TYR cc_start: 0.7560 (OUTLIER) cc_final: 0.6988 (t80) REVERT: A 1092 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.6812 (pp) REVERT: A 1118 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7989 (mm) REVERT: A 1127 PHE cc_start: 0.8530 (t80) cc_final: 0.8159 (t80) REVERT: B 440 SER cc_start: 0.8762 (OUTLIER) cc_final: 0.8279 (p) REVERT: B 486 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8189 (m) REVERT: B 488 ASP cc_start: 0.9212 (p0) cc_final: 0.8882 (p0) REVERT: B 528 PHE cc_start: 0.7562 (OUTLIER) cc_final: 0.6811 (m-10) REVERT: B 709 LEU cc_start: 0.9794 (OUTLIER) cc_final: 0.9493 (mt) REVERT: B 716 MET cc_start: 0.9604 (mmp) cc_final: 0.9292 (mmp) REVERT: B 817 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8663 (mm) REVERT: B 824 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.8350 (m-40) REVERT: B 988 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9142 (mt) REVERT: B 1009 THR cc_start: 0.9266 (OUTLIER) cc_final: 0.9046 (p) REVERT: B 1078 THR cc_start: 0.9251 (OUTLIER) cc_final: 0.8926 (t) REVERT: B 1127 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8116 (pp20) outliers start: 96 outliers final: 66 residues processed: 209 average time/residue: 0.2531 time to fit residues: 85.8544 Evaluate side-chains 207 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 121 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 163 PHE 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 368 ILE Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 626 THR 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 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 1022 LEU 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 1118 LEU 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 1245 SER 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 1334 SER 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 236 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 422 LYS Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 486 THR 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 780 CYS Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 824 ASN Chi-restraints excluded: chain B residue 924 LEU 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 1002 PHE Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain B residue 1086 LEU 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 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 1260 ILE Chi-restraints excluded: chain B residue 1267 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 144 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 202 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.056586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.041804 restraints weight = 105258.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.042626 restraints weight = 62245.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.042805 restraints weight = 36132.140| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3545 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3576 | |-----------------------------------------------------------------------------| r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2361 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= 0.505 Angle : 0.806 38.942 23997 Z= 0.389 Chirality : 0.042 0.424 2831 Planarity : 0.005 0.085 2874 Dihedral : 16.335 177.696 2617 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.19 % Favored : 93.76 % Rotamer: Outliers : 4.49 % Allowed : 30.64 % Favored : 64.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.19), residues: 2018 helix: 0.80 (0.14), residues: 1459 sheet: None (None), residues: 0 loop : -2.45 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1073 HIS 0.004 0.001 HIS A 212 PHE 0.022 0.002 PHE A 163 TYR 0.025 0.001 TYR A 461 ARG 0.005 0.000 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.04004 ( 1063) hydrogen bonds : angle 4.40114 ( 3096) covalent geometry : bond 0.01315 (17634) covalent geometry : angle 0.80574 (23997) ********************** 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 208 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 124 time to evaluate : 2.071 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 74 GLN cc_start: 0.6558 (OUTLIER) cc_final: 0.4977 (mt0) REVERT: A 200 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7155 (mpp) REVERT: A 279 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7470 (pp20) REVERT: A 420 MET cc_start: 0.8436 (ptm) cc_final: 0.8106 (ppp) REVERT: A 538 ILE cc_start: 0.8059 (mm) cc_final: 0.7786 (tt) REVERT: A 745 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8344 (tm-30) REVERT: A 764 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.6304 (mp) REVERT: A 920 TYR cc_start: 0.8718 (OUTLIER) cc_final: 0.8402 (t80) REVERT: A 1029 MET cc_start: 0.9020 (ppp) cc_final: 0.8599 (ppp) REVERT: A 1056 MET cc_start: 0.6480 (OUTLIER) cc_final: 0.5909 (ttm) REVERT: A 1060 TYR cc_start: 0.7352 (OUTLIER) cc_final: 0.6772 (t80) REVERT: A 1069 LEU cc_start: 0.8054 (mt) cc_final: 0.7469 (mm) REVERT: A 1092 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.6735 (pp) REVERT: A 1118 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7980 (mm) REVERT: A 1127 PHE cc_start: 0.8563 (t80) cc_final: 0.8203 (t80) REVERT: B 275 LEU cc_start: 0.7876 (pp) cc_final: 0.7532 (mt) REVERT: B 363 THR cc_start: 0.9278 (p) cc_final: 0.8949 (t) REVERT: B 368 GLU cc_start: 0.9049 (pp20) cc_final: 0.8817 (tm-30) REVERT: B 440 SER cc_start: 0.8511 (OUTLIER) cc_final: 0.8024 (p) REVERT: B 486 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8206 (m) REVERT: B 488 ASP cc_start: 0.9200 (p0) cc_final: 0.8870 (p0) REVERT: B 528 PHE cc_start: 0.7561 (OUTLIER) cc_final: 0.6781 (m-10) REVERT: B 590 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8787 (mt) REVERT: B 709 LEU cc_start: 0.9791 (OUTLIER) cc_final: 0.9504 (mt) REVERT: B 716 MET cc_start: 0.9640 (mmp) cc_final: 0.9315 (mmp) REVERT: B 817 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8657 (mm) REVERT: B 988 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9078 (mt) REVERT: B 1078 THR cc_start: 0.9181 (OUTLIER) cc_final: 0.8833 (t) REVERT: B 1127 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8115 (pp20) outliers start: 84 outliers final: 62 residues processed: 197 average time/residue: 0.2534 time to fit residues: 82.0488 Evaluate side-chains 205 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 124 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 163 PHE 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 368 ILE Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 626 THR 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 920 TYR 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 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 1118 LEU 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 1245 SER 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 1334 SER 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 355 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 372 ASN Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 486 THR 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 780 CYS 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 988 LEU Chi-restraints excluded: chain B residue 991 LEU Chi-restraints excluded: chain B residue 1002 PHE Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain B residue 1086 LEU 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 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 1267 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 101 optimal weight: 0.8980 chunk 57 optimal weight: 0.0970 chunk 15 optimal weight: 0.0270 chunk 91 optimal weight: 1.9990 chunk 165 optimal weight: 0.0020 chunk 173 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 201 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 overall best weight: 0.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3695 r_free = 0.3695 target = 0.056918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.042200 restraints weight = 104891.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.043047 restraints weight = 61995.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.043164 restraints weight = 35642.359| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3576 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | 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: 3592 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2383 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= 0.503 Angle : 0.808 38.957 23997 Z= 0.388 Chirality : 0.041 0.217 2831 Planarity : 0.005 0.085 2874 Dihedral : 16.312 177.333 2617 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.10 % Favored : 93.86 % Rotamer: Outliers : 3.85 % Allowed : 31.39 % Favored : 64.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.19), residues: 2018 helix: 0.80 (0.14), residues: 1461 sheet: None (None), residues: 0 loop : -2.48 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1165 HIS 0.004 0.001 HIS A1192 PHE 0.027 0.002 PHE A1231 TYR 0.023 0.001 TYR A 461 ARG 0.005 0.000 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 1063) hydrogen bonds : angle 4.34553 ( 3096) covalent geometry : bond 0.01309 (17634) covalent geometry : angle 0.80788 (23997) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6317.38 seconds wall clock time: 110 minutes 51.43 seconds (6651.43 seconds total)