Starting phenix.real_space_refine on Mon May 4 15:07:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m80_63699/05_2026/9m80_63699.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m80_63699/05_2026/9m80_63699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m80_63699/05_2026/9m80_63699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m80_63699/05_2026/9m80_63699.map" model { file = "/net/cci-nas-00/data/ceres_data/9m80_63699/05_2026/9m80_63699.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m80_63699/05_2026/9m80_63699.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 13841 2.51 5 N 3691 2.21 5 O 4047 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21667 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 4157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4157 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 29, 'TRANS': 494} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 4157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4157 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 29, 'TRANS': 494} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 6656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6656 Classifications: {'peptide': 836} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 33, 'TRANS': 802} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 6662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6662 Classifications: {'peptide': 836} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 802} Chain breaks: 1 Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'GLC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.98, per 1000 atoms: 0.23 Number of scatterers: 21667 At special positions: 0 Unit cell: (135.136, 131.84, 183.752, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 4047 8.00 N 3691 7.00 C 13841 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 Links applied ALPHA1-4 " GLC E 1 " - " GLC E 2 " Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 1.0 seconds 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5072 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 14 sheets defined 56.7% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 117 through 130 Processing helix chain 'C' and resid 152 through 156 removed outlier: 3.950A pdb=" N GLY C 156 " --> pdb=" O PRO C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 168 through 175 Processing helix chain 'C' and resid 179 through 183 removed outlier: 3.619A pdb=" N LEU C 183 " --> pdb=" O GLU C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 215 removed outlier: 3.648A pdb=" N ASN C 199 " --> pdb=" O ASP C 195 " (cutoff:3.500A) Proline residue: C 203 - end of helix Processing helix chain 'C' and resid 217 through 227 removed outlier: 3.730A pdb=" N THR C 221 " --> pdb=" O GLY C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 250 Processing helix chain 'C' and resid 253 through 257 removed outlier: 3.509A pdb=" N TRP C 257 " --> pdb=" O TRP C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 Processing helix chain 'C' and resid 265 through 276 Processing helix chain 'C' and resid 277 through 304 Processing helix chain 'C' and resid 320 through 326 Processing helix chain 'C' and resid 327 through 330 Processing helix chain 'C' and resid 362 through 370 Processing helix chain 'C' and resid 371 through 385 Processing helix chain 'C' and resid 392 through 396 Processing helix chain 'C' and resid 419 through 430 removed outlier: 4.237A pdb=" N PHE C 423 " --> pdb=" O ARG C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 454 Processing helix chain 'C' and resid 463 through 465 No H-bonds generated for 'chain 'C' and resid 463 through 465' Processing helix chain 'C' and resid 475 through 479 removed outlier: 3.859A pdb=" N HIS C 479 " --> pdb=" O PRO C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'C' and resid 503 through 514 Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.960A pdb=" N ASN C 518 " --> pdb=" O PRO C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 532 Processing helix chain 'C' and resid 542 through 546 Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 577 through 591 Processing helix chain 'D' and resid 103 through 107 Processing helix chain 'D' and resid 117 through 131 Processing helix chain 'D' and resid 152 through 156 removed outlier: 3.790A pdb=" N GLY D 156 " --> pdb=" O PRO D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 167 Processing helix chain 'D' and resid 169 through 174 removed outlier: 3.914A pdb=" N LYS D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 179 through 183 Processing helix chain 'D' and resid 193 through 215 Proline residue: D 203 - end of helix Processing helix chain 'D' and resid 217 through 228 Processing helix chain 'D' and resid 229 through 234 removed outlier: 4.287A pdb=" N GLY D 234 " --> pdb=" O PRO D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 249 Processing helix chain 'D' and resid 253 through 257 removed outlier: 3.562A pdb=" N TRP D 257 " --> pdb=" O TRP D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 Processing helix chain 'D' and resid 265 through 276 Processing helix chain 'D' and resid 276 through 304 Processing helix chain 'D' and resid 320 through 326 Processing helix chain 'D' and resid 327 through 330 removed outlier: 3.655A pdb=" N PHE D 330 " --> pdb=" O ARG D 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 327 through 330' Processing helix chain 'D' and resid 362 through 370 removed outlier: 3.704A pdb=" N MET D 366 " --> pdb=" O ASP D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 385 Processing helix chain 'D' and resid 392 through 396 Processing helix chain 'D' and resid 419 through 430 removed outlier: 4.211A pdb=" N PHE D 423 " --> pdb=" O ARG D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 454 removed outlier: 3.659A pdb=" N VAL D 448 " --> pdb=" O THR D 444 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE D 454 " --> pdb=" O LEU D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 removed outlier: 3.528A pdb=" N HIS D 479 " --> pdb=" O PRO D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 501 removed outlier: 3.507A pdb=" N GLN D 500 " --> pdb=" O ILE D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 514 Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 521 through 532 Processing helix chain 'D' and resid 542 through 546 Processing helix chain 'D' and resid 549 through 553 Processing helix chain 'D' and resid 577 through 591 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 101 through 132 Processing helix chain 'A' and resid 148 through 156 Processing helix chain 'A' and resid 158 through 169 removed outlier: 3.510A pdb=" N LEU A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 178 removed outlier: 3.532A pdb=" N THR A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 309 through 315 Processing helix chain 'A' and resid 317 through 322 Processing helix chain 'A' and resid 322 through 330 Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 341 through 372 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 391 through 394 removed outlier: 3.745A pdb=" N THR A 394 " --> pdb=" O THR A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 391 through 394' Processing helix chain 'A' and resid 395 through 407 Processing helix chain 'A' and resid 411 through 422 Processing helix chain 'A' and resid 431 through 435 removed outlier: 3.849A pdb=" N LEU A 435 " --> pdb=" O PRO A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 447 Processing helix chain 'A' and resid 447 through 470 Processing helix chain 'A' and resid 474 through 485 Processing helix chain 'A' and resid 580 through 588 Processing helix chain 'A' and resid 595 through 605 Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 626 through 631 Processing helix chain 'A' and resid 635 through 647 Processing helix chain 'A' and resid 649 through 653 removed outlier: 3.706A pdb=" N VAL A 652 " --> pdb=" O ASP A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 662 Processing helix chain 'A' and resid 667 through 694 Processing helix chain 'A' and resid 715 through 733 removed outlier: 3.565A pdb=" N ASN A 719 " --> pdb=" O ARG A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 742 removed outlier: 3.881A pdb=" N ILE A 739 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN A 740 " --> pdb=" O LYS A 736 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE A 742 " --> pdb=" O ARG A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 776 removed outlier: 3.613A pdb=" N LYS A 761 " --> pdb=" O TYR A 757 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS A 776 " --> pdb=" O ALA A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 782 No H-bonds generated for 'chain 'A' and resid 780 through 782' Processing helix chain 'A' and resid 793 through 801 Processing helix chain 'A' and resid 802 through 804 No H-bonds generated for 'chain 'A' and resid 802 through 804' Processing helix chain 'A' and resid 819 through 828 removed outlier: 4.116A pdb=" N MET A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN A 828 " --> pdb=" O LYS A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 848 Processing helix chain 'A' and resid 849 through 852 removed outlier: 3.520A pdb=" N PHE A 852 " --> pdb=" O GLU A 849 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 849 through 852' Processing helix chain 'A' and resid 860 through 871 removed outlier: 4.089A pdb=" N GLY A 864 " --> pdb=" O HIS A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 889 Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 921 through 938 removed outlier: 3.705A pdb=" N ASP A 938 " --> pdb=" O LYS A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 952 Processing helix chain 'A' and resid 957 through 969 removed outlier: 3.666A pdb=" N THR A 961 " --> pdb=" O ASN A 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 91 removed outlier: 3.904A pdb=" N ALA B 82 " --> pdb=" O SER B 78 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ASN B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 132 removed outlier: 3.967A pdb=" N THR B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 156 Processing helix chain 'B' and resid 158 through 169 Processing helix chain 'B' and resid 172 through 178 removed outlier: 3.590A pdb=" N THR B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 309 through 315 Processing helix chain 'B' and resid 317 through 322 removed outlier: 3.578A pdb=" N ALA B 321 " --> pdb=" O ASP B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 330 Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 341 through 372 Processing helix chain 'B' and resid 376 through 380 Processing helix chain 'B' and resid 395 through 407 Processing helix chain 'B' and resid 411 through 422 Processing helix chain 'B' and resid 431 through 435 removed outlier: 3.637A pdb=" N ALA B 434 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU B 435 " --> pdb=" O PRO B 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 431 through 435' Processing helix chain 'B' and resid 440 through 447 Processing helix chain 'B' and resid 447 through 470 Processing helix chain 'B' and resid 473 through 485 Processing helix chain 'B' and resid 580 through 588 Processing helix chain 'B' and resid 595 through 605 Processing helix chain 'B' and resid 607 through 614 Processing helix chain 'B' and resid 626 through 631 Processing helix chain 'B' and resid 635 through 647 Processing helix chain 'B' and resid 648 through 652 removed outlier: 4.168A pdb=" N TRP B 651 " --> pdb=" O SER B 648 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 652 " --> pdb=" O ASP B 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 648 through 652' Processing helix chain 'B' and resid 654 through 665 removed outlier: 3.503A pdb=" N GLU B 660 " --> pdb=" O LYS B 657 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS B 663 " --> pdb=" O GLU B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 694 Processing helix chain 'B' and resid 715 through 732 removed outlier: 3.609A pdb=" N ASN B 719 " --> pdb=" O ARG B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 742 removed outlier: 4.095A pdb=" N ILE B 739 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN B 740 " --> pdb=" O LYS B 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 776 removed outlier: 3.734A pdb=" N HIS B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 804 Proline residue: B 802 - end of helix Processing helix chain 'B' and resid 819 through 828 removed outlier: 3.815A pdb=" N MET B 823 " --> pdb=" O GLY B 819 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN B 828 " --> pdb=" O LYS B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 848 Processing helix chain 'B' and resid 849 through 852 removed outlier: 3.766A pdb=" N PHE B 852 " --> pdb=" O GLU B 849 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 849 through 852' Processing helix chain 'B' and resid 858 through 860 No H-bonds generated for 'chain 'B' and resid 858 through 860' Processing helix chain 'B' and resid 861 through 871 Processing helix chain 'B' and resid 877 through 889 Processing helix chain 'B' and resid 897 through 903 removed outlier: 3.579A pdb=" N SER B 903 " --> pdb=" O ASP B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 938 Proline residue: B 923 - end of helix removed outlier: 3.852A pdb=" N ASP B 938 " --> pdb=" O LYS B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 952 Processing helix chain 'B' and resid 957 through 969 removed outlier: 3.658A pdb=" N THR B 961 " --> pdb=" O ASN B 957 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 435 through 437 removed outlier: 6.895A pdb=" N PHE C 388 " --> pdb=" O ILE C 436 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N TRP C 135 " --> pdb=" O MET C 309 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ASP C 311 " --> pdb=" O TRP C 135 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA C 98 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLN C 136 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL C 100 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLN C 483 " --> pdb=" O THR C 537 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N MET C 539 " --> pdb=" O GLN C 483 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL C 485 " --> pdb=" O MET C 539 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N THR C 541 " --> pdb=" O VAL C 485 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 354 through 359 removed outlier: 6.098A pdb=" N SER C 342 " --> pdb=" O TRP C 356 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER C 358 " --> pdb=" O PHE C 340 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N PHE C 340 " --> pdb=" O SER C 358 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY C 343 " --> pdb=" O TRP C 400 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TRP C 400 " --> pdb=" O GLY C 343 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 435 through 437 removed outlier: 3.722A pdb=" N ILE D 436 " --> pdb=" O PHE D 388 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU D 387 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG D 389 " --> pdb=" O GLY D 310 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N TRP D 135 " --> pdb=" O MET D 309 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N ASP D 311 " --> pdb=" O TRP D 135 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA D 98 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N GLN D 136 " --> pdb=" O ALA D 98 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL D 100 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLN D 483 " --> pdb=" O THR D 537 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N MET D 539 " --> pdb=" O GLN D 483 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL D 485 " --> pdb=" O MET D 539 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N THR D 541 " --> pdb=" O VAL D 485 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLY D 458 " --> pdb=" O VAL D 484 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR D 486 " --> pdb=" O GLY D 458 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ALA D 460 " --> pdb=" O TYR D 486 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 354 through 359 removed outlier: 6.339A pdb=" N SER D 342 " --> pdb=" O TRP D 356 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N SER D 358 " --> pdb=" O PHE D 340 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N PHE D 340 " --> pdb=" O SER D 358 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY D 343 " --> pdb=" O TRP D 400 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TRP D 400 " --> pdb=" O GLY D 343 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 245 through 255 removed outlier: 4.039A pdb=" N ALA A 280 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N ASP A 249 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 10.176A pdb=" N VAL A 278 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 9.728A pdb=" N SER A 251 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 10.809A pdb=" N ILE A 276 " --> pdb=" O SER A 251 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ALA A 208 " --> pdb=" O ASN A 295 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ARG A 297 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY A 210 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N TRP A 299 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N GLY A 212 " --> pdb=" O TRP A 299 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N THR A 301 " --> pdb=" O GLY A 212 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N LEU A 213 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLN A 135 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N GLN A 387 " --> pdb=" O GLN A 135 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TYR A 137 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ASN A 389 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU A 139 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N ASN A 592 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N TYR A 425 " --> pdb=" O ASN A 592 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL A 591 " --> pdb=" O GLN A 619 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 221 through 225 removed outlier: 3.511A pdb=" N GLY A 228 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 262 Processing sheet with id=AA8, first strand: chain 'A' and resid 437 through 439 Processing sheet with id=AA9, first strand: chain 'A' and resid 784 through 788 removed outlier: 6.573A pdb=" N MET A 702 " --> pdb=" O VAL A 746 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE A 748 " --> pdb=" O MET A 702 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ASP A 704 " --> pdb=" O ILE A 748 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLY A 750 " --> pdb=" O ASP A 704 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLN A 706 " --> pdb=" O GLY A 750 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE A 703 " --> pdb=" O LEU A 806 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLN A 808 " --> pdb=" O PHE A 703 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL A 705 " --> pdb=" O GLN A 808 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N SER A 807 " --> pdb=" O ILE A 833 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 245 through 256 removed outlier: 12.224A pdb=" N VAL B 246 " --> pdb=" O PRO B 284 " (cutoff:3.500A) removed outlier: 10.657A pdb=" N THR B 248 " --> pdb=" O ASP B 282 " (cutoff:3.500A) removed outlier: 11.520A pdb=" N ASP B 282 " --> pdb=" O THR B 248 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL B 250 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ALA B 208 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N ARG B 297 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLY B 210 " --> pdb=" O ARG B 297 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N TRP B 299 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLY B 212 " --> pdb=" O TRP B 299 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N THR B 301 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N ASN B 592 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TYR B 425 " --> pdb=" O ASN B 592 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL B 591 " --> pdb=" O GLN B 619 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 221 through 225 Processing sheet with id=AB3, first strand: chain 'B' and resid 259 through 262 Processing sheet with id=AB4, first strand: chain 'B' and resid 437 through 439 Processing sheet with id=AB5, first strand: chain 'B' and resid 784 through 788 removed outlier: 6.332A pdb=" N MET B 702 " --> pdb=" O VAL B 746 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE B 748 " --> pdb=" O MET B 702 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP B 704 " --> pdb=" O ILE B 748 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N GLY B 750 " --> pdb=" O ASP B 704 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLN B 706 " --> pdb=" O GLY B 750 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N VAL B 707 " --> pdb=" O GLN B 808 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N SER B 807 " --> pdb=" O ILE B 833 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU B 832 " --> pdb=" O PHE B 853 " (cutoff:3.500A) 1061 hydrogen bonds defined for protein. 2979 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.57 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6312 1.33 - 1.45: 3814 1.45 - 1.57: 11913 1.57 - 1.70: 0 1.70 - 1.82: 152 Bond restraints: 22191 Sorted by residual: bond pdb=" CA TYR A 336 " pdb=" C TYR A 336 " ideal model delta sigma weight residual 1.531 1.495 0.037 7.40e-03 1.83e+04 2.46e+01 bond pdb=" CA SER A 953 " pdb=" CB SER A 953 " ideal model delta sigma weight residual 1.528 1.462 0.065 1.35e-02 5.49e+03 2.34e+01 bond pdb=" CA SER A 952 " pdb=" CB SER A 952 " ideal model delta sigma weight residual 1.528 1.464 0.064 1.37e-02 5.33e+03 2.17e+01 bond pdb=" CA TYR A 713 " pdb=" C TYR A 713 " ideal model delta sigma weight residual 1.522 1.467 0.054 1.37e-02 5.33e+03 1.57e+01 bond pdb=" CA ALA B 913 " pdb=" CB ALA B 913 " ideal model delta sigma weight residual 1.532 1.485 0.047 1.33e-02 5.65e+03 1.23e+01 ... (remaining 22186 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 29347 1.96 - 3.93: 608 3.93 - 5.89: 102 5.89 - 7.85: 24 7.85 - 9.81: 9 Bond angle restraints: 30090 Sorted by residual: angle pdb=" CA ASP A 877 " pdb=" CB ASP A 877 " pdb=" CG ASP A 877 " ideal model delta sigma weight residual 112.60 118.97 -6.37 1.00e+00 1.00e+00 4.06e+01 angle pdb=" CA PHE C 393 " pdb=" CB PHE C 393 " pdb=" CG PHE C 393 " ideal model delta sigma weight residual 113.80 119.92 -6.12 1.00e+00 1.00e+00 3.75e+01 angle pdb=" N ARG A 912 " pdb=" CA ARG A 912 " pdb=" C ARG A 912 " ideal model delta sigma weight residual 110.44 117.60 -7.16 1.20e+00 6.94e-01 3.56e+01 angle pdb=" CA GLY B 906 " pdb=" C GLY B 906 " pdb=" O GLY B 906 " ideal model delta sigma weight residual 122.29 117.52 4.77 8.10e-01 1.52e+00 3.47e+01 angle pdb=" N ALA A 913 " pdb=" CA ALA A 913 " pdb=" C ALA A 913 " ideal model delta sigma weight residual 108.79 100.01 8.78 1.53e+00 4.27e-01 3.29e+01 ... (remaining 30085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.93: 12135 24.93 - 49.87: 981 49.87 - 74.80: 135 74.80 - 99.74: 27 99.74 - 124.67: 2 Dihedral angle restraints: 13280 sinusoidal: 5402 harmonic: 7878 Sorted by residual: dihedral pdb=" CA PHE A 256 " pdb=" C PHE A 256 " pdb=" N TYR A 257 " pdb=" CA TYR A 257 " ideal model delta harmonic sigma weight residual 180.00 -158.80 -21.20 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" N PHE A 956 " pdb=" C PHE A 956 " pdb=" CA PHE A 956 " pdb=" CB PHE A 956 " ideal model delta harmonic sigma weight residual 122.80 112.42 10.38 0 2.50e+00 1.60e-01 1.72e+01 dihedral pdb=" C2 GLC D 601 " pdb=" C1 GLC D 601 " pdb=" O5 GLC D 601 " pdb=" C5 GLC D 601 " ideal model delta sinusoidal sigma weight residual -59.66 65.01 -124.67 1 3.00e+01 1.11e-03 1.67e+01 ... (remaining 13277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2642 0.055 - 0.110: 524 0.110 - 0.165: 74 0.165 - 0.220: 21 0.220 - 0.275: 4 Chirality restraints: 3265 Sorted by residual: chirality pdb=" C1 GLC E 2 " pdb=" O4 GLC E 1 " pdb=" C2 GLC E 2 " pdb=" O5 GLC E 2 " both_signs ideal model delta sigma weight residual False 2.40 2.23 0.17 2.00e-02 2.50e+03 6.82e+01 chirality pdb=" CA GLU C 580 " pdb=" N GLU C 580 " pdb=" C GLU C 580 " pdb=" CB GLU C 580 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA ILE D 436 " pdb=" N ILE D 436 " pdb=" C ILE D 436 " pdb=" CB ILE D 436 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 3262 not shown) Planarity restraints: 3879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 663 " -0.020 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C LYS A 663 " 0.069 2.00e-02 2.50e+03 pdb=" O LYS A 663 " -0.026 2.00e-02 2.50e+03 pdb=" N PHE A 664 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 394 " 0.262 9.50e-02 1.11e+02 1.18e-01 8.52e+00 pdb=" NE ARG C 394 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG C 394 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG C 394 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 394 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 911 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.77e+00 pdb=" C GLY A 911 " -0.048 2.00e-02 2.50e+03 pdb=" O GLY A 911 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG A 912 " 0.017 2.00e-02 2.50e+03 ... (remaining 3876 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1976 2.74 - 3.28: 21240 3.28 - 3.82: 37229 3.82 - 4.36: 46472 4.36 - 4.90: 79776 Nonbonded interactions: 186693 Sorted by model distance: nonbonded pdb=" O PHE B 91 " pdb=" OG1 THR B 92 " model vdw 2.201 3.040 nonbonded pdb=" OG1 THR A 835 " pdb=" OD1 ASP A 837 " model vdw 2.274 3.040 nonbonded pdb=" CD1 LEU B 806 " pdb=" O ILE B 831 " model vdw 2.331 3.460 nonbonded pdb=" O ALA A 665 " pdb=" NE2 GLN A 671 " model vdw 2.389 3.120 nonbonded pdb=" O ASP C 482 " pdb=" OD1 ASP C 482 " model vdw 2.409 3.040 ... (remaining 186688 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 77 through 911 or (resid 912 through 913 and (name N or na \ me CA or name C or name O or name CB )) or resid 914 through 978)) } ncs_group { reference = chain 'C' selection = (chain 'D' and resid 71 through 594) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.390 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 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 : 0.005 0.065 22192 Z= 0.276 Angle : 0.704 15.927 30093 Z= 0.419 Chirality : 0.047 0.275 3265 Planarity : 0.005 0.118 3879 Dihedral : 17.390 124.674 8208 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.35 % Allowed : 23.51 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.16), residues: 2708 helix: 0.95 (0.14), residues: 1322 sheet: -0.44 (0.29), residues: 343 loop : -0.44 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 960 TYR 0.034 0.002 TYR D 385 PHE 0.028 0.002 PHE A 956 TRP 0.017 0.001 TRP A 645 HIS 0.007 0.001 HIS A 809 Details of bonding type rmsd covalent geometry : bond 0.00537 (22191) covalent geometry : angle 0.69617 (30090) hydrogen bonds : bond 0.14140 ( 1061) hydrogen bonds : angle 6.17363 ( 2979) link_ALPHA1-4 : bond 0.04610 ( 1) link_ALPHA1-4 : angle 10.28060 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 255 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: D 171 GLU cc_start: 0.7463 (tm-30) cc_final: 0.6583 (tp30) REVERT: D 237 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6566 (pt0) REVERT: D 256 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6724 (mt-10) REVERT: D 274 GLN cc_start: 0.7820 (mp10) cc_final: 0.7372 (mm-40) REVERT: D 298 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7385 (ttt180) REVERT: D 445 GLU cc_start: 0.6719 (tp30) cc_final: 0.6371 (mt-10) REVERT: A 174 GLU cc_start: 0.7975 (mp0) cc_final: 0.7641 (mp0) REVERT: A 226 LYS cc_start: 0.8451 (mmtp) cc_final: 0.7606 (pttm) REVERT: A 669 ASP cc_start: 0.7565 (m-30) cc_final: 0.7293 (m-30) REVERT: A 737 ASP cc_start: 0.7514 (m-30) cc_final: 0.7284 (m-30) REVERT: A 827 MET cc_start: 0.8759 (mtt) cc_final: 0.8305 (mtm) REVERT: A 971 ASP cc_start: 0.8861 (t0) cc_final: 0.8264 (t0) REVERT: B 164 GLU cc_start: 0.8390 (pt0) cc_final: 0.8109 (pt0) REVERT: B 340 GLU cc_start: 0.7808 (mm-30) cc_final: 0.6952 (pm20) REVERT: B 482 LYS cc_start: 0.8321 (mtpm) cc_final: 0.6686 (mptt) REVERT: B 602 VAL cc_start: 0.8158 (t) cc_final: 0.7641 (m) REVERT: B 637 GLU cc_start: 0.8199 (mp0) cc_final: 0.7846 (mp0) REVERT: B 908 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7236 (pm20) REVERT: B 971 ASP cc_start: 0.8660 (t0) cc_final: 0.8179 (t0) outliers start: 8 outliers final: 3 residues processed: 262 average time/residue: 0.1841 time to fit residues: 71.8559 Evaluate side-chains 237 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 233 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 551 SER Chi-restraints excluded: chain D residue 298 ARG Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 883 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.0170 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 overall best weight: 0.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 490 HIS D 263 ASN D 518 ASN A 719 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.128066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.105164 restraints weight = 26602.885| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.57 r_work: 0.2954 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.0673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22192 Z= 0.112 Angle : 0.477 6.984 30093 Z= 0.248 Chirality : 0.040 0.237 3265 Planarity : 0.003 0.033 3879 Dihedral : 4.907 59.541 3016 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.43 % Allowed : 21.43 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.16), residues: 2708 helix: 1.30 (0.14), residues: 1336 sheet: -0.36 (0.30), residues: 331 loop : -0.28 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 419 TYR 0.010 0.001 TYR A 353 PHE 0.018 0.001 PHE A 956 TRP 0.010 0.001 TRP A 630 HIS 0.004 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00255 (22191) covalent geometry : angle 0.47579 (30090) hydrogen bonds : bond 0.03939 ( 1061) hydrogen bonds : angle 4.79396 ( 2979) link_ALPHA1-4 : bond 0.00757 ( 1) link_ALPHA1-4 : angle 3.38943 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 254 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: C 87 MET cc_start: 0.6496 (ptm) cc_final: 0.5753 (ptm) REVERT: C 218 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6755 (pm20) REVERT: C 281 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7851 (mm-30) REVERT: C 419 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.6326 (mtp85) REVERT: D 171 GLU cc_start: 0.7643 (tm-30) cc_final: 0.6922 (tp30) REVERT: D 237 GLU cc_start: 0.6925 (mm-30) cc_final: 0.6658 (pt0) REVERT: D 274 GLN cc_start: 0.7744 (mp10) cc_final: 0.7313 (mm-40) REVERT: D 299 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7504 (mmtp) REVERT: D 385 TYR cc_start: 0.8716 (m-80) cc_final: 0.8356 (m-80) REVERT: D 445 GLU cc_start: 0.6808 (tp30) cc_final: 0.6513 (mt-10) REVERT: A 174 GLU cc_start: 0.8031 (mp0) cc_final: 0.7724 (mp0) REVERT: A 226 LYS cc_start: 0.8389 (mmtp) cc_final: 0.7578 (pttm) REVERT: A 239 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.7539 (ttm) REVERT: A 669 ASP cc_start: 0.7411 (m-30) cc_final: 0.7087 (m-30) REVERT: A 704 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.8049 (m-30) REVERT: A 737 ASP cc_start: 0.7508 (m-30) cc_final: 0.7248 (m-30) REVERT: A 815 MET cc_start: 0.8637 (ttm) cc_final: 0.8389 (mtp) REVERT: A 827 MET cc_start: 0.8694 (mtt) cc_final: 0.8249 (mtm) REVERT: A 858 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.7572 (mm-30) REVERT: A 867 LYS cc_start: 0.8106 (ttmt) cc_final: 0.7721 (ttpp) REVERT: A 955 LYS cc_start: 0.8873 (tttp) cc_final: 0.8536 (ttpp) REVERT: A 971 ASP cc_start: 0.8934 (t0) cc_final: 0.8397 (t0) REVERT: B 230 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7857 (mt-10) REVERT: B 239 MET cc_start: 0.8089 (tpp) cc_final: 0.7882 (tpp) REVERT: B 323 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8155 (tt0) REVERT: B 340 GLU cc_start: 0.7819 (mm-30) cc_final: 0.6989 (pm20) REVERT: B 473 ASP cc_start: 0.6230 (t0) cc_final: 0.5612 (m-30) REVERT: B 491 ASP cc_start: 0.7283 (m-30) cc_final: 0.6561 (p0) REVERT: B 602 VAL cc_start: 0.8295 (t) cc_final: 0.7845 (m) REVERT: B 604 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: B 637 GLU cc_start: 0.8218 (mp0) cc_final: 0.7893 (mp0) REVERT: B 908 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7521 (pm20) REVERT: B 971 ASP cc_start: 0.8747 (t0) cc_final: 0.8289 (t0) outliers start: 56 outliers final: 20 residues processed: 293 average time/residue: 0.1725 time to fit residues: 76.9733 Evaluate side-chains 268 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 239 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 482 ASP Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 333 HIS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 691 GLU Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 894 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 265 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 263 ASN D 518 ASN A 719 ASN B 99 HIS B 463 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.143502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.124056 restraints weight = 24325.925| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.13 r_work: 0.3196 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.0677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 22192 Z= 0.268 Angle : 0.578 6.234 30093 Z= 0.300 Chirality : 0.045 0.169 3265 Planarity : 0.004 0.046 3879 Dihedral : 4.799 64.527 3008 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.30 % Allowed : 21.43 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.16), residues: 2708 helix: 1.09 (0.14), residues: 1335 sheet: -0.38 (0.30), residues: 327 loop : -0.50 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 394 TYR 0.016 0.002 TYR D 591 PHE 0.021 0.002 PHE B 220 TRP 0.013 0.002 TRP A 630 HIS 0.007 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00660 (22191) covalent geometry : angle 0.57645 (30090) hydrogen bonds : bond 0.04855 ( 1061) hydrogen bonds : angle 4.84526 ( 2979) link_ALPHA1-4 : bond 0.00582 ( 1) link_ALPHA1-4 : angle 4.48958 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 244 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: C 87 MET cc_start: 0.6912 (ptm) cc_final: 0.6577 (ptm) REVERT: C 170 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7961 (mp0) REVERT: C 218 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6843 (pm20) REVERT: C 281 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7791 (mm-30) REVERT: C 419 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.6626 (mtp85) REVERT: D 171 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7702 (tp30) REVERT: D 256 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6713 (mt-10) REVERT: D 299 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7730 (mptt) REVERT: A 174 GLU cc_start: 0.8235 (mp0) cc_final: 0.7981 (mp0) REVERT: A 226 LYS cc_start: 0.8404 (mmtp) cc_final: 0.7747 (pttm) REVERT: A 239 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.7922 (ttm) REVERT: A 669 ASP cc_start: 0.7875 (m-30) cc_final: 0.7450 (m-30) REVERT: A 827 MET cc_start: 0.8889 (mtt) cc_final: 0.8521 (mtm) REVERT: A 858 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.7880 (mm-30) REVERT: A 867 LYS cc_start: 0.8505 (ttmt) cc_final: 0.8144 (ttpp) REVERT: B 230 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8051 (mt-10) REVERT: B 306 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8374 (pt0) REVERT: B 340 GLU cc_start: 0.7801 (mm-30) cc_final: 0.6953 (pm20) REVERT: B 473 ASP cc_start: 0.6217 (t0) cc_final: 0.5705 (m-30) REVERT: B 482 LYS cc_start: 0.8587 (mtpm) cc_final: 0.7115 (mptt) REVERT: B 604 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: B 908 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7617 (pm20) REVERT: B 971 ASP cc_start: 0.8733 (t0) cc_final: 0.8291 (t0) outliers start: 76 outliers final: 47 residues processed: 300 average time/residue: 0.1764 time to fit residues: 79.8150 Evaluate side-chains 290 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 234 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 539 MET Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 733 MET Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 691 GLU Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 894 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 24 optimal weight: 0.8980 chunk 72 optimal weight: 9.9990 chunk 209 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 175 optimal weight: 0.3980 chunk 28 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 263 ASN D 518 ASN A 719 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.127340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.104314 restraints weight = 26650.627| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.58 r_work: 0.2937 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22192 Z= 0.110 Angle : 0.461 6.334 30093 Z= 0.241 Chirality : 0.040 0.156 3265 Planarity : 0.003 0.036 3879 Dihedral : 4.373 61.996 3008 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.39 % Allowed : 22.25 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.16), residues: 2708 helix: 1.42 (0.14), residues: 1338 sheet: -0.36 (0.30), residues: 331 loop : -0.32 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 394 TYR 0.011 0.001 TYR A 353 PHE 0.013 0.001 PHE B 220 TRP 0.014 0.001 TRP B 645 HIS 0.003 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00256 (22191) covalent geometry : angle 0.46041 (30090) hydrogen bonds : bond 0.03723 ( 1061) hydrogen bonds : angle 4.55329 ( 2979) link_ALPHA1-4 : bond 0.00611 ( 1) link_ALPHA1-4 : angle 3.05852 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 250 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: C 218 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6811 (pm20) REVERT: C 419 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.6356 (mtp85) REVERT: C 438 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: D 171 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7475 (tp30) REVERT: D 299 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7640 (mptt) REVERT: D 385 TYR cc_start: 0.8716 (m-80) cc_final: 0.8482 (m-80) REVERT: A 174 GLU cc_start: 0.8094 (mp0) cc_final: 0.7819 (mp0) REVERT: A 226 LYS cc_start: 0.8469 (mmtp) cc_final: 0.7622 (pttm) REVERT: A 239 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.7683 (ttm) REVERT: A 669 ASP cc_start: 0.7584 (m-30) cc_final: 0.7106 (m-30) REVERT: A 827 MET cc_start: 0.8764 (mtt) cc_final: 0.8369 (mtm) REVERT: A 858 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7608 (mm-30) REVERT: A 867 LYS cc_start: 0.8204 (ttmt) cc_final: 0.7830 (ttpp) REVERT: A 971 ASP cc_start: 0.8962 (t0) cc_final: 0.8409 (t0) REVERT: B 230 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7920 (mt-10) REVERT: B 340 GLU cc_start: 0.7812 (mm-30) cc_final: 0.6829 (pm20) REVERT: B 473 ASP cc_start: 0.6199 (t0) cc_final: 0.5624 (m-30) REVERT: B 491 ASP cc_start: 0.7306 (m-30) cc_final: 0.6625 (p0) REVERT: B 602 VAL cc_start: 0.8343 (t) cc_final: 0.7890 (m) REVERT: B 637 GLU cc_start: 0.8205 (mp0) cc_final: 0.7924 (mp0) REVERT: B 908 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7575 (pm20) REVERT: B 971 ASP cc_start: 0.8782 (t0) cc_final: 0.8238 (t0) outliers start: 55 outliers final: 28 residues processed: 292 average time/residue: 0.1742 time to fit residues: 76.2217 Evaluate side-chains 270 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 235 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 539 MET Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 576 ARG Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 691 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 894 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 160 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 204 optimal weight: 4.9990 chunk 141 optimal weight: 0.0870 chunk 201 optimal weight: 0.7980 overall best weight: 1.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 263 ASN D 518 ASN A 719 ASN B 463 ASN B 808 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.125617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.102509 restraints weight = 26689.854| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.58 r_work: 0.2914 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22192 Z= 0.175 Angle : 0.500 5.849 30093 Z= 0.259 Chirality : 0.042 0.144 3265 Planarity : 0.003 0.036 3879 Dihedral : 4.460 62.435 3008 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.96 % Allowed : 21.77 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.16), residues: 2708 helix: 1.39 (0.14), residues: 1337 sheet: -0.34 (0.30), residues: 327 loop : -0.36 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 394 TYR 0.017 0.001 TYR B 469 PHE 0.017 0.001 PHE B 220 TRP 0.011 0.001 TRP A 630 HIS 0.005 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00427 (22191) covalent geometry : angle 0.49867 (30090) hydrogen bonds : bond 0.04082 ( 1061) hydrogen bonds : angle 4.55875 ( 2979) link_ALPHA1-4 : bond 0.00660 ( 1) link_ALPHA1-4 : angle 3.53516 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 238 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: C 218 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6842 (pm20) REVERT: C 419 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.6420 (mtp85) REVERT: C 438 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8135 (tm-30) REVERT: D 171 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7501 (tp30) REVERT: D 189 MET cc_start: 0.5094 (OUTLIER) cc_final: 0.4347 (pmm) REVERT: D 299 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7582 (mptt) REVERT: A 174 GLU cc_start: 0.8057 (mp0) cc_final: 0.7778 (mp0) REVERT: A 226 LYS cc_start: 0.8436 (mmtp) cc_final: 0.7574 (pttm) REVERT: A 239 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.7716 (ttm) REVERT: A 827 MET cc_start: 0.8783 (mtt) cc_final: 0.8382 (mtm) REVERT: A 858 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7619 (mm-30) REVERT: A 867 LYS cc_start: 0.8182 (ttmt) cc_final: 0.7779 (ttpp) REVERT: A 971 ASP cc_start: 0.8943 (t0) cc_final: 0.8384 (t0) REVERT: B 230 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7998 (mt-10) REVERT: B 306 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8330 (pt0) REVERT: B 340 GLU cc_start: 0.7810 (mm-30) cc_final: 0.6815 (pm20) REVERT: B 473 ASP cc_start: 0.6125 (t0) cc_final: 0.5489 (m-30) REVERT: B 602 VAL cc_start: 0.8272 (t) cc_final: 0.7753 (m) REVERT: B 637 GLU cc_start: 0.8204 (mp0) cc_final: 0.7893 (mp0) REVERT: B 971 ASP cc_start: 0.8776 (t0) cc_final: 0.8305 (t0) outliers start: 68 outliers final: 41 residues processed: 290 average time/residue: 0.1783 time to fit residues: 77.9979 Evaluate side-chains 283 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 233 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 539 MET Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 576 ARG Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 691 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 808 GLN Chi-restraints excluded: chain B residue 830 CYS Chi-restraints excluded: chain B residue 894 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 19 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 223 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 180 optimal weight: 8.9990 chunk 204 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 47 optimal weight: 0.0570 chunk 79 optimal weight: 6.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 263 ASN D 518 ASN A 719 ASN A 860 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.125005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.101891 restraints weight = 26822.560| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.59 r_work: 0.3212 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 22192 Z= 0.190 Angle : 0.513 5.893 30093 Z= 0.266 Chirality : 0.042 0.146 3265 Planarity : 0.004 0.036 3879 Dihedral : 4.532 63.832 3008 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.39 % Allowed : 21.38 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.16), residues: 2708 helix: 1.35 (0.14), residues: 1337 sheet: -0.37 (0.29), residues: 328 loop : -0.40 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 366 TYR 0.013 0.002 TYR D 591 PHE 0.019 0.002 PHE B 664 TRP 0.013 0.001 TRP B 645 HIS 0.005 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00464 (22191) covalent geometry : angle 0.51131 (30090) hydrogen bonds : bond 0.04190 ( 1061) hydrogen bonds : angle 4.57630 ( 2979) link_ALPHA1-4 : bond 0.00673 ( 1) link_ALPHA1-4 : angle 3.66809 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 239 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: C 218 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6922 (pm20) REVERT: C 281 GLU cc_start: 0.8267 (mm-30) cc_final: 0.8051 (mm-30) REVERT: C 419 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.6609 (mtp85) REVERT: C 438 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8176 (tm-30) REVERT: D 171 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7766 (tp30) REVERT: D 299 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7668 (mptt) REVERT: A 174 GLU cc_start: 0.8245 (mp0) cc_final: 0.7988 (mp0) REVERT: A 226 LYS cc_start: 0.8474 (mmtp) cc_final: 0.7695 (pttm) REVERT: A 239 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.7875 (ttm) REVERT: A 827 MET cc_start: 0.8887 (mtt) cc_final: 0.8532 (mtm) REVERT: A 858 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.7853 (mm-30) REVERT: A 867 LYS cc_start: 0.8393 (ttmt) cc_final: 0.7982 (ttpp) REVERT: A 971 ASP cc_start: 0.9025 (t0) cc_final: 0.8472 (t0) REVERT: B 230 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8348 (mt-10) REVERT: B 306 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8448 (pt0) REVERT: B 340 GLU cc_start: 0.7938 (mm-30) cc_final: 0.6925 (pm20) REVERT: B 473 ASP cc_start: 0.6312 (t0) cc_final: 0.5627 (m-30) REVERT: B 602 VAL cc_start: 0.8491 (t) cc_final: 0.7978 (m) REVERT: B 637 GLU cc_start: 0.8332 (mp0) cc_final: 0.8026 (mp0) REVERT: B 908 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7376 (pm20) REVERT: B 971 ASP cc_start: 0.8803 (t0) cc_final: 0.8353 (t0) outliers start: 78 outliers final: 57 residues processed: 299 average time/residue: 0.1634 time to fit residues: 73.6964 Evaluate side-chains 299 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 234 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 539 MET Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 385 TYR Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 576 ARG Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 691 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 804 SER Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 830 CYS Chi-restraints excluded: chain B residue 894 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 99 optimal weight: 5.9990 chunk 145 optimal weight: 0.0170 chunk 228 optimal weight: 0.1980 chunk 74 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 269 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 overall best weight: 1.6424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 263 ASN D 518 ASN A 719 ASN B 463 ASN B 808 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.125461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.102411 restraints weight = 26714.241| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.59 r_work: 0.3224 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22192 Z= 0.163 Angle : 0.496 7.181 30093 Z= 0.258 Chirality : 0.041 0.142 3265 Planarity : 0.003 0.036 3879 Dihedral : 4.487 64.823 3008 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.17 % Allowed : 21.38 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.16), residues: 2708 helix: 1.39 (0.14), residues: 1337 sheet: -0.39 (0.29), residues: 332 loop : -0.37 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 394 TYR 0.012 0.001 TYR D 591 PHE 0.016 0.001 PHE B 220 TRP 0.015 0.001 TRP B 645 HIS 0.004 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00398 (22191) covalent geometry : angle 0.49477 (30090) hydrogen bonds : bond 0.04024 ( 1061) hydrogen bonds : angle 4.53293 ( 2979) link_ALPHA1-4 : bond 0.00661 ( 1) link_ALPHA1-4 : angle 3.47190 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 241 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: C 218 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6920 (pm20) REVERT: C 281 GLU cc_start: 0.8245 (mm-30) cc_final: 0.8040 (mm-30) REVERT: C 419 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.6476 (mtp85) REVERT: C 438 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8007 (tm-30) REVERT: D 150 ASP cc_start: 0.7882 (t0) cc_final: 0.6905 (p0) REVERT: D 171 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7797 (tp30) REVERT: D 189 MET cc_start: 0.5190 (OUTLIER) cc_final: 0.4287 (pmm) REVERT: D 299 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7677 (mptt) REVERT: D 385 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.8333 (m-80) REVERT: A 174 GLU cc_start: 0.8223 (mp0) cc_final: 0.7961 (mp0) REVERT: A 226 LYS cc_start: 0.8482 (mmtp) cc_final: 0.7663 (pttt) REVERT: A 239 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7849 (ttm) REVERT: A 827 MET cc_start: 0.8875 (mtt) cc_final: 0.8511 (mtm) REVERT: A 858 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.7860 (mm-30) REVERT: A 867 LYS cc_start: 0.8378 (ttmt) cc_final: 0.7972 (ttpp) REVERT: A 971 ASP cc_start: 0.9029 (t0) cc_final: 0.8484 (t0) REVERT: B 164 GLU cc_start: 0.8526 (pt0) cc_final: 0.8318 (pt0) REVERT: B 230 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8333 (mt-10) REVERT: B 306 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8408 (pt0) REVERT: B 340 GLU cc_start: 0.7904 (mm-30) cc_final: 0.6898 (pm20) REVERT: B 473 ASP cc_start: 0.6320 (t0) cc_final: 0.5652 (m-30) REVERT: B 602 VAL cc_start: 0.8491 (t) cc_final: 0.7989 (m) REVERT: B 637 GLU cc_start: 0.8346 (mp0) cc_final: 0.8038 (mp0) REVERT: B 908 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7350 (pm20) REVERT: B 971 ASP cc_start: 0.8799 (t0) cc_final: 0.8351 (t0) outliers start: 73 outliers final: 56 residues processed: 295 average time/residue: 0.1681 time to fit residues: 75.3796 Evaluate side-chains 302 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 236 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 539 MET Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 385 TYR Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 576 ARG Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 691 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 804 SER Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 808 GLN Chi-restraints excluded: chain B residue 830 CYS Chi-restraints excluded: chain B residue 894 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 244 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 266 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 269 optimal weight: 0.4980 chunk 225 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 94 optimal weight: 7.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 263 ASN D 518 ASN A 719 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.125866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.102854 restraints weight = 26692.748| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.59 r_work: 0.3228 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22192 Z= 0.149 Angle : 0.489 6.634 30093 Z= 0.254 Chirality : 0.041 0.142 3265 Planarity : 0.003 0.036 3879 Dihedral : 4.453 65.059 3008 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.22 % Allowed : 21.25 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.16), residues: 2708 helix: 1.43 (0.14), residues: 1337 sheet: -0.49 (0.29), residues: 345 loop : -0.37 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 366 TYR 0.011 0.001 TYR D 591 PHE 0.016 0.001 PHE B 220 TRP 0.018 0.001 TRP B 645 HIS 0.004 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00359 (22191) covalent geometry : angle 0.48821 (30090) hydrogen bonds : bond 0.03934 ( 1061) hydrogen bonds : angle 4.50246 ( 2979) link_ALPHA1-4 : bond 0.00814 ( 1) link_ALPHA1-4 : angle 3.34040 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 239 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: C 218 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6917 (pm20) REVERT: C 419 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.6444 (mtp85) REVERT: C 438 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.7995 (tm-30) REVERT: D 150 ASP cc_start: 0.7857 (t0) cc_final: 0.6877 (p0) REVERT: D 171 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7782 (tp30) REVERT: D 189 MET cc_start: 0.5173 (OUTLIER) cc_final: 0.4279 (pmm) REVERT: D 274 GLN cc_start: 0.7920 (mp10) cc_final: 0.7525 (mm-40) REVERT: D 299 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7672 (mptt) REVERT: D 385 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.8338 (m-80) REVERT: A 174 GLU cc_start: 0.8213 (mp0) cc_final: 0.7945 (mp0) REVERT: A 226 LYS cc_start: 0.8500 (mmtp) cc_final: 0.7668 (pttt) REVERT: A 239 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.7798 (ttm) REVERT: A 827 MET cc_start: 0.8868 (mtt) cc_final: 0.8523 (mtm) REVERT: A 858 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.7866 (mm-30) REVERT: A 867 LYS cc_start: 0.8369 (ttmt) cc_final: 0.7960 (ttpp) REVERT: A 971 ASP cc_start: 0.9019 (t0) cc_final: 0.8473 (t0) REVERT: B 164 GLU cc_start: 0.8489 (pt0) cc_final: 0.8279 (pt0) REVERT: B 230 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8270 (mt-10) REVERT: B 306 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8391 (pt0) REVERT: B 340 GLU cc_start: 0.7900 (mm-30) cc_final: 0.6918 (pm20) REVERT: B 473 ASP cc_start: 0.6282 (t0) cc_final: 0.5657 (m-30) REVERT: B 491 ASP cc_start: 0.7369 (m-30) cc_final: 0.6686 (p0) REVERT: B 602 VAL cc_start: 0.8475 (t) cc_final: 0.7971 (m) REVERT: B 637 GLU cc_start: 0.8329 (mp0) cc_final: 0.8020 (mp0) REVERT: B 971 ASP cc_start: 0.8786 (t0) cc_final: 0.8338 (t0) outliers start: 74 outliers final: 55 residues processed: 292 average time/residue: 0.1733 time to fit residues: 76.7276 Evaluate side-chains 303 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 238 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 539 MET Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 385 TYR Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 576 ARG Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 691 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 804 SER Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 830 CYS Chi-restraints excluded: chain B residue 894 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 2 optimal weight: 9.9990 chunk 212 optimal weight: 2.9990 chunk 181 optimal weight: 6.9990 chunk 246 optimal weight: 0.7980 chunk 257 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 33 optimal weight: 0.0980 chunk 147 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 263 ASN D 518 ASN A 719 ASN A 808 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.125713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.102742 restraints weight = 26711.083| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.58 r_work: 0.2917 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22192 Z= 0.159 Angle : 0.498 7.162 30093 Z= 0.258 Chirality : 0.041 0.142 3265 Planarity : 0.003 0.036 3879 Dihedral : 4.482 65.977 3008 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.22 % Allowed : 21.34 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.16), residues: 2708 helix: 1.43 (0.14), residues: 1337 sheet: -0.39 (0.30), residues: 328 loop : -0.38 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 366 TYR 0.011 0.001 TYR D 591 PHE 0.017 0.001 PHE B 220 TRP 0.022 0.001 TRP B 645 HIS 0.004 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00388 (22191) covalent geometry : angle 0.49640 (30090) hydrogen bonds : bond 0.03983 ( 1061) hydrogen bonds : angle 4.50162 ( 2979) link_ALPHA1-4 : bond 0.00768 ( 1) link_ALPHA1-4 : angle 3.39062 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 241 time to evaluate : 0.861 Fit side-chains revert: symmetry clash REVERT: C 218 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6868 (pm20) REVERT: C 419 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.6394 (mtp85) REVERT: C 438 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.7914 (tm-30) REVERT: D 150 ASP cc_start: 0.7754 (t0) cc_final: 0.6756 (p0) REVERT: D 171 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7647 (tp30) REVERT: D 189 MET cc_start: 0.5115 (OUTLIER) cc_final: 0.4240 (pmm) REVERT: D 193 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7192 (mt-10) REVERT: D 274 GLN cc_start: 0.7786 (mp10) cc_final: 0.7455 (mm-40) REVERT: D 299 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7585 (mptt) REVERT: D 385 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.8227 (m-80) REVERT: A 174 GLU cc_start: 0.8046 (mp0) cc_final: 0.7759 (mp0) REVERT: A 226 LYS cc_start: 0.8465 (mmtp) cc_final: 0.7518 (pttt) REVERT: A 239 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7732 (ttm) REVERT: A 827 MET cc_start: 0.8789 (mtt) cc_final: 0.8404 (mtm) REVERT: A 858 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7670 (mm-30) REVERT: A 867 LYS cc_start: 0.8172 (ttmt) cc_final: 0.7764 (ttpp) REVERT: A 971 ASP cc_start: 0.8957 (t0) cc_final: 0.8398 (t0) REVERT: B 164 GLU cc_start: 0.8409 (pt0) cc_final: 0.8179 (pt0) REVERT: B 230 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7988 (mt-10) REVERT: B 306 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8349 (pt0) REVERT: B 340 GLU cc_start: 0.7838 (mm-30) cc_final: 0.6815 (pm20) REVERT: B 473 ASP cc_start: 0.6301 (t0) cc_final: 0.5670 (m-30) REVERT: B 491 ASP cc_start: 0.7362 (m-30) cc_final: 0.6672 (p0) REVERT: B 602 VAL cc_start: 0.8249 (t) cc_final: 0.7716 (m) REVERT: B 637 GLU cc_start: 0.8225 (mp0) cc_final: 0.7905 (mp0) REVERT: B 971 ASP cc_start: 0.8774 (t0) cc_final: 0.8300 (t0) outliers start: 74 outliers final: 55 residues processed: 295 average time/residue: 0.1720 time to fit residues: 76.8535 Evaluate side-chains 302 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 237 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 539 MET Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 385 TYR Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 576 ARG Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 691 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 830 CYS Chi-restraints excluded: chain B residue 894 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 132 optimal weight: 3.9990 chunk 235 optimal weight: 0.5980 chunk 199 optimal weight: 0.9980 chunk 187 optimal weight: 0.0020 chunk 163 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 145 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 263 ASN D 518 ASN A 719 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.127939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.105067 restraints weight = 26578.887| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.58 r_work: 0.2947 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22192 Z= 0.106 Angle : 0.461 6.339 30093 Z= 0.239 Chirality : 0.040 0.142 3265 Planarity : 0.003 0.036 3879 Dihedral : 4.261 63.583 3008 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.26 % Allowed : 22.34 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.16), residues: 2708 helix: 1.58 (0.14), residues: 1337 sheet: -0.37 (0.30), residues: 333 loop : -0.27 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 394 TYR 0.009 0.001 TYR A 353 PHE 0.012 0.001 PHE B 220 TRP 0.024 0.001 TRP B 645 HIS 0.003 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00249 (22191) covalent geometry : angle 0.46010 (30090) hydrogen bonds : bond 0.03546 ( 1061) hydrogen bonds : angle 4.39347 ( 2979) link_ALPHA1-4 : bond 0.00854 ( 1) link_ALPHA1-4 : angle 2.88018 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 256 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: C 218 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6845 (pm20) REVERT: C 419 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.6325 (mtp85) REVERT: C 438 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7447 (tm-30) REVERT: D 150 ASP cc_start: 0.7763 (t0) cc_final: 0.6786 (p0) REVERT: D 171 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7613 (tp30) REVERT: D 193 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7151 (mt-10) REVERT: D 274 GLN cc_start: 0.7833 (mp10) cc_final: 0.7464 (mm-40) REVERT: D 299 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7615 (mptt) REVERT: D 385 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.8154 (m-80) REVERT: A 174 GLU cc_start: 0.8054 (mp0) cc_final: 0.7782 (mp0) REVERT: A 226 LYS cc_start: 0.8434 (mmtp) cc_final: 0.7534 (pttm) REVERT: A 239 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7636 (ttm) REVERT: A 827 MET cc_start: 0.8756 (mtt) cc_final: 0.8368 (mtm) REVERT: A 858 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.7651 (mm-30) REVERT: A 867 LYS cc_start: 0.8162 (ttmt) cc_final: 0.7758 (ttpp) REVERT: A 971 ASP cc_start: 0.8955 (t0) cc_final: 0.8378 (t0) REVERT: B 164 GLU cc_start: 0.8389 (pt0) cc_final: 0.8180 (pt0) REVERT: B 230 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7932 (mt-10) REVERT: B 340 GLU cc_start: 0.7807 (mm-30) cc_final: 0.6835 (pm20) REVERT: B 473 ASP cc_start: 0.6165 (t0) cc_final: 0.5619 (m-30) REVERT: B 491 ASP cc_start: 0.7185 (m-30) cc_final: 0.6533 (p0) REVERT: B 602 VAL cc_start: 0.8297 (t) cc_final: 0.7803 (m) REVERT: B 637 GLU cc_start: 0.8209 (mp0) cc_final: 0.7904 (mp0) REVERT: B 971 ASP cc_start: 0.8779 (t0) cc_final: 0.8243 (t0) outliers start: 52 outliers final: 40 residues processed: 291 average time/residue: 0.1750 time to fit residues: 77.5175 Evaluate side-chains 292 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 244 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 539 MET Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 385 TYR Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 576 ARG Chi-restraints excluded: chain B residue 691 GLU Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 830 CYS Chi-restraints excluded: chain B residue 894 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 150 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 162 optimal weight: 0.7980 chunk 7 optimal weight: 9.9990 chunk 179 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 262 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 263 ASN D 518 ASN A 719 ASN A 808 GLN B 463 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.125404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.102221 restraints weight = 26715.073| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.52 r_work: 0.3225 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22192 Z= 0.184 Angle : 0.519 8.724 30093 Z= 0.268 Chirality : 0.042 0.157 3265 Planarity : 0.004 0.036 3879 Dihedral : 4.505 65.129 3008 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.39 % Allowed : 22.29 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.16), residues: 2708 helix: 1.46 (0.14), residues: 1337 sheet: -0.41 (0.30), residues: 328 loop : -0.37 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 366 TYR 0.013 0.001 TYR D 591 PHE 0.019 0.002 PHE B 220 TRP 0.025 0.001 TRP B 645 HIS 0.005 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00449 (22191) covalent geometry : angle 0.51803 (30090) hydrogen bonds : bond 0.04110 ( 1061) hydrogen bonds : angle 4.51003 ( 2979) link_ALPHA1-4 : bond 0.00781 ( 1) link_ALPHA1-4 : angle 3.48477 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6217.85 seconds wall clock time: 107 minutes 9.42 seconds (6429.42 seconds total)