Starting phenix.real_space_refine on Fri Aug 7 15:31:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/13eu_77027/08_2026/13eu_77027.cif Found real_map, /net/cci-nas-00/data/ceres_data/13eu_77027/08_2026/13eu_77027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/13eu_77027/08_2026/13eu_77027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/13eu_77027/08_2026/13eu_77027.map" model { file = "/net/cci-nas-00/data/ceres_data/13eu_77027/08_2026/13eu_77027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/13eu_77027/08_2026/13eu_77027.cif" } resolution = 3.26 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 ------------------------------------------------------------------------------- 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= 0.005 sd= 0.051 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: 5 Type Number sf(0) Gaussians Ca 7 9.91 5 S 114 5.16 5 C 14116 2.51 5 N 3765 2.21 5 O 4259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22261 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 912, 7286 Classifications: {'peptide': 912} Link IDs: {'PTRANS': 52, 'TRANS': 859} Chain breaks: 3 Chain: "B" Number of atoms: 7275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 911, 7275 Classifications: {'peptide': 911} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 51, 'TRANS': 859} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 7285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 912, 7285 Classifications: {'peptide': 912} Link IDs: {'PTRANS': 52, 'TRANS': 859} Chain breaks: 3 Chain: "G" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 408 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Planarities with less than four sites: {'CGU:plan-1': 11} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' CA': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 4.48, per 1000 atoms: 0.20 Number of scatterers: 22261 At special positions: 0 Unit cell: (113.9, 116.45, 141.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 7 19.99 S 114 16.00 O 4259 8.00 N 3765 7.00 C 14116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 986.0 milliseconds 5454 Ramachandran restraints generated. 2727 Oldfield, 0 Emsley, 2727 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5208 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 46 sheets defined 17.5% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 7 through 13 removed outlier: 4.061A pdb=" N SER A 11 " --> pdb=" O MET A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 24 removed outlier: 3.802A pdb=" N TYR A 23 " --> pdb=" O ASP A 19 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 19 through 24' Processing helix chain 'A' and resid 25 through 35 Processing helix chain 'A' and resid 41 through 45 removed outlier: 4.076A pdb=" N LYS A 44 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE A 45 " --> pdb=" O ASN A 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 41 through 45' Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'A' and resid 319 through 325 removed outlier: 4.049A pdb=" N GLY A 324 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN A 325 " --> pdb=" O MET A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 342 Processing helix chain 'A' and resid 374 through 386 Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 511 through 517 Processing helix chain 'A' and resid 521 through 526 removed outlier: 3.590A pdb=" N LEU A 524 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 525 " --> pdb=" O PRO A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 562 Processing helix chain 'A' and resid 577 through 582 removed outlier: 4.708A pdb=" N ASN A 582 " --> pdb=" O PHE A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'A' and resid 611 through 616 removed outlier: 3.617A pdb=" N GLY A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 646 Processing helix chain 'A' and resid 716 through 721 Processing helix chain 'A' and resid 773 through 786 Processing helix chain 'A' and resid 829 through 833 removed outlier: 3.520A pdb=" N GLN A 833 " --> pdb=" O ILE A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 907 removed outlier: 4.063A pdb=" N ASN A 907 " --> pdb=" O LEU A 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 14 Processing helix chain 'B' and resid 19 through 24 removed outlier: 3.697A pdb=" N LEU B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 35 Processing helix chain 'B' and resid 97 through 99 No H-bonds generated for 'chain 'B' and resid 97 through 99' Processing helix chain 'B' and resid 319 through 323 Processing helix chain 'B' and resid 339 through 342 Processing helix chain 'B' and resid 375 through 386 removed outlier: 3.697A pdb=" N GLY B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.680A pdb=" N ARG B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE B 408 " --> pdb=" O PRO B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 408' Processing helix chain 'B' and resid 475 through 488 Processing helix chain 'B' and resid 493 through 497 Processing helix chain 'B' and resid 511 through 517 Processing helix chain 'B' and resid 521 through 526 removed outlier: 3.686A pdb=" N ASP B 526 " --> pdb=" O GLY B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 removed outlier: 4.055A pdb=" N ASN B 542 " --> pdb=" O TYR B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 562 Processing helix chain 'B' and resid 577 through 581 removed outlier: 3.896A pdb=" N LYS B 581 " --> pdb=" O PHE B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 603 Processing helix chain 'B' and resid 611 through 616 removed outlier: 3.621A pdb=" N ASP B 615 " --> pdb=" O ASP B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 646 Processing helix chain 'B' and resid 697 through 699 No H-bonds generated for 'chain 'B' and resid 697 through 699' Processing helix chain 'B' and resid 716 through 721 Processing helix chain 'B' and resid 725 through 727 No H-bonds generated for 'chain 'B' and resid 725 through 727' Processing helix chain 'B' and resid 774 through 786 Processing helix chain 'B' and resid 898 through 902 Processing helix chain 'C' and resid 8 through 13 Processing helix chain 'C' and resid 25 through 35 Processing helix chain 'C' and resid 283 through 288 removed outlier: 3.644A pdb=" N ASN C 286 " --> pdb=" O ASN C 283 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE C 288 " --> pdb=" O VAL C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 325 removed outlier: 3.925A pdb=" N GLY C 324 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN C 325 " --> pdb=" O MET C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 386 Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.507A pdb=" N ARG C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE C 408 " --> pdb=" O PRO C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 408' Processing helix chain 'C' and resid 474 through 488 Processing helix chain 'C' and resid 489 through 492 Processing helix chain 'C' and resid 493 through 497 Processing helix chain 'C' and resid 511 through 518 Processing helix chain 'C' and resid 521 through 525 removed outlier: 3.589A pdb=" N LEU C 524 " --> pdb=" O ALA C 521 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL C 525 " --> pdb=" O PRO C 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 521 through 525' Processing helix chain 'C' and resid 551 through 562 Processing helix chain 'C' and resid 577 through 581 removed outlier: 3.869A pdb=" N LYS C 581 " --> pdb=" O PHE C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 603 Processing helix chain 'C' and resid 634 through 645 Processing helix chain 'C' and resid 773 through 785 Processing helix chain 'C' and resid 829 through 833 removed outlier: 3.622A pdb=" N GLN C 833 " --> pdb=" O ILE C 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 908 removed outlier: 4.596A pdb=" N ASN C 907 " --> pdb=" O LEU C 903 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER C 908 " --> pdb=" O LEU C 904 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 903 through 908' Processing helix chain 'G' and resid 5 through 9 Processing helix chain 'G' and resid 34 through 40 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.834A pdb=" N ARG A 104 " --> pdb=" O ASP A 622 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A 624 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASP A 102 " --> pdb=" O ILE A 624 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LEU A 626 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TYR A 100 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A 105 " --> pdb=" O PHE A 569 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 569 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 removed outlier: 3.913A pdb=" N ASP A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 82 " --> pdb=" O TRP A 594 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TRP A 594 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 removed outlier: 3.860A pdb=" N LEU A 94 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 133 through 137 Processing sheet with id=AA5, first strand: chain 'A' and resid 174 through 175 Processing sheet with id=AA6, first strand: chain 'A' and resid 182 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 228 through 233 removed outlier: 7.132A pdb=" N ALA A 228 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N TYR A 295 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLY A 230 " --> pdb=" O TYR A 295 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N GLU A 297 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL A 232 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.176A pdb=" N GLN A 326 " --> pdb=" O SER A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 336 through 337 Processing sheet with id=AB1, first strand: chain 'A' and resid 420 through 421 removed outlier: 3.920A pdb=" N ASN A 420 " --> pdb=" O ILE A 473 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN C 420 " --> pdb=" O ILE C 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB3, first strand: chain 'A' and resid 453 through 454 removed outlier: 3.827A pdb=" N LYS A 453 " --> pdb=" O LYS A 438 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE C 274 " --> pdb=" O VAL A 437 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 292 " --> pdb=" O PHE C 275 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 463 through 465 removed outlier: 6.750A pdb=" N GLY A 464 " --> pdb=" O ALA C 175 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 652 through 655 removed outlier: 3.624A pdb=" N GLN A 652 " --> pdb=" O VAL A 939 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 660 through 667 removed outlier: 3.514A pdb=" N TYR A 665 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY A 688 " --> pdb=" O GLU A 932 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 673 through 681 removed outlier: 4.304A pdb=" N SER A 680 " --> pdb=" O HIS A 910 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N HIS A 910 " --> pdb=" O SER A 680 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA A 911 " --> pdb=" O PHE A 736 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N PHE A 736 " --> pdb=" O ALA A 911 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ASP A 913 " --> pdb=" O ILE A 734 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE A 734 " --> pdb=" O ASP A 913 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR A 915 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL A 732 " --> pdb=" O THR A 915 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLU A 917 " --> pdb=" O LYS A 730 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 673 through 681 removed outlier: 4.304A pdb=" N SER A 680 " --> pdb=" O HIS A 910 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N HIS A 910 " --> pdb=" O SER A 680 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA A 911 " --> pdb=" O PHE A 736 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N PHE A 736 " --> pdb=" O ALA A 911 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ASP A 913 " --> pdb=" O ILE A 734 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE A 734 " --> pdb=" O ASP A 913 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR A 915 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL A 732 " --> pdb=" O THR A 915 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLU A 917 " --> pdb=" O LYS A 730 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 810 through 817 removed outlier: 3.528A pdb=" N LYS A 874 " --> pdb=" O MET A 812 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 65 through 68 removed outlier: 3.640A pdb=" N ALA B 628 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 626 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ARG B 104 " --> pdb=" O ASP B 622 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE B 624 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASP B 102 " --> pdb=" O ILE B 624 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU B 626 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N TYR B 100 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 105 " --> pdb=" O PHE B 569 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 65 through 68 removed outlier: 3.640A pdb=" N ALA B 628 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 626 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ARG B 104 " --> pdb=" O ASP B 622 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE B 624 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASP B 102 " --> pdb=" O ILE B 624 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU B 626 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N TYR B 100 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 72 through 75 removed outlier: 3.809A pdb=" N ASP B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 82 " --> pdb=" O TRP B 594 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TRP B 594 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 94 through 95 removed outlier: 3.775A pdb=" N LEU B 94 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 133 through 137 removed outlier: 3.571A pdb=" N LYS B 168 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 173 " --> pdb=" O GLU C 462 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP C 432 " --> pdb=" O ILE C 463 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 437 " --> pdb=" O PHE B 274 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE B 274 " --> pdb=" O VAL C 437 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA B 228 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N TYR B 295 " --> pdb=" O ALA B 228 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLY B 230 " --> pdb=" O TYR B 295 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N GLU B 297 " --> pdb=" O GLY B 230 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL B 232 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 133 through 137 removed outlier: 3.571A pdb=" N LYS B 168 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 173 " --> pdb=" O GLU C 462 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP C 432 " --> pdb=" O ILE C 463 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 182 through 183 removed outlier: 3.568A pdb=" N GLY B 190 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 203 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.268A pdb=" N GLN B 326 " --> pdb=" O SER B 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 336 through 337 Processing sheet with id=AD1, first strand: chain 'B' and resid 438 through 439 Processing sheet with id=AD2, first strand: chain 'B' and resid 652 through 655 removed outlier: 3.539A pdb=" N LEU B 952 " --> pdb=" O VAL B 936 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 660 through 667 removed outlier: 4.324A pdb=" N GLY B 688 " --> pdb=" O GLU B 932 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TRP B 882 " --> pdb=" O PHE B 691 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 674 through 681 removed outlier: 3.625A pdb=" N VAL B 674 " --> pdb=" O PHE B 916 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER B 680 " --> pdb=" O HIS B 910 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N HIS B 910 " --> pdb=" O SER B 680 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA B 911 " --> pdb=" O PHE B 736 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE B 736 " --> pdb=" O ALA B 911 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP B 913 " --> pdb=" O ILE B 734 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE B 734 " --> pdb=" O ASP B 913 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR B 915 " --> pdb=" O VAL B 732 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL B 732 " --> pdb=" O THR B 915 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLU B 917 " --> pdb=" O LYS B 730 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 674 through 681 removed outlier: 3.625A pdb=" N VAL B 674 " --> pdb=" O PHE B 916 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER B 680 " --> pdb=" O HIS B 910 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N HIS B 910 " --> pdb=" O SER B 680 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA B 911 " --> pdb=" O PHE B 736 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE B 736 " --> pdb=" O ALA B 911 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP B 913 " --> pdb=" O ILE B 734 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE B 734 " --> pdb=" O ASP B 913 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR B 915 " --> pdb=" O VAL B 732 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL B 732 " --> pdb=" O THR B 915 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLU B 917 " --> pdb=" O LYS B 730 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 766 through 767 removed outlier: 4.710A pdb=" N MET B 772 " --> pdb=" O VAL B 767 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 809 through 817 Processing sheet with id=AD8, first strand: chain 'C' and resid 65 through 68 removed outlier: 5.072A pdb=" N ILE C 619 " --> pdb=" O ASP C 108 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASP C 108 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N PHE C 621 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL C 106 " --> pdb=" O PHE C 621 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 65 through 68 removed outlier: 5.072A pdb=" N ILE C 619 " --> pdb=" O ASP C 108 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASP C 108 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N PHE C 621 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL C 106 " --> pdb=" O PHE C 621 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 72 through 75 removed outlier: 3.773A pdb=" N ASP C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE C 596 " --> pdb=" O TYR C 80 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR C 592 " --> pdb=" O PHE C 84 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 94 through 95 removed outlier: 3.573A pdb=" N LEU C 94 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 190 through 191 removed outlier: 3.572A pdb=" N ILE C 203 " --> pdb=" O GLY C 190 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.408A pdb=" N GLN C 326 " --> pdb=" O SER C 309 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 336 through 337 Processing sheet with id=AE6, first strand: chain 'C' and resid 409 through 410 removed outlier: 3.684A pdb=" N ILE C 409 " --> pdb=" O TRP C 535 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 652 through 655 Processing sheet with id=AE8, first strand: chain 'C' and resid 660 through 667 Processing sheet with id=AE9, first strand: chain 'C' and resid 673 through 681 removed outlier: 5.012A pdb=" N ASN C 673 " --> pdb=" O VAL C 918 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL C 918 " --> pdb=" O ASN C 673 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE C 916 " --> pdb=" O PRO C 675 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N SER C 677 " --> pdb=" O MET C 914 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N MET C 914 " --> pdb=" O SER C 677 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU C 912 " --> pdb=" O PRO C 679 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA C 911 " --> pdb=" O PHE C 736 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE C 736 " --> pdb=" O ALA C 911 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ASP C 913 " --> pdb=" O ILE C 734 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ILE C 734 " --> pdb=" O ASP C 913 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR C 915 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N VAL C 732 " --> pdb=" O THR C 915 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLU C 917 " --> pdb=" O LYS C 730 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 810 through 817 removed outlier: 3.720A pdb=" N LYS C 874 " --> pdb=" O MET C 812 " (cutoff:3.500A) 563 hydrogen bonds defined for protein. 1440 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: 4.02 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7300 1.34 - 1.47: 5778 1.47 - 1.60: 9548 1.60 - 1.72: 0 1.72 - 1.85: 205 Bond restraints: 22831 Sorted by residual: bond pdb=" C GLU B 538 " pdb=" N TYR B 539 " ideal model delta sigma weight residual 1.335 1.286 0.049 1.30e-02 5.92e+03 1.41e+01 bond pdb=" N MET B 540 " pdb=" CA MET B 540 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.10e-02 8.26e+03 1.19e+01 bond pdb=" CA ASP C 541 " pdb=" C ASP C 541 " ideal model delta sigma weight residual 1.523 1.489 0.034 1.34e-02 5.57e+03 6.56e+00 bond pdb=" C SER A 536 " pdb=" N LEU A 537 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.31e-02 5.83e+03 6.56e+00 bond pdb=" N CGU G 25 " pdb=" CA CGU G 25 " ideal model delta sigma weight residual 1.458 1.507 -0.049 1.90e-02 2.77e+03 6.53e+00 ... (remaining 22826 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 30524 1.81 - 3.62: 431 3.62 - 5.43: 75 5.43 - 7.24: 6 7.24 - 9.05: 7 Bond angle restraints: 31043 Sorted by residual: angle pdb=" N TYR C 539 " pdb=" CA TYR C 539 " pdb=" C TYR C 539 " ideal model delta sigma weight residual 111.28 103.97 7.31 1.09e+00 8.42e-01 4.49e+01 angle pdb=" C GLU B 538 " pdb=" CA GLU B 538 " pdb=" CB GLU B 538 " ideal model delta sigma weight residual 110.88 119.51 -8.63 1.57e+00 4.06e-01 3.02e+01 angle pdb=" CA TYR B 539 " pdb=" C TYR B 539 " pdb=" O TYR B 539 " ideal model delta sigma weight residual 120.63 115.41 5.22 1.08e+00 8.57e-01 2.34e+01 angle pdb=" CA TYR A 539 " pdb=" C TYR A 539 " pdb=" O TYR A 539 " ideal model delta sigma weight residual 120.51 114.75 5.76 1.43e+00 4.89e-01 1.62e+01 angle pdb=" N ASP C 541 " pdb=" CA ASP C 541 " pdb=" C ASP C 541 " ideal model delta sigma weight residual 110.80 102.49 8.31 2.13e+00 2.20e-01 1.52e+01 ... (remaining 31038 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 12787 17.18 - 34.37: 594 34.37 - 51.55: 129 51.55 - 68.73: 20 68.73 - 85.91: 1 Dihedral angle restraints: 13531 sinusoidal: 5393 harmonic: 8138 Sorted by residual: dihedral pdb=" CA ASN A 221 " pdb=" C ASN A 221 " pdb=" N GLU A 222 " pdb=" CA GLU A 222 " ideal model delta harmonic sigma weight residual 180.00 -157.12 -22.88 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA PHE B 209 " pdb=" C PHE B 209 " pdb=" N GLN B 210 " pdb=" CA GLN B 210 " ideal model delta harmonic sigma weight residual -180.00 -157.47 -22.53 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA ALA A 223 " pdb=" C ALA A 223 " pdb=" N ASP A 224 " pdb=" CA ASP A 224 " ideal model delta harmonic sigma weight residual -180.00 -157.95 -22.05 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 13528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2699 0.055 - 0.111: 526 0.111 - 0.166: 63 0.166 - 0.222: 1 0.222 - 0.277: 2 Chirality restraints: 3291 Sorted by residual: chirality pdb=" CA GLU B 538 " pdb=" N GLU B 538 " pdb=" C GLU B 538 " pdb=" CB GLU B 538 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA GLU A 538 " pdb=" N GLU A 538 " pdb=" C GLU A 538 " pdb=" CB GLU A 538 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA MET B 540 " pdb=" N MET B 540 " pdb=" C MET B 540 " pdb=" CB MET B 540 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 3288 not shown) Planarity restraints: 4089 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 539 " 0.023 2.00e-02 2.50e+03 1.68e-02 5.67e+00 pdb=" CG TYR C 539 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR C 539 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR C 539 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 539 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 539 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR C 539 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 539 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 539 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C TYR C 539 " -0.034 2.00e-02 2.50e+03 pdb=" O TYR C 539 " 0.013 2.00e-02 2.50e+03 pdb=" N MET C 540 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 567 " -0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO A 568 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 568 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 568 " -0.025 5.00e-02 4.00e+02 ... (remaining 4086 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 311 2.63 - 3.20: 19238 3.20 - 3.77: 31750 3.77 - 4.33: 45791 4.33 - 4.90: 77131 Nonbonded interactions: 174221 Sorted by model distance: nonbonded pdb="CA CA G 403 " pdb="CA CA G 404 " model vdw 2.066 1.980 nonbonded pdb=" N ASP A 919 " pdb=" OD1 ASP A 919 " model vdw 2.155 3.120 nonbonded pdb=" OD1 ASN B 662 " pdb=" OH TYR B 928 " model vdw 2.226 3.040 nonbonded pdb=" OD1 ASP A 55 " pdb=" OG1 THR A 637 " model vdw 2.253 3.040 nonbonded pdb=" O ASN C 283 " pdb=" ND2 ASN C 286 " model vdw 2.259 3.120 ... (remaining 174216 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 436 or (resid 437 and (name N or name CA or name \ C or name O or name CB )) or resid 438 through 439 or resid 449 through 958)) selection = (chain 'B' and (resid 8 through 439 or resid 449 through 958)) selection = (chain 'C' and (resid 8 through 436 or (resid 437 and (name N or name CA or name \ C or name O or name CB )) or resid 438 through 439 or resid 449 through 958)) } 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 19.030 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 22831 Z= 0.151 Angle : 0.573 9.049 31043 Z= 0.323 Chirality : 0.044 0.277 3291 Planarity : 0.004 0.046 4089 Dihedral : 10.479 85.913 8323 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.56 % Favored : 93.33 % Rotamer: Outliers : 3.79 % Allowed : 6.54 % Favored : 89.67 % Cbeta Deviations : 0.04 % 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: -1.74 (0.16), residues: 2727 helix: 0.76 (0.31), residues: 325 sheet: -0.53 (0.22), residues: 581 loop : -1.85 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 814 TYR 0.041 0.001 TYR C 539 PHE 0.016 0.001 PHE A 754 TRP 0.007 0.001 TRP B 535 HIS 0.004 0.001 HIS C 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (22831) covalent geometry : angle 0.57305 / 0.32 (31043) hydrogen bonds : bond 0.26880 / 17.94 ( 522) hydrogen bonds : angle 9.51058 / 6.53 ( 1440) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5454 Ramachandran restraints generated. 2727 Oldfield, 0 Emsley, 2727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5454 Ramachandran restraints generated. 2727 Oldfield, 0 Emsley, 2727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 774 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 TYR cc_start: 0.8504 (p90) cc_final: 0.8289 (p90) REVERT: A 36 GLU cc_start: 0.8155 (tp30) cc_final: 0.7919 (tp30) REVERT: A 73 ARG cc_start: 0.7894 (ttt180) cc_final: 0.7681 (ttt180) REVERT: A 81 LYS cc_start: 0.8058 (pttt) cc_final: 0.7856 (ptpp) REVERT: A 102 ASP cc_start: 0.7008 (t0) cc_final: 0.6775 (m-30) REVERT: A 171 VAL cc_start: 0.8082 (t) cc_final: 0.7842 (p) REVERT: A 217 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6465 (mp0) REVERT: A 218 SER cc_start: 0.6845 (m) cc_final: 0.6630 (p) REVERT: A 308 LEU cc_start: 0.6421 (mt) cc_final: 0.6045 (mm) REVERT: A 349 SER cc_start: 0.7520 (m) cc_final: 0.7293 (t) REVERT: A 527 CYS cc_start: 0.6355 (t) cc_final: 0.5986 (p) REVERT: A 618 SER cc_start: 0.8701 (t) cc_final: 0.8426 (p) REVERT: A 631 PHE cc_start: 0.8369 (t80) cc_final: 0.8129 (t80) REVERT: A 674 VAL cc_start: 0.7786 (t) cc_final: 0.7563 (p) REVERT: A 687 ARG cc_start: 0.8267 (mtp180) cc_final: 0.7927 (mtm-85) REVERT: A 718 TYR cc_start: 0.7520 (t80) cc_final: 0.7243 (t80) REVERT: A 730 LYS cc_start: 0.5942 (mtmm) cc_final: 0.5687 (mtmm) REVERT: A 736 PHE cc_start: 0.7169 (OUTLIER) cc_final: 0.6800 (m-10) REVERT: A 767 VAL cc_start: 0.6825 (OUTLIER) cc_final: 0.6536 (p) REVERT: A 802 MET cc_start: 0.7776 (ttm) cc_final: 0.7535 (ttm) REVERT: A 818 ASP cc_start: 0.7635 (t0) cc_final: 0.7313 (t0) REVERT: A 823 LYS cc_start: 0.8028 (mmtt) cc_final: 0.7778 (mmtt) REVERT: A 825 TYR cc_start: 0.7317 (t80) cc_final: 0.6998 (t80) REVERT: A 865 THR cc_start: 0.7470 (p) cc_final: 0.7203 (t) REVERT: A 870 ILE cc_start: 0.7237 (OUTLIER) cc_final: 0.6885 (pt) REVERT: A 935 ASP cc_start: 0.7845 (t0) cc_final: 0.7554 (t0) REVERT: A 952 LEU cc_start: 0.7435 (tp) cc_final: 0.7174 (tp) REVERT: B 13 MET cc_start: 0.7753 (mpp) cc_final: 0.7390 (mmm) REVERT: B 58 THR cc_start: 0.8498 (t) cc_final: 0.8192 (m) REVERT: B 94 LEU cc_start: 0.7726 (tp) cc_final: 0.7452 (tt) REVERT: B 135 TRP cc_start: 0.6376 (p90) cc_final: 0.6087 (p90) REVERT: B 258 VAL cc_start: 0.6111 (t) cc_final: 0.5902 (m) REVERT: B 414 THR cc_start: 0.6249 (p) cc_final: 0.5851 (p) REVERT: B 525 VAL cc_start: 0.7200 (OUTLIER) cc_final: 0.6958 (p) REVERT: B 527 CYS cc_start: 0.6751 (t) cc_final: 0.6158 (m) REVERT: B 606 SER cc_start: 0.7755 (m) cc_final: 0.7073 (p) REVERT: B 710 TYR cc_start: 0.7371 (t80) cc_final: 0.6946 (t80) REVERT: B 730 LYS cc_start: 0.8339 (tttt) cc_final: 0.7855 (ttmm) REVERT: B 731 LYS cc_start: 0.7435 (pttt) cc_final: 0.7230 (ptpp) REVERT: B 847 MET cc_start: 0.5356 (ptp) cc_final: 0.5115 (ptt) REVERT: B 881 LEU cc_start: 0.8125 (mp) cc_final: 0.7631 (mt) REVERT: B 884 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7407 (mt) REVERT: C 30 GLN cc_start: 0.8094 (tt0) cc_final: 0.7830 (mm-40) REVERT: C 31 PHE cc_start: 0.8310 (t80) cc_final: 0.8037 (t80) REVERT: C 74 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7407 (mm-30) REVERT: C 75 ASP cc_start: 0.7876 (m-30) cc_final: 0.7605 (t0) REVERT: C 184 LYS cc_start: 0.7814 (ttmt) cc_final: 0.7396 (mmtt) REVERT: C 222 GLU cc_start: 0.4149 (OUTLIER) cc_final: 0.3824 (pp20) REVERT: C 273 GLN cc_start: 0.6546 (mp10) cc_final: 0.5792 (mp10) REVERT: C 349 SER cc_start: 0.7241 (m) cc_final: 0.6885 (t) REVERT: C 382 LEU cc_start: 0.8395 (mt) cc_final: 0.8148 (mm) REVERT: C 405 ASP cc_start: 0.7506 (m-30) cc_final: 0.7201 (t0) REVERT: C 467 ASN cc_start: 0.6945 (p0) cc_final: 0.6680 (p0) REVERT: C 494 ASP cc_start: 0.6456 (t0) cc_final: 0.6217 (t0) REVERT: C 555 ARG cc_start: 0.7706 (mtm-85) cc_final: 0.7459 (mtm180) REVERT: C 565 ARG cc_start: 0.7357 (ttt180) cc_final: 0.6993 (ttt180) REVERT: C 618 SER cc_start: 0.8253 (t) cc_final: 0.8041 (p) REVERT: C 663 MET cc_start: 0.7637 (mtp) cc_final: 0.7414 (mmm) REVERT: C 701 SER cc_start: 0.7337 (m) cc_final: 0.7081 (p) REVERT: C 730 LYS cc_start: 0.7392 (mtpt) cc_final: 0.7122 (mtpt) REVERT: C 732 VAL cc_start: 0.7941 (t) cc_final: 0.7468 (p) REVERT: C 758 ARG cc_start: 0.8233 (mtp180) cc_final: 0.7978 (mtp85) REVERT: C 877 CYS cc_start: 0.7518 (OUTLIER) cc_final: 0.7282 (t) outliers start: 91 outliers final: 37 residues processed: 835 average time/residue: 0.1503 time to fit residues: 192.4309 Evaluate side-chains 695 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 650 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 736 PHE Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain B residue 884 ILE Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 352 ASN Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 877 CYS Chi-restraints excluded: chain G residue 43 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN A 47 ASN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 ASN A 348 ASN ** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 ASN A 547 ASN A 601 ASN A 662 ASN A 790 GLN ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN B 370 GLN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 ASN B 563 ASN B 582 ASN B 940 HIS ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS C 467 ASN C 548 HIS C 636 ASN C 771 ASN C 808 ASN C 836 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.119173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.105997 restraints weight = 31046.014| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.93 r_work: 0.3184 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22831 Z= 0.145 Angle : 0.563 8.691 31043 Z= 0.298 Chirality : 0.045 0.230 3291 Planarity : 0.005 0.046 4089 Dihedral : 7.090 55.971 3190 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 4.21 % Allowed : 12.99 % Favored : 82.80 % 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: -1.68 (0.16), residues: 2727 helix: 0.53 (0.30), residues: 348 sheet: -0.30 (0.23), residues: 550 loop : -1.82 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 848 TYR 0.025 0.002 TYR B 724 PHE 0.025 0.002 PHE G 4 TRP 0.011 0.001 TRP A 882 HIS 0.006 0.001 HIS C 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (22831) covalent geometry : angle 0.56335 / 0.30 (31043) hydrogen bonds : bond 0.04731 / 3.16 ( 522) hydrogen bonds : angle 6.47232 / 4.43 ( 1440) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5454 Ramachandran restraints generated. 2727 Oldfield, 0 Emsley, 2727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5454 Ramachandran restraints generated. 2727 Oldfield, 0 Emsley, 2727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 686 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7738 (tp30) cc_final: 0.7042 (tp30) REVERT: A 55 ASP cc_start: 0.7321 (t0) cc_final: 0.6826 (t0) REVERT: A 168 LYS cc_start: 0.7780 (mttp) cc_final: 0.7574 (mmtp) REVERT: A 218 SER cc_start: 0.8028 (m) cc_final: 0.7736 (p) REVERT: A 318 ASN cc_start: 0.7266 (OUTLIER) cc_final: 0.7040 (p0) REVERT: A 320 LYS cc_start: 0.7893 (tttt) cc_final: 0.7670 (tttt) REVERT: A 325 GLN cc_start: 0.8289 (pt0) cc_final: 0.7694 (mt0) REVERT: A 631 PHE cc_start: 0.8318 (t80) cc_final: 0.8101 (t80) REVERT: A 718 TYR cc_start: 0.7732 (t80) cc_final: 0.7379 (t80) REVERT: A 730 LYS cc_start: 0.7639 (mtmm) cc_final: 0.7372 (mttp) REVERT: A 751 PRO cc_start: 0.6685 (Cg_endo) cc_final: 0.6249 (Cg_exo) REVERT: A 799 LYS cc_start: 0.8213 (ttmm) cc_final: 0.7798 (mttm) REVERT: A 802 MET cc_start: 0.7780 (ttm) cc_final: 0.7553 (ttm) REVERT: A 823 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7938 (mmtt) REVERT: A 825 TYR cc_start: 0.8022 (t80) cc_final: 0.7676 (t80) REVERT: A 865 THR cc_start: 0.8118 (p) cc_final: 0.7853 (t) REVERT: A 870 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8120 (pt) REVERT: B 13 MET cc_start: 0.7419 (mpp) cc_final: 0.7182 (mmm) REVERT: B 58 THR cc_start: 0.8296 (t) cc_final: 0.7942 (m) REVERT: B 258 VAL cc_start: 0.7658 (t) cc_final: 0.7232 (m) REVERT: B 422 CYS cc_start: 0.7835 (p) cc_final: 0.7570 (p) REVERT: B 525 VAL cc_start: 0.7257 (OUTLIER) cc_final: 0.7027 (p) REVERT: B 527 CYS cc_start: 0.7639 (t) cc_final: 0.7329 (m) REVERT: B 606 SER cc_start: 0.8387 (m) cc_final: 0.7988 (p) REVERT: B 642 GLU cc_start: 0.7418 (tt0) cc_final: 0.7132 (tt0) REVERT: B 651 ASP cc_start: 0.6726 (m-30) cc_final: 0.6477 (m-30) REVERT: B 702 LEU cc_start: 0.8471 (tp) cc_final: 0.8199 (tp) REVERT: B 724 TYR cc_start: 0.7657 (p90) cc_final: 0.7448 (p90) REVERT: B 730 LYS cc_start: 0.8216 (tttt) cc_final: 0.7805 (ttmm) REVERT: B 731 LYS cc_start: 0.7990 (pttt) cc_final: 0.7763 (ptpp) REVERT: B 796 GLU cc_start: 0.7901 (mp0) cc_final: 0.7380 (mp0) REVERT: B 810 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7756 (mt0) REVERT: B 847 MET cc_start: 0.7369 (ptp) cc_final: 0.7126 (ptp) REVERT: C 31 PHE cc_start: 0.8406 (t80) cc_final: 0.8141 (t80) REVERT: C 50 VAL cc_start: 0.8647 (OUTLIER) cc_final: 0.8445 (m) REVERT: C 72 ASP cc_start: 0.7657 (t0) cc_final: 0.7420 (t0) REVERT: C 74 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7149 (mm-30) REVERT: C 75 ASP cc_start: 0.8029 (m-30) cc_final: 0.7744 (t0) REVERT: C 184 LYS cc_start: 0.8471 (ttmt) cc_final: 0.8190 (mmtt) REVERT: C 222 GLU cc_start: 0.4686 (OUTLIER) cc_final: 0.4037 (pp20) REVERT: C 273 GLN cc_start: 0.7329 (mp10) cc_final: 0.6016 (mp10) REVERT: C 276 SER cc_start: 0.8212 (t) cc_final: 0.7718 (p) REVERT: C 302 GLU cc_start: 0.7305 (pt0) cc_final: 0.6964 (pt0) REVERT: C 349 SER cc_start: 0.7954 (m) cc_final: 0.7717 (t) REVERT: C 396 ASN cc_start: 0.8374 (t0) cc_final: 0.8154 (t0) REVERT: C 494 ASP cc_start: 0.7001 (t0) cc_final: 0.6723 (t0) REVERT: C 495 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8050 (ptmm) REVERT: C 618 SER cc_start: 0.8158 (t) cc_final: 0.7892 (p) REVERT: C 653 SER cc_start: 0.8827 (m) cc_final: 0.8479 (p) REVERT: C 662 ASN cc_start: 0.8146 (m-40) cc_final: 0.7867 (m110) REVERT: C 701 SER cc_start: 0.8115 (m) cc_final: 0.7754 (p) REVERT: C 732 VAL cc_start: 0.8081 (t) cc_final: 0.7721 (p) REVERT: C 812 MET cc_start: 0.7874 (mtm) cc_final: 0.7655 (mtt) REVERT: C 821 LYS cc_start: 0.8329 (mttt) cc_final: 0.8049 (mttt) REVERT: C 836 ASN cc_start: 0.8126 (m-40) cc_final: 0.7908 (m110) REVERT: C 849 GLU cc_start: 0.7771 (pt0) cc_final: 0.7500 (pt0) REVERT: C 873 LYS cc_start: 0.8377 (mttt) cc_final: 0.8136 (mttm) REVERT: C 877 CYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7374 (t) REVERT: G 5 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7333 (mt) outliers start: 101 outliers final: 67 residues processed: 741 average time/residue: 0.1361 time to fit residues: 154.9954 Evaluate side-chains 716 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 640 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 548 HIS Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain B residue 810 GLN Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 913 ASP Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 495 LYS Chi-restraints excluded: chain C residue 513 ASP Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 771 ASN Chi-restraints excluded: chain C residue 824 ASP Chi-restraints excluded: chain C residue 830 ILE Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 877 CYS Chi-restraints excluded: chain C residue 892 SER Chi-restraints excluded: chain C residue 914 MET Chi-restraints excluded: chain C residue 923 GLU Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 8 MET Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 43 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 36 optimal weight: 1.9990 chunk 201 optimal weight: 6.9990 chunk 202 optimal weight: 4.9990 chunk 273 optimal weight: 5.9990 chunk 248 optimal weight: 0.4980 chunk 68 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 216 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 ASN A 122 ASN A 318 ASN A 348 ASN A 359 GLN A 379 GLN A 516 ASN A 940 HIS ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN B 412 HIS B 499 ASN B 502 ASN B 510 ASN B 563 ASN B 902 ASN B 940 HIS ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS C 548 HIS ** C 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 940 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.119222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.105953 restraints weight = 31214.402| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.94 r_work: 0.3184 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22831 Z= 0.137 Angle : 0.541 7.552 31043 Z= 0.287 Chirality : 0.044 0.241 3291 Planarity : 0.005 0.044 4089 Dihedral : 6.818 57.514 3164 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.83 % Allowed : 13.79 % Favored : 81.38 % 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: -1.59 (0.16), residues: 2727 helix: 0.58 (0.30), residues: 348 sheet: -0.19 (0.22), residues: 566 loop : -1.79 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 646 TYR 0.018 0.002 TYR A 23 PHE 0.029 0.002 PHE B 875 TRP 0.021 0.001 TRP B 135 HIS 0.008 0.001 HIS C 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (22831) covalent geometry : angle 0.54139 / 0.29 (31043) hydrogen bonds : bond 0.04088 / 2.73 ( 522) hydrogen bonds : angle 5.97298 / 4.09 ( 1440) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5454 Ramachandran restraints generated. 2727 Oldfield, 0 Emsley, 2727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5454 Ramachandran restraints generated. 2727 Oldfield, 0 Emsley, 2727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 662 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7777 (tp30) cc_final: 0.7072 (tp30) REVERT: A 55 ASP cc_start: 0.7289 (t0) cc_final: 0.6749 (t0) REVERT: A 320 LYS cc_start: 0.7894 (tttt) cc_final: 0.7682 (tttt) REVERT: A 325 GLN cc_start: 0.8290 (pt0) cc_final: 0.7781 (mt0) REVERT: A 631 PHE cc_start: 0.8317 (t80) cc_final: 0.8087 (t80) REVERT: A 718 TYR cc_start: 0.7716 (t80) cc_final: 0.7385 (t80) REVERT: A 730 LYS cc_start: 0.7655 (mtmm) cc_final: 0.7410 (mttp) REVERT: A 751 PRO cc_start: 0.6664 (Cg_endo) cc_final: 0.6252 (Cg_exo) REVERT: A 799 LYS cc_start: 0.8228 (ttmm) cc_final: 0.7851 (mttm) REVERT: A 802 MET cc_start: 0.7835 (ttm) cc_final: 0.7620 (ttm) REVERT: A 823 LYS cc_start: 0.8165 (mmtt) cc_final: 0.7929 (mmtt) REVERT: A 825 TYR cc_start: 0.8013 (t80) cc_final: 0.7749 (t80) REVERT: A 865 THR cc_start: 0.8102 (p) cc_final: 0.7836 (t) REVERT: A 870 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8089 (pt) REVERT: B 58 THR cc_start: 0.8286 (t) cc_final: 0.7967 (m) REVERT: B 258 VAL cc_start: 0.7611 (t) cc_final: 0.7212 (m) REVERT: B 525 VAL cc_start: 0.7180 (OUTLIER) cc_final: 0.6964 (p) REVERT: B 527 CYS cc_start: 0.7637 (t) cc_final: 0.7352 (m) REVERT: B 606 SER cc_start: 0.8381 (m) cc_final: 0.7993 (p) REVERT: B 642 GLU cc_start: 0.7476 (tt0) cc_final: 0.7270 (tt0) REVERT: B 651 ASP cc_start: 0.6780 (m-30) cc_final: 0.6465 (m-30) REVERT: B 674 VAL cc_start: 0.8371 (t) cc_final: 0.8078 (m) REVERT: B 702 LEU cc_start: 0.8475 (tp) cc_final: 0.8253 (tp) REVERT: B 730 LYS cc_start: 0.8205 (tttt) cc_final: 0.7775 (ttmm) REVERT: B 731 LYS cc_start: 0.7980 (pttt) cc_final: 0.7748 (ptpp) REVERT: B 796 GLU cc_start: 0.7895 (mp0) cc_final: 0.7520 (mp0) REVERT: B 810 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7770 (mt0) REVERT: B 814 ARG cc_start: 0.7996 (ptt180) cc_final: 0.7297 (ttp-170) REVERT: B 825 TYR cc_start: 0.8363 (t80) cc_final: 0.7917 (t80) REVERT: B 847 MET cc_start: 0.7331 (ptp) cc_final: 0.7097 (ptp) REVERT: C 31 PHE cc_start: 0.8380 (t80) cc_final: 0.8105 (t80) REVERT: C 49 THR cc_start: 0.8093 (t) cc_final: 0.7765 (p) REVERT: C 50 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8371 (m) REVERT: C 72 ASP cc_start: 0.7666 (t0) cc_final: 0.7450 (t0) REVERT: C 74 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7250 (mm-30) REVERT: C 75 ASP cc_start: 0.8037 (m-30) cc_final: 0.7773 (t0) REVERT: C 80 TYR cc_start: 0.8254 (p90) cc_final: 0.7990 (p90) REVERT: C 95 ASP cc_start: 0.7284 (t0) cc_final: 0.6971 (t0) REVERT: C 184 LYS cc_start: 0.8434 (ttmt) cc_final: 0.8202 (mmtt) REVERT: C 222 GLU cc_start: 0.4645 (OUTLIER) cc_final: 0.3996 (pp20) REVERT: C 273 GLN cc_start: 0.7355 (mp10) cc_final: 0.5978 (mp10) REVERT: C 276 SER cc_start: 0.8205 (t) cc_final: 0.7727 (p) REVERT: C 302 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6851 (pt0) REVERT: C 349 SER cc_start: 0.8018 (m) cc_final: 0.7801 (t) REVERT: C 380 LEU cc_start: 0.7347 (mt) cc_final: 0.7078 (mt) REVERT: C 396 ASN cc_start: 0.8329 (t0) cc_final: 0.8087 (t0) REVERT: C 486 SER cc_start: 0.8566 (t) cc_final: 0.8333 (m) REVERT: C 494 ASP cc_start: 0.7094 (t0) cc_final: 0.6786 (t0) REVERT: C 495 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8026 (ptmm) REVERT: C 520 VAL cc_start: 0.8106 (OUTLIER) cc_final: 0.7823 (t) REVERT: C 618 SER cc_start: 0.8086 (t) cc_final: 0.7807 (p) REVERT: C 653 SER cc_start: 0.8810 (m) cc_final: 0.8452 (p) REVERT: C 664 LEU cc_start: 0.8590 (mp) cc_final: 0.8258 (mt) REVERT: C 678 ILE cc_start: 0.8463 (mm) cc_final: 0.8245 (mm) REVERT: C 701 SER cc_start: 0.8109 (m) cc_final: 0.7741 (p) REVERT: C 812 MET cc_start: 0.7905 (mtm) cc_final: 0.7697 (mtt) REVERT: C 821 LYS cc_start: 0.8309 (mttt) cc_final: 0.7995 (mttt) REVERT: C 836 ASN cc_start: 0.8006 (m-40) cc_final: 0.7782 (m110) REVERT: C 849 GLU cc_start: 0.7780 (pt0) cc_final: 0.7549 (pt0) REVERT: C 873 LYS cc_start: 0.8320 (mttt) cc_final: 0.8065 (mttm) REVERT: C 877 CYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7396 (t) outliers start: 116 outliers final: 79 residues processed: 729 average time/residue: 0.1411 time to fit residues: 159.1050 Evaluate side-chains 720 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 632 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 873 LYS Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 548 HIS Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 663 MET Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain B residue 810 GLN Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 913 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 495 LYS Chi-restraints excluded: chain C residue 513 ASP Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 667 ILE Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 804 SER Chi-restraints excluded: chain C residue 830 ILE Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 877 CYS Chi-restraints excluded: chain C residue 888 SER Chi-restraints excluded: chain C residue 892 SER Chi-restraints excluded: chain C residue 914 MET Chi-restraints excluded: chain C residue 923 GLU Chi-restraints excluded: chain G residue 8 MET Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 43 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 168 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 199 optimal weight: 1.9990 chunk 251 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 112 optimal weight: 0.5980 chunk 213 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN A 516 ASN B 370 GLN B 499 ASN B 510 ASN B 563 ASN B 647 ASN ** B 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 902 ASN C 269 GLN C 326 GLN C 548 HIS ** C 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 ASN C 940 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.118580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.105249 restraints weight = 31107.835| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.95 r_work: 0.3197 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22831 Z= 0.149 Angle : 0.548 8.554 31043 Z= 0.288 Chirality : 0.045 0.222 3291 Planarity : 0.004 0.048 4089 Dihedral : 6.665 59.203 3160 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 4.96 % Allowed : 14.24 % Favored : 80.80 % 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: -1.56 (0.16), residues: 2727 helix: 0.53 (0.30), residues: 348 sheet: -0.21 (0.22), residues: 587 loop : -1.76 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 848 TYR 0.028 0.002 TYR B 724 PHE 0.030 0.002 PHE B 875 TRP 0.022 0.002 TRP B 135 HIS 0.009 0.001 HIS C 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (22831) covalent geometry : angle 0.54829 / 0.29 (31043) hydrogen bonds : bond 0.04006 / 2.65 ( 522) hydrogen bonds : angle 5.76703 / 3.96 ( 1440) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5454 Ramachandran restraints generated. 2727 Oldfield, 0 Emsley, 2727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5454 Ramachandran restraints generated. 2727 Oldfield, 0 Emsley, 2727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 644 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7787 (tp30) cc_final: 0.7090 (tp30) REVERT: A 55 ASP cc_start: 0.7400 (t0) cc_final: 0.6875 (t0) REVERT: A 240 LYS cc_start: 0.8329 (mmtt) cc_final: 0.8112 (mmmm) REVERT: A 320 LYS cc_start: 0.7877 (tttt) cc_final: 0.7668 (tttt) REVERT: A 325 GLN cc_start: 0.8270 (pt0) cc_final: 0.7762 (mt0) REVERT: A 631 PHE cc_start: 0.8301 (t80) cc_final: 0.8057 (t80) REVERT: A 676 ILE cc_start: 0.7977 (mt) cc_final: 0.7714 (mp) REVERT: A 718 TYR cc_start: 0.7751 (t80) cc_final: 0.7303 (t80) REVERT: A 719 LEU cc_start: 0.7520 (mt) cc_final: 0.7256 (mp) REVERT: A 751 PRO cc_start: 0.6639 (Cg_endo) cc_final: 0.6254 (Cg_exo) REVERT: A 799 LYS cc_start: 0.8210 (ttmm) cc_final: 0.7836 (mttm) REVERT: A 823 LYS cc_start: 0.8171 (mmtt) cc_final: 0.7936 (mmtt) REVERT: A 825 TYR cc_start: 0.8023 (t80) cc_final: 0.7773 (t80) REVERT: A 865 THR cc_start: 0.8124 (p) cc_final: 0.7855 (t) REVERT: A 870 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8122 (pt) REVERT: B 13 MET cc_start: 0.7389 (mmm) cc_final: 0.7102 (mmm) REVERT: B 58 THR cc_start: 0.8288 (t) cc_final: 0.7969 (m) REVERT: B 96 MET cc_start: 0.6981 (mmp) cc_final: 0.6771 (mmm) REVERT: B 98 SER cc_start: 0.8063 (p) cc_final: 0.7856 (t) REVERT: B 176 PRO cc_start: 0.8294 (Cg_endo) cc_final: 0.7966 (Cg_exo) REVERT: B 259 MET cc_start: 0.7290 (mmm) cc_final: 0.6488 (mmm) REVERT: B 525 VAL cc_start: 0.7187 (OUTLIER) cc_final: 0.6965 (p) REVERT: B 527 CYS cc_start: 0.7692 (t) cc_final: 0.7397 (m) REVERT: B 606 SER cc_start: 0.8379 (m) cc_final: 0.7971 (p) REVERT: B 674 VAL cc_start: 0.8388 (t) cc_final: 0.8125 (m) REVERT: B 730 LYS cc_start: 0.8232 (tttt) cc_final: 0.7831 (ttmm) REVERT: B 731 LYS cc_start: 0.7920 (pttt) cc_final: 0.7694 (ptpp) REVERT: B 796 GLU cc_start: 0.7887 (mp0) cc_final: 0.7352 (mp0) REVERT: B 810 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7775 (mt0) REVERT: B 814 ARG cc_start: 0.8008 (ptt180) cc_final: 0.7296 (ttp-170) REVERT: B 825 TYR cc_start: 0.8372 (t80) cc_final: 0.7891 (t80) REVERT: B 847 MET cc_start: 0.7326 (ptp) cc_final: 0.7097 (ptp) REVERT: B 889 ASN cc_start: 0.8072 (p0) cc_final: 0.7835 (p0) REVERT: C 31 PHE cc_start: 0.8409 (t80) cc_final: 0.8152 (t80) REVERT: C 50 VAL cc_start: 0.8675 (OUTLIER) cc_final: 0.8465 (m) REVERT: C 74 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7305 (mm-30) REVERT: C 75 ASP cc_start: 0.8024 (m-30) cc_final: 0.7790 (t0) REVERT: C 184 LYS cc_start: 0.8469 (ttmt) cc_final: 0.8202 (mmtt) REVERT: C 273 GLN cc_start: 0.7404 (mp10) cc_final: 0.6053 (mp10) REVERT: C 276 SER cc_start: 0.8253 (t) cc_final: 0.7814 (p) REVERT: C 302 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6875 (pt0) REVERT: C 317 LYS cc_start: 0.8152 (mttt) cc_final: 0.7844 (mttt) REVERT: C 369 LEU cc_start: 0.8383 (mt) cc_final: 0.8164 (mt) REVERT: C 396 ASN cc_start: 0.8320 (t0) cc_final: 0.8062 (t0) REVERT: C 486 SER cc_start: 0.8568 (t) cc_final: 0.8318 (m) REVERT: C 494 ASP cc_start: 0.7154 (t0) cc_final: 0.6858 (t0) REVERT: C 495 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8020 (ptmm) REVERT: C 520 VAL cc_start: 0.8105 (OUTLIER) cc_final: 0.7803 (t) REVERT: C 618 SER cc_start: 0.8108 (t) cc_final: 0.7829 (p) REVERT: C 653 SER cc_start: 0.8840 (m) cc_final: 0.8439 (p) REVERT: C 664 LEU cc_start: 0.8590 (mp) cc_final: 0.8302 (mt) REVERT: C 678 ILE cc_start: 0.8508 (mm) cc_final: 0.8264 (mm) REVERT: C 701 SER cc_start: 0.8109 (m) cc_final: 0.7742 (p) REVERT: C 731 LYS cc_start: 0.8493 (ptpt) cc_final: 0.8273 (ptpt) REVERT: C 732 VAL cc_start: 0.8010 (t) cc_final: 0.7739 (p) REVERT: C 821 LYS cc_start: 0.8346 (mttt) cc_final: 0.8008 (mttt) REVERT: C 873 LYS cc_start: 0.8278 (mttt) cc_final: 0.8028 (mttm) REVERT: C 947 ILE cc_start: 0.7903 (mt) cc_final: 0.7679 (mt) outliers start: 119 outliers final: 94 residues processed: 702 average time/residue: 0.1531 time to fit residues: 165.2300 Evaluate side-chains 725 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 624 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 707 ASP Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 819 ASP Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 873 LYS Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain B residue 662 ASN Chi-restraints excluded: chain B residue 663 MET Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain B residue 810 GLN Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 913 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 352 ASN Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 495 LYS Chi-restraints excluded: chain C residue 513 ASP Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 667 ILE Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 804 SER Chi-restraints excluded: chain C residue 824 ASP Chi-restraints excluded: chain C residue 830 ILE Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 888 SER Chi-restraints excluded: chain C residue 892 SER Chi-restraints excluded: chain C residue 914 MET Chi-restraints excluded: chain C residue 923 GLU Chi-restraints excluded: chain G residue 8 MET Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 43 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 268 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 264 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 221 optimal weight: 8.9990 chunk 249 optimal weight: 0.8980 chunk 257 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 182 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN A 516 ASN B 370 GLN B 499 ASN B 510 ASN B 563 ASN B 769 GLN ** B 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 HIS ** C 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 940 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.113811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.100293 restraints weight = 31362.144| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.91 r_work: 0.3120 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.084 22831 Z= 0.380 Angle : 0.721 9.733 31043 Z= 0.386 Chirality : 0.053 0.298 3291 Planarity : 0.006 0.057 4089 Dihedral : 7.366 59.975 3156 Min Nonbonded Distance : 1.570 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.90 % Favored : 90.06 % Rotamer: Outliers : 5.37 % Allowed : 14.70 % Favored : 79.93 % 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: -2.01 (0.15), residues: 2727 helix: -0.18 (0.28), residues: 355 sheet: -0.40 (0.22), residues: 559 loop : -2.01 (0.13), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 848 TYR 0.036 0.003 TYR B 724 PHE 0.035 0.003 PHE B 875 TRP 0.024 0.003 TRP B 135 HIS 0.014 0.002 HIS C 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00893 / 0.38 (22831) covalent geometry : angle 0.72148 / 0.39 (31043) hydrogen bonds : bond 0.05971 / 3.92 ( 522) hydrogen bonds : angle 6.21794 / 4.28 ( 1440) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5454 Ramachandran restraints generated. 2727 Oldfield, 0 Emsley, 2727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5454 Ramachandran restraints generated. 2727 Oldfield, 0 Emsley, 2727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 675 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7753 (tp30) cc_final: 0.7113 (tp30) REVERT: A 55 ASP cc_start: 0.7603 (t0) cc_final: 0.7067 (t0) REVERT: A 240 LYS cc_start: 0.8366 (mmtt) cc_final: 0.8136 (mmmm) REVERT: A 388 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8190 (tpt-90) REVERT: A 645 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7791 (mm) REVERT: A 676 ILE cc_start: 0.7947 (mt) cc_final: 0.7582 (mp) REVERT: A 677 SER cc_start: 0.7827 (t) cc_final: 0.7524 (m) REVERT: A 707 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7566 (p0) REVERT: A 718 TYR cc_start: 0.7839 (t80) cc_final: 0.7276 (t80) REVERT: A 748 LEU cc_start: 0.7920 (mt) cc_final: 0.7680 (mt) REVERT: A 751 PRO cc_start: 0.6729 (Cg_endo) cc_final: 0.6283 (Cg_exo) REVERT: A 798 TYR cc_start: 0.7942 (p90) cc_final: 0.7683 (p90) REVERT: A 799 LYS cc_start: 0.8169 (ttmm) cc_final: 0.7729 (mttm) REVERT: A 823 LYS cc_start: 0.8211 (mmtt) cc_final: 0.7924 (mmtt) REVERT: A 825 TYR cc_start: 0.8122 (t80) cc_final: 0.7848 (t80) REVERT: A 870 ILE cc_start: 0.8506 (tt) cc_final: 0.8140 (pt) REVERT: B 58 THR cc_start: 0.8274 (t) cc_final: 0.7972 (m) REVERT: B 259 MET cc_start: 0.7400 (mmm) cc_final: 0.6566 (mmm) REVERT: B 525 VAL cc_start: 0.7315 (OUTLIER) cc_final: 0.7091 (p) REVERT: B 527 CYS cc_start: 0.7836 (t) cc_final: 0.7600 (m) REVERT: B 559 MET cc_start: 0.7348 (mmt) cc_final: 0.7027 (mmt) REVERT: B 606 SER cc_start: 0.8305 (m) cc_final: 0.7854 (p) REVERT: B 702 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8205 (mp) REVERT: B 730 LYS cc_start: 0.8362 (tttt) cc_final: 0.7945 (ttmm) REVERT: B 731 LYS cc_start: 0.8102 (pttt) cc_final: 0.7860 (ptpp) REVERT: B 746 ASP cc_start: 0.7697 (t0) cc_final: 0.7461 (t0) REVERT: B 796 GLU cc_start: 0.7889 (mp0) cc_final: 0.7507 (mp0) REVERT: B 810 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7758 (mt0) REVERT: B 847 MET cc_start: 0.7256 (ptp) cc_final: 0.7033 (ptp) REVERT: B 889 ASN cc_start: 0.8089 (p0) cc_final: 0.7810 (p0) REVERT: C 31 PHE cc_start: 0.8505 (t80) cc_final: 0.8228 (t80) REVERT: C 50 VAL cc_start: 0.8797 (OUTLIER) cc_final: 0.8556 (m) REVERT: C 63 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7505 (mtp-110) REVERT: C 74 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7527 (mm-30) REVERT: C 184 LYS cc_start: 0.8545 (ttmt) cc_final: 0.8164 (mtmm) REVERT: C 235 LYS cc_start: 0.8281 (pttt) cc_final: 0.7986 (ptpp) REVERT: C 273 GLN cc_start: 0.7405 (mp10) cc_final: 0.6026 (mp10) REVERT: C 276 SER cc_start: 0.8331 (t) cc_final: 0.7874 (p) REVERT: C 302 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7093 (pt0) REVERT: C 317 LYS cc_start: 0.8200 (mttt) cc_final: 0.7918 (mttt) REVERT: C 494 ASP cc_start: 0.7261 (t0) cc_final: 0.6962 (t0) REVERT: C 495 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8104 (ptmm) REVERT: C 618 SER cc_start: 0.8200 (t) cc_final: 0.7908 (p) REVERT: C 651 ASP cc_start: 0.7482 (m-30) cc_final: 0.7241 (m-30) REVERT: C 664 LEU cc_start: 0.8650 (mp) cc_final: 0.8314 (mt) REVERT: C 701 SER cc_start: 0.8055 (m) cc_final: 0.7831 (p) REVERT: C 758 ARG cc_start: 0.8403 (mtp85) cc_final: 0.8009 (mtp85) REVERT: C 761 ASP cc_start: 0.6694 (OUTLIER) cc_final: 0.6384 (t70) REVERT: C 821 LYS cc_start: 0.8341 (mttt) cc_final: 0.8104 (mttt) REVERT: C 873 LYS cc_start: 0.8267 (mttt) cc_final: 0.8026 (mttm) REVERT: C 930 LEU cc_start: 0.8279 (mm) cc_final: 0.7942 (mt) REVERT: C 944 ARG cc_start: 0.7295 (ttt90) cc_final: 0.6801 (ttt90) REVERT: C 947 ILE cc_start: 0.7754 (mt) cc_final: 0.7540 (mt) outliers start: 129 outliers final: 93 residues processed: 736 average time/residue: 0.1533 time to fit residues: 174.2924 Evaluate side-chains 747 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 643 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 707 ASP Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 819 ASP Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 873 LYS Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain B residue 810 GLN Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 913 ASP Chi-restraints excluded: chain B residue 949 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 352 ASN Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 461 ASN Chi-restraints excluded: chain C residue 495 LYS Chi-restraints excluded: chain C residue 513 ASP Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 667 ILE Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 761 ASP Chi-restraints excluded: chain C residue 804 SER Chi-restraints excluded: chain C residue 824 ASP Chi-restraints excluded: chain C residue 830 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 888 SER Chi-restraints excluded: chain C residue 892 SER Chi-restraints excluded: chain C residue 914 MET Chi-restraints excluded: chain C residue 923 GLU Chi-restraints excluded: chain G residue 8 MET Chi-restraints excluded: chain G residue 43 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 97 optimal weight: 0.3980 chunk 25 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 274 optimal weight: 9.9990 chunk 110 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 160 optimal weight: 0.0870 chunk 104 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 120 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN A 516 ASN B 370 GLN B 499 ASN B 510 ASN B 563 ASN B 836 ASN B 902 ASN B 940 HIS C 138 ASN C 548 HIS C 771 ASN C 940 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.120085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.106836 restraints weight = 30954.583| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.94 r_work: 0.3198 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 22831 Z= 0.099 Angle : 0.533 9.224 31043 Z= 0.280 Chirality : 0.044 0.203 3291 Planarity : 0.005 0.058 4089 Dihedral : 6.433 54.416 3152 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.92 % Allowed : 17.53 % Favored : 78.55 % 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: -1.61 (0.16), residues: 2727 helix: 0.41 (0.29), residues: 349 sheet: -0.26 (0.22), residues: 577 loop : -1.75 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 848 TYR 0.028 0.001 TYR B 724 PHE 0.032 0.001 PHE C 113 TRP 0.025 0.001 TRP B 135 HIS 0.009 0.001 HIS C 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (22831) covalent geometry : angle 0.53276 / 0.28 (31043) hydrogen bonds : bond 0.03223 / 2.15 ( 522) hydrogen bonds : angle 5.60077 / 3.85 ( 1440) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5454 Ramachandran restraints generated. 2727 Oldfield, 0 Emsley, 2727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5454 Ramachandran restraints generated. 2727 Oldfield, 0 Emsley, 2727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 631 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7728 (tp30) cc_final: 0.7102 (tp30) REVERT: A 55 ASP cc_start: 0.7520 (t0) cc_final: 0.7024 (t0) REVERT: A 134 GLU cc_start: 0.7712 (pt0) cc_final: 0.7438 (mt-10) REVERT: A 240 LYS cc_start: 0.8364 (mmtt) cc_final: 0.8111 (mmmm) REVERT: A 323 LEU cc_start: 0.8369 (mt) cc_final: 0.8042 (mm) REVERT: A 325 GLN cc_start: 0.8255 (pt0) cc_final: 0.7755 (mt0) REVERT: A 328 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7358 (ttp) REVERT: A 388 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8330 (tpt90) REVERT: A 676 ILE cc_start: 0.7936 (mt) cc_final: 0.7611 (mp) REVERT: A 677 SER cc_start: 0.7866 (t) cc_final: 0.7536 (m) REVERT: A 718 TYR cc_start: 0.7699 (t80) cc_final: 0.7311 (t80) REVERT: A 719 LEU cc_start: 0.7501 (mt) cc_final: 0.7169 (mp) REVERT: A 748 LEU cc_start: 0.7708 (mt) cc_final: 0.7478 (mt) REVERT: A 751 PRO cc_start: 0.6735 (Cg_endo) cc_final: 0.6282 (Cg_exo) REVERT: A 799 LYS cc_start: 0.8186 (ttmm) cc_final: 0.7823 (mttm) REVERT: A 825 TYR cc_start: 0.8010 (t80) cc_final: 0.7751 (t80) REVERT: A 870 ILE cc_start: 0.8441 (tt) cc_final: 0.8089 (pt) REVERT: B 13 MET cc_start: 0.7391 (mmm) cc_final: 0.6892 (mmm) REVERT: B 58 THR cc_start: 0.8378 (t) cc_final: 0.8035 (m) REVERT: B 176 PRO cc_start: 0.8234 (Cg_endo) cc_final: 0.7867 (Cg_exo) REVERT: B 259 MET cc_start: 0.7296 (mmm) cc_final: 0.6438 (mmm) REVERT: B 321 VAL cc_start: 0.8801 (t) cc_final: 0.8598 (p) REVERT: B 417 GLU cc_start: 0.7387 (mp0) cc_final: 0.7134 (mp0) REVERT: B 525 VAL cc_start: 0.7208 (OUTLIER) cc_final: 0.6980 (p) REVERT: B 527 CYS cc_start: 0.7628 (t) cc_final: 0.7307 (m) REVERT: B 559 MET cc_start: 0.7181 (mmt) cc_final: 0.6934 (mmt) REVERT: B 606 SER cc_start: 0.8342 (m) cc_final: 0.7962 (p) REVERT: B 674 VAL cc_start: 0.8354 (t) cc_final: 0.8078 (m) REVERT: B 730 LYS cc_start: 0.8188 (tttt) cc_final: 0.7801 (ttmm) REVERT: B 731 LYS cc_start: 0.7936 (pttt) cc_final: 0.7708 (ptpp) REVERT: B 786 ASN cc_start: 0.7948 (m-40) cc_final: 0.7688 (t0) REVERT: B 810 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7715 (mt0) REVERT: B 836 ASN cc_start: 0.7967 (OUTLIER) cc_final: 0.7721 (m-40) REVERT: B 847 MET cc_start: 0.7350 (ptp) cc_final: 0.7131 (ptp) REVERT: B 889 ASN cc_start: 0.8047 (p0) cc_final: 0.7845 (p0) REVERT: C 31 PHE cc_start: 0.8443 (t80) cc_final: 0.8158 (t80) REVERT: C 74 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7281 (mm-30) REVERT: C 75 ASP cc_start: 0.8037 (m-30) cc_final: 0.7759 (t0) REVERT: C 184 LYS cc_start: 0.8449 (ttmt) cc_final: 0.8098 (mmtt) REVERT: C 185 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7441 (mp0) REVERT: C 273 GLN cc_start: 0.7364 (mp10) cc_final: 0.6033 (mp10) REVERT: C 276 SER cc_start: 0.8271 (t) cc_final: 0.7841 (p) REVERT: C 317 LYS cc_start: 0.8128 (mttt) cc_final: 0.7820 (mttt) REVERT: C 396 ASN cc_start: 0.8308 (t0) cc_final: 0.8102 (t0) REVERT: C 486 SER cc_start: 0.8554 (t) cc_final: 0.8345 (m) REVERT: C 494 ASP cc_start: 0.7221 (t0) cc_final: 0.6891 (t0) REVERT: C 495 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8051 (ptmm) REVERT: C 618 SER cc_start: 0.7995 (t) cc_final: 0.7701 (p) REVERT: C 664 LEU cc_start: 0.8559 (mp) cc_final: 0.8281 (mt) REVERT: C 678 ILE cc_start: 0.8498 (mm) cc_final: 0.8241 (mm) REVERT: C 701 SER cc_start: 0.8113 (m) cc_final: 0.7720 (p) REVERT: C 731 LYS cc_start: 0.8500 (ptpt) cc_final: 0.8292 (ptpt) REVERT: C 758 ARG cc_start: 0.8406 (mtp85) cc_final: 0.7799 (mtp85) REVERT: C 761 ASP cc_start: 0.6820 (OUTLIER) cc_final: 0.6458 (t70) REVERT: C 821 LYS cc_start: 0.8402 (mttt) cc_final: 0.8057 (mttt) REVERT: C 848 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8009 (ppt-90) REVERT: C 873 LYS cc_start: 0.8187 (mttt) cc_final: 0.7939 (mttm) REVERT: C 930 LEU cc_start: 0.8318 (mm) cc_final: 0.8058 (mt) REVERT: C 944 ARG cc_start: 0.7225 (ttt90) cc_final: 0.6689 (ttt90) REVERT: C 947 ILE cc_start: 0.7773 (mt) cc_final: 0.7518 (tp) outliers start: 94 outliers final: 70 residues processed: 677 average time/residue: 0.1494 time to fit residues: 155.0212 Evaluate side-chains 687 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 609 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 707 ASP Chi-restraints excluded: chain A residue 715 SER Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 873 LYS Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain B residue 810 GLN Chi-restraints excluded: chain B residue 836 ASN Chi-restraints excluded: chain B residue 913 ASP Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 352 ASN Chi-restraints excluded: chain C residue 476 ASN Chi-restraints excluded: chain C residue 495 LYS Chi-restraints excluded: chain C residue 513 ASP Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 667 ILE Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 761 ASP Chi-restraints excluded: chain C residue 771 ASN Chi-restraints excluded: chain C residue 804 SER Chi-restraints excluded: chain C residue 830 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 888 SER Chi-restraints excluded: chain C residue 892 SER Chi-restraints excluded: chain C residue 923 GLU Chi-restraints excluded: chain C residue 929 VAL Chi-restraints excluded: chain G residue 8 MET Chi-restraints excluded: chain G residue 43 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 86 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 247 optimal weight: 0.0870 chunk 83 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 176 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 overall best weight: 2.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN A 516 ASN B 370 GLN B 510 ASN B 563 ASN ** B 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C 548 HIS ** C 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 940 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.117205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.103970 restraints weight = 31113.385| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.93 r_work: 0.3152 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 22831 Z= 0.223 Angle : 0.606 8.864 31043 Z= 0.321 Chirality : 0.047 0.228 3291 Planarity : 0.005 0.064 4089 Dihedral : 6.768 58.126 3152 Min Nonbonded Distance : 1.654 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 4.46 % Allowed : 17.49 % Favored : 78.05 % 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: -1.71 (0.16), residues: 2727 helix: 0.29 (0.29), residues: 348 sheet: -0.29 (0.22), residues: 567 loop : -1.82 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 848 TYR 0.033 0.002 TYR B 724 PHE 0.033 0.002 PHE B 875 TRP 0.027 0.002 TRP B 135 HIS 0.011 0.001 HIS C 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.22 (22831) covalent geometry : angle 0.60635 / 0.32 (31043) hydrogen bonds : bond 0.04590 / 3.02 ( 522) hydrogen bonds : angle 5.76897 / 3.97 ( 1440) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5454 Ramachandran restraints generated. 2727 Oldfield, 0 Emsley, 2727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5454 Ramachandran restraints generated. 2727 Oldfield, 0 Emsley, 2727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 635 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7761 (tp30) cc_final: 0.7159 (tp30) REVERT: A 55 ASP cc_start: 0.7603 (t0) cc_final: 0.7116 (t0) REVERT: A 134 GLU cc_start: 0.7705 (pt0) cc_final: 0.7437 (mt-10) REVERT: A 240 LYS cc_start: 0.8403 (mmtt) cc_final: 0.8137 (mmmm) REVERT: A 325 GLN cc_start: 0.8290 (pt0) cc_final: 0.7901 (mt0) REVERT: A 384 SER cc_start: 0.8190 (t) cc_final: 0.7909 (p) REVERT: A 388 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8227 (tpt-90) REVERT: A 627 TYR cc_start: 0.8075 (m-80) cc_final: 0.7866 (m-80) REVERT: A 645 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7684 (mm) REVERT: A 676 ILE cc_start: 0.7915 (mt) cc_final: 0.7602 (mp) REVERT: A 677 SER cc_start: 0.7814 (t) cc_final: 0.7505 (m) REVERT: A 707 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7284 (p0) REVERT: A 718 TYR cc_start: 0.7734 (t80) cc_final: 0.7322 (t80) REVERT: A 748 LEU cc_start: 0.7779 (mt) cc_final: 0.7535 (mt) REVERT: A 751 PRO cc_start: 0.6715 (Cg_endo) cc_final: 0.6286 (Cg_exo) REVERT: A 799 LYS cc_start: 0.8159 (ttmm) cc_final: 0.7811 (mttm) REVERT: A 825 TYR cc_start: 0.8068 (t80) cc_final: 0.7848 (t80) REVERT: A 870 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8099 (pt) REVERT: A 881 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7414 (mp) REVERT: A 893 MET cc_start: 0.7481 (mtm) cc_final: 0.7267 (mtm) REVERT: B 13 MET cc_start: 0.7425 (mmm) cc_final: 0.6865 (mmm) REVERT: B 58 THR cc_start: 0.8313 (t) cc_final: 0.7988 (m) REVERT: B 258 VAL cc_start: 0.7683 (OUTLIER) cc_final: 0.7326 (m) REVERT: B 259 MET cc_start: 0.7279 (mmm) cc_final: 0.6372 (mmm) REVERT: B 525 VAL cc_start: 0.7278 (OUTLIER) cc_final: 0.7070 (p) REVERT: B 527 CYS cc_start: 0.7780 (t) cc_final: 0.7488 (m) REVERT: B 606 SER cc_start: 0.8327 (m) cc_final: 0.7909 (p) REVERT: B 674 VAL cc_start: 0.8412 (t) cc_final: 0.8200 (m) REVERT: B 730 LYS cc_start: 0.8304 (tttt) cc_final: 0.7894 (ttmm) REVERT: B 731 LYS cc_start: 0.8059 (pttt) cc_final: 0.7818 (ptpp) REVERT: B 786 ASN cc_start: 0.7937 (m-40) cc_final: 0.7625 (t0) REVERT: B 810 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7740 (mt0) REVERT: B 847 MET cc_start: 0.7265 (ptp) cc_final: 0.7052 (ptp) REVERT: C 13 MET cc_start: 0.8330 (tpp) cc_final: 0.7998 (mmt) REVERT: C 31 PHE cc_start: 0.8465 (t80) cc_final: 0.8182 (t80) REVERT: C 74 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7298 (mm-30) REVERT: C 75 ASP cc_start: 0.8020 (m-30) cc_final: 0.7717 (t0) REVERT: C 184 LYS cc_start: 0.8513 (ttmt) cc_final: 0.8176 (mmtt) REVERT: C 185 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7493 (mp0) REVERT: C 273 GLN cc_start: 0.7413 (mp10) cc_final: 0.6040 (mp10) REVERT: C 276 SER cc_start: 0.8271 (t) cc_final: 0.7846 (p) REVERT: C 302 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7030 (pt0) REVERT: C 317 LYS cc_start: 0.8145 (mttt) cc_final: 0.7830 (mttt) REVERT: C 486 SER cc_start: 0.8603 (t) cc_final: 0.8386 (m) REVERT: C 494 ASP cc_start: 0.7293 (t0) cc_final: 0.6972 (t0) REVERT: C 495 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8060 (ptmm) REVERT: C 618 SER cc_start: 0.8155 (t) cc_final: 0.7842 (p) REVERT: C 664 LEU cc_start: 0.8596 (mp) cc_final: 0.8294 (mt) REVERT: C 678 ILE cc_start: 0.8537 (mm) cc_final: 0.8287 (mm) REVERT: C 701 SER cc_start: 0.8094 (m) cc_final: 0.7776 (p) REVERT: C 758 ARG cc_start: 0.8418 (mtp85) cc_final: 0.7911 (mtp85) REVERT: C 761 ASP cc_start: 0.6822 (OUTLIER) cc_final: 0.6519 (t70) REVERT: C 821 LYS cc_start: 0.8398 (mttt) cc_final: 0.8039 (mttt) REVERT: C 848 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8145 (ppt170) REVERT: C 873 LYS cc_start: 0.8268 (mttt) cc_final: 0.8017 (mttm) REVERT: C 930 LEU cc_start: 0.8349 (mm) cc_final: 0.8004 (mt) REVERT: C 944 ARG cc_start: 0.7329 (ttt90) cc_final: 0.6844 (ttt90) outliers start: 107 outliers final: 87 residues processed: 685 average time/residue: 0.1612 time to fit residues: 169.5212 Evaluate side-chains 722 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 623 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 707 ASP Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 819 ASP Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 873 LYS Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain B residue 810 GLN Chi-restraints excluded: chain B residue 913 ASP Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 352 ASN Chi-restraints excluded: chain C residue 476 ASN Chi-restraints excluded: chain C residue 495 LYS Chi-restraints excluded: chain C residue 513 ASP Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 667 ILE Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 761 ASP Chi-restraints excluded: chain C residue 804 SER Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 830 ILE Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 888 SER Chi-restraints excluded: chain C residue 892 SER Chi-restraints excluded: chain C residue 914 MET Chi-restraints excluded: chain C residue 923 GLU Chi-restraints excluded: chain C residue 929 VAL Chi-restraints excluded: chain G residue 8 MET Chi-restraints excluded: chain G residue 43 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 19 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 258 optimal weight: 0.7980 chunk 131 optimal weight: 0.2980 chunk 124 optimal weight: 0.7980 chunk 214 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 33 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN A 516 ASN B 370 GLN B 499 ASN B 510 ASN B 563 ASN B 647 ASN B 836 ASN ** B 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 HIS C 771 ASN C 940 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.118895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105354 restraints weight = 30614.069| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.92 r_work: 0.3199 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 22831 Z= 0.098 Angle : 0.530 10.109 31043 Z= 0.277 Chirality : 0.044 0.198 3291 Planarity : 0.004 0.054 4089 Dihedral : 6.282 55.372 3152 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.92 % Allowed : 18.91 % Favored : 77.18 % 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: -1.51 (0.16), residues: 2727 helix: 0.52 (0.30), residues: 349 sheet: -0.25 (0.22), residues: 578 loop : -1.67 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 73 TYR 0.026 0.001 TYR B 724 PHE 0.030 0.001 PHE B 875 TRP 0.032 0.002 TRP C 535 HIS 0.008 0.001 HIS C 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (22831) covalent geometry : angle 0.52966 / 0.28 (31043) hydrogen bonds : bond 0.03166 / 2.11 ( 522) hydrogen bonds : angle 5.48748 / 3.77 ( 1440) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5454 Ramachandran restraints generated. 2727 Oldfield, 0 Emsley, 2727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5454 Ramachandran restraints generated. 2727 Oldfield, 0 Emsley, 2727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 626 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7757 (tp30) cc_final: 0.7145 (tp30) REVERT: A 55 ASP cc_start: 0.7565 (t0) cc_final: 0.7080 (t0) REVERT: A 240 LYS cc_start: 0.8365 (mmtt) cc_final: 0.8131 (mttm) REVERT: A 325 GLN cc_start: 0.8159 (pt0) cc_final: 0.7837 (mt0) REVERT: A 328 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7348 (ttp) REVERT: A 388 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8315 (tpt90) REVERT: A 645 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7576 (mm) REVERT: A 647 ASN cc_start: 0.7355 (t0) cc_final: 0.7036 (t0) REVERT: A 676 ILE cc_start: 0.7960 (mt) cc_final: 0.7649 (mp) REVERT: A 677 SER cc_start: 0.7836 (t) cc_final: 0.7571 (m) REVERT: A 718 TYR cc_start: 0.7667 (t80) cc_final: 0.7319 (t80) REVERT: A 719 LEU cc_start: 0.7524 (mt) cc_final: 0.7248 (mp) REVERT: A 751 PRO cc_start: 0.6782 (Cg_endo) cc_final: 0.6352 (Cg_exo) REVERT: A 799 LYS cc_start: 0.8187 (ttmm) cc_final: 0.7859 (mttm) REVERT: A 870 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8132 (pt) REVERT: A 881 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7357 (mp) REVERT: A 893 MET cc_start: 0.7420 (mtm) cc_final: 0.7175 (mtm) REVERT: B 13 MET cc_start: 0.7335 (mmm) cc_final: 0.6830 (mmm) REVERT: B 58 THR cc_start: 0.8321 (t) cc_final: 0.7990 (m) REVERT: B 176 PRO cc_start: 0.8258 (Cg_endo) cc_final: 0.7953 (Cg_exo) REVERT: B 258 VAL cc_start: 0.7553 (OUTLIER) cc_final: 0.7155 (m) REVERT: B 259 MET cc_start: 0.7308 (mmm) cc_final: 0.6545 (mmm) REVERT: B 417 GLU cc_start: 0.7386 (mp0) cc_final: 0.7093 (mp0) REVERT: B 525 VAL cc_start: 0.7190 (OUTLIER) cc_final: 0.6977 (p) REVERT: B 527 CYS cc_start: 0.7653 (t) cc_final: 0.7341 (m) REVERT: B 559 MET cc_start: 0.7156 (mmt) cc_final: 0.6950 (mmt) REVERT: B 606 SER cc_start: 0.8336 (m) cc_final: 0.7949 (p) REVERT: B 647 ASN cc_start: 0.8328 (OUTLIER) cc_final: 0.8013 (t0) REVERT: B 674 VAL cc_start: 0.8380 (t) cc_final: 0.8112 (m) REVERT: B 730 LYS cc_start: 0.8166 (tttt) cc_final: 0.7797 (ttmm) REVERT: B 810 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7759 (mt0) REVERT: B 847 MET cc_start: 0.7256 (ptp) cc_final: 0.6832 (ptt) REVERT: C 13 MET cc_start: 0.8249 (tpp) cc_final: 0.7979 (mmt) REVERT: C 31 PHE cc_start: 0.8491 (t80) cc_final: 0.8186 (t80) REVERT: C 49 THR cc_start: 0.8064 (t) cc_final: 0.7711 (p) REVERT: C 50 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8377 (m) REVERT: C 73 ARG cc_start: 0.8163 (ttt-90) cc_final: 0.7938 (ttt-90) REVERT: C 74 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7140 (mm-30) REVERT: C 184 LYS cc_start: 0.8471 (ttmt) cc_final: 0.8135 (mmtt) REVERT: C 185 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7472 (mp0) REVERT: C 273 GLN cc_start: 0.7415 (mp10) cc_final: 0.6111 (mp10) REVERT: C 276 SER cc_start: 0.8344 (t) cc_final: 0.7975 (p) REVERT: C 317 LYS cc_start: 0.7963 (mttt) cc_final: 0.7689 (mttt) REVERT: C 380 LEU cc_start: 0.7262 (mt) cc_final: 0.6988 (mt) REVERT: C 486 SER cc_start: 0.8564 (t) cc_final: 0.8325 (m) REVERT: C 494 ASP cc_start: 0.7304 (t0) cc_final: 0.6966 (t0) REVERT: C 495 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8041 (ptmm) REVERT: C 618 SER cc_start: 0.7996 (t) cc_final: 0.7708 (p) REVERT: C 664 LEU cc_start: 0.8558 (mp) cc_final: 0.8326 (mt) REVERT: C 678 ILE cc_start: 0.8512 (mm) cc_final: 0.8260 (mm) REVERT: C 701 SER cc_start: 0.8127 (m) cc_final: 0.7807 (p) REVERT: C 713 SER cc_start: 0.7468 (m) cc_final: 0.7066 (p) REVERT: C 731 LYS cc_start: 0.8457 (ptpt) cc_final: 0.8227 (ptpt) REVERT: C 758 ARG cc_start: 0.8369 (mtp85) cc_final: 0.7910 (mtp85) REVERT: C 761 ASP cc_start: 0.6875 (OUTLIER) cc_final: 0.6564 (t70) REVERT: C 805 PHE cc_start: 0.8259 (t80) cc_final: 0.7958 (t80) REVERT: C 821 LYS cc_start: 0.8388 (mttt) cc_final: 0.8074 (mttt) REVERT: C 848 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8001 (ppt-90) REVERT: C 873 LYS cc_start: 0.8087 (mttt) cc_final: 0.7841 (mttm) REVERT: C 930 LEU cc_start: 0.8310 (mm) cc_final: 0.7968 (mt) REVERT: C 944 ARG cc_start: 0.7222 (ttt90) cc_final: 0.6765 (ttt90) outliers start: 94 outliers final: 73 residues processed: 673 average time/residue: 0.1429 time to fit residues: 147.3522 Evaluate side-chains 695 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 609 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 707 ASP Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 873 LYS Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 810 GLN Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 913 ASP Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 352 ASN Chi-restraints excluded: chain C residue 476 ASN Chi-restraints excluded: chain C residue 495 LYS Chi-restraints excluded: chain C residue 513 ASP Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 667 ILE Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 761 ASP Chi-restraints excluded: chain C residue 771 ASN Chi-restraints excluded: chain C residue 804 SER Chi-restraints excluded: chain C residue 830 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 888 SER Chi-restraints excluded: chain C residue 892 SER Chi-restraints excluded: chain C residue 914 MET Chi-restraints excluded: chain C residue 923 GLU Chi-restraints excluded: chain C residue 929 VAL Chi-restraints excluded: chain G residue 8 MET Chi-restraints excluded: chain G residue 43 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 187 optimal weight: 8.9990 chunk 228 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 79 optimal weight: 0.0070 chunk 216 optimal weight: 0.9990 chunk 200 optimal weight: 6.9990 chunk 224 optimal weight: 3.9990 chunk 227 optimal weight: 0.0370 chunk 156 optimal weight: 2.9990 chunk 276 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN A 516 ASN A 582 ASN B 370 GLN B 510 ASN B 563 ASN B 647 ASN ** B 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 HIS ** C 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 940 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.117310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.103678 restraints weight = 31010.004| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.92 r_work: 0.3184 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22831 Z= 0.164 Angle : 0.574 9.959 31043 Z= 0.301 Chirality : 0.045 0.245 3291 Planarity : 0.005 0.061 4089 Dihedral : 6.465 56.393 3150 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 4.33 % Allowed : 18.78 % Favored : 76.88 % 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: -1.54 (0.16), residues: 2727 helix: 0.48 (0.30), residues: 349 sheet: -0.22 (0.22), residues: 572 loop : -1.71 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 92 TYR 0.031 0.002 TYR B 724 PHE 0.034 0.002 PHE B 875 TRP 0.032 0.002 TRP C 535 HIS 0.010 0.001 HIS C 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (22831) covalent geometry : angle 0.57427 / 0.30 (31043) hydrogen bonds : bond 0.03978 / 2.63 ( 522) hydrogen bonds : angle 5.54575 / 3.81 ( 1440) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5454 Ramachandran restraints generated. 2727 Oldfield, 0 Emsley, 2727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5454 Ramachandran restraints generated. 2727 Oldfield, 0 Emsley, 2727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 613 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7781 (tp30) cc_final: 0.7162 (tp30) REVERT: A 55 ASP cc_start: 0.7610 (t0) cc_final: 0.7123 (t0) REVERT: A 240 LYS cc_start: 0.8404 (mmtt) cc_final: 0.8165 (mttm) REVERT: A 325 GLN cc_start: 0.8246 (pt0) cc_final: 0.7818 (mt0) REVERT: A 631 PHE cc_start: 0.8318 (t80) cc_final: 0.8088 (t80) REVERT: A 676 ILE cc_start: 0.7953 (mt) cc_final: 0.7638 (mp) REVERT: A 677 SER cc_start: 0.7879 (t) cc_final: 0.7605 (m) REVERT: A 707 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7262 (p0) REVERT: A 718 TYR cc_start: 0.7710 (t80) cc_final: 0.7357 (t80) REVERT: A 719 LEU cc_start: 0.7544 (mt) cc_final: 0.7301 (mp) REVERT: A 751 PRO cc_start: 0.6774 (Cg_endo) cc_final: 0.6358 (Cg_exo) REVERT: A 799 LYS cc_start: 0.8174 (ttmm) cc_final: 0.7814 (mttm) REVERT: A 827 GLN cc_start: 0.7781 (tp40) cc_final: 0.7481 (tp40) REVERT: A 870 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8143 (pt) REVERT: A 881 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7410 (mt) REVERT: A 893 MET cc_start: 0.7480 (mtm) cc_final: 0.7255 (mtm) REVERT: B 13 MET cc_start: 0.7430 (mmm) cc_final: 0.6899 (mmm) REVERT: B 58 THR cc_start: 0.8364 (t) cc_final: 0.8024 (m) REVERT: B 176 PRO cc_start: 0.8265 (Cg_endo) cc_final: 0.8047 (Cg_exo) REVERT: B 240 LYS cc_start: 0.8866 (mmtt) cc_final: 0.8657 (mmtp) REVERT: B 258 VAL cc_start: 0.7625 (OUTLIER) cc_final: 0.7246 (m) REVERT: B 259 MET cc_start: 0.7294 (mmm) cc_final: 0.6481 (mmm) REVERT: B 417 GLU cc_start: 0.7397 (mp0) cc_final: 0.7138 (mp0) REVERT: B 525 VAL cc_start: 0.7278 (OUTLIER) cc_final: 0.7076 (p) REVERT: B 527 CYS cc_start: 0.7738 (t) cc_final: 0.7438 (m) REVERT: B 606 SER cc_start: 0.8340 (m) cc_final: 0.7933 (p) REVERT: B 674 VAL cc_start: 0.8430 (OUTLIER) cc_final: 0.8207 (m) REVERT: B 730 LYS cc_start: 0.8258 (tttt) cc_final: 0.7880 (ttmm) REVERT: B 786 ASN cc_start: 0.8047 (t0) cc_final: 0.7674 (t0) REVERT: B 810 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7713 (mt0) REVERT: B 891 MET cc_start: 0.7558 (mtp) cc_final: 0.7231 (mmm) REVERT: C 13 MET cc_start: 0.8259 (tpp) cc_final: 0.7998 (mmt) REVERT: C 31 PHE cc_start: 0.8452 (t80) cc_final: 0.8136 (t80) REVERT: C 49 THR cc_start: 0.8118 (t) cc_final: 0.7783 (p) REVERT: C 50 VAL cc_start: 0.8706 (OUTLIER) cc_final: 0.8426 (m) REVERT: C 73 ARG cc_start: 0.8313 (ttt-90) cc_final: 0.8063 (ttt-90) REVERT: C 74 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7315 (mm-30) REVERT: C 184 LYS cc_start: 0.8500 (ttmt) cc_final: 0.8051 (mtmm) REVERT: C 185 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7498 (mp0) REVERT: C 235 LYS cc_start: 0.8176 (pttt) cc_final: 0.7888 (ptpp) REVERT: C 273 GLN cc_start: 0.7437 (mp10) cc_final: 0.6100 (mp10) REVERT: C 276 SER cc_start: 0.8337 (t) cc_final: 0.7932 (p) REVERT: C 302 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7014 (pt0) REVERT: C 317 LYS cc_start: 0.8046 (mttt) cc_final: 0.7742 (mttt) REVERT: C 486 SER cc_start: 0.8586 (t) cc_final: 0.8372 (m) REVERT: C 494 ASP cc_start: 0.7343 (t0) cc_final: 0.7021 (t0) REVERT: C 495 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8046 (ptmm) REVERT: C 618 SER cc_start: 0.8112 (t) cc_final: 0.7810 (p) REVERT: C 664 LEU cc_start: 0.8538 (mp) cc_final: 0.8298 (mt) REVERT: C 678 ILE cc_start: 0.8528 (mm) cc_final: 0.8276 (mm) REVERT: C 701 SER cc_start: 0.8109 (m) cc_final: 0.7788 (p) REVERT: C 758 ARG cc_start: 0.8438 (mtp85) cc_final: 0.7928 (mtp85) REVERT: C 761 ASP cc_start: 0.6926 (OUTLIER) cc_final: 0.6587 (t70) REVERT: C 821 LYS cc_start: 0.8419 (mttt) cc_final: 0.8064 (mttt) REVERT: C 848 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8156 (ppt170) REVERT: C 873 LYS cc_start: 0.8118 (mttt) cc_final: 0.7863 (mttm) REVERT: C 930 LEU cc_start: 0.8312 (mm) cc_final: 0.7980 (mt) REVERT: C 944 ARG cc_start: 0.7277 (ttt90) cc_final: 0.6852 (ttt90) outliers start: 104 outliers final: 83 residues processed: 661 average time/residue: 0.1484 time to fit residues: 150.3572 Evaluate side-chains 702 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 607 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 707 ASP Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 873 LYS Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 913 ASP Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 810 GLN Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 913 ASP Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 352 ASN Chi-restraints excluded: chain C residue 476 ASN Chi-restraints excluded: chain C residue 495 LYS Chi-restraints excluded: chain C residue 513 ASP Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 667 ILE Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 761 ASP Chi-restraints excluded: chain C residue 804 SER Chi-restraints excluded: chain C residue 830 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 888 SER Chi-restraints excluded: chain C residue 892 SER Chi-restraints excluded: chain C residue 914 MET Chi-restraints excluded: chain C residue 923 GLU Chi-restraints excluded: chain C residue 929 VAL Chi-restraints excluded: chain G residue 8 MET Chi-restraints excluded: chain G residue 43 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 233 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 203 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 213 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN A 516 ASN B 14 HIS B 370 GLN B 499 ASN B 510 ASN B 563 ASN ** B 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 HIS ** C 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 940 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.116118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.102874 restraints weight = 31328.440| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.93 r_work: 0.3148 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 22831 Z= 0.314 Angle : 0.687 9.847 31043 Z= 0.365 Chirality : 0.051 0.266 3291 Planarity : 0.006 0.067 4089 Dihedral : 6.963 60.641 3147 Min Nonbonded Distance : 1.603 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 4.29 % Allowed : 18.78 % Favored : 76.93 % 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: -1.89 (0.15), residues: 2727 helix: 0.10 (0.29), residues: 349 sheet: -0.43 (0.22), residues: 571 loop : -1.93 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 646 TYR 0.038 0.003 TYR B 724 PHE 0.037 0.003 PHE B 875 TRP 0.040 0.003 TRP C 535 HIS 0.015 0.002 HIS C 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00738 / 0.31 (22831) covalent geometry : angle 0.68740 / 0.37 (31043) hydrogen bonds : bond 0.05366 / 3.53 ( 522) hydrogen bonds : angle 5.95411 / 4.10 ( 1440) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5454 Ramachandran restraints generated. 2727 Oldfield, 0 Emsley, 2727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5454 Ramachandran restraints generated. 2727 Oldfield, 0 Emsley, 2727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 636 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7802 (tp30) cc_final: 0.7204 (tp30) REVERT: A 55 ASP cc_start: 0.7685 (t0) cc_final: 0.7244 (t0) REVERT: A 240 LYS cc_start: 0.8466 (mmtt) cc_final: 0.8201 (mttm) REVERT: A 325 GLN cc_start: 0.8341 (pt0) cc_final: 0.7810 (mt0) REVERT: A 676 ILE cc_start: 0.7932 (mt) cc_final: 0.7613 (mp) REVERT: A 677 SER cc_start: 0.7857 (t) cc_final: 0.7548 (m) REVERT: A 707 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7486 (p0) REVERT: A 718 TYR cc_start: 0.7778 (t80) cc_final: 0.7229 (t80) REVERT: A 719 LEU cc_start: 0.7538 (mt) cc_final: 0.7282 (mp) REVERT: A 748 LEU cc_start: 0.7819 (mt) cc_final: 0.7575 (mt) REVERT: A 751 PRO cc_start: 0.6764 (Cg_endo) cc_final: 0.6331 (Cg_exo) REVERT: A 799 LYS cc_start: 0.8184 (ttmm) cc_final: 0.7777 (mttm) REVERT: A 823 LYS cc_start: 0.8265 (mmtt) cc_final: 0.7967 (mmtt) REVERT: A 870 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8109 (pt) REVERT: B 13 MET cc_start: 0.7451 (mmm) cc_final: 0.6830 (mmm) REVERT: B 258 VAL cc_start: 0.7727 (OUTLIER) cc_final: 0.7371 (m) REVERT: B 259 MET cc_start: 0.7363 (mmm) cc_final: 0.6466 (mmm) REVERT: B 298 ASP cc_start: 0.7562 (t0) cc_final: 0.7295 (t0) REVERT: B 417 GLU cc_start: 0.7433 (mp0) cc_final: 0.7188 (mp0) REVERT: B 525 VAL cc_start: 0.7330 (OUTLIER) cc_final: 0.7121 (p) REVERT: B 527 CYS cc_start: 0.7846 (t) cc_final: 0.7569 (m) REVERT: B 606 SER cc_start: 0.8266 (m) cc_final: 0.7851 (p) REVERT: B 647 ASN cc_start: 0.8383 (t0) cc_final: 0.7983 (t0) REVERT: B 674 VAL cc_start: 0.8448 (OUTLIER) cc_final: 0.8244 (m) REVERT: B 702 LEU cc_start: 0.8410 (tp) cc_final: 0.8190 (mp) REVERT: B 730 LYS cc_start: 0.8373 (tttt) cc_final: 0.7968 (ttmm) REVERT: B 786 ASN cc_start: 0.8023 (t0) cc_final: 0.7796 (t0) REVERT: B 810 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7776 (mt0) REVERT: C 31 PHE cc_start: 0.8435 (t80) cc_final: 0.8138 (t80) REVERT: C 50 VAL cc_start: 0.8786 (OUTLIER) cc_final: 0.8551 (m) REVERT: C 73 ARG cc_start: 0.8385 (ttt-90) cc_final: 0.8010 (ttt-90) REVERT: C 74 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7393 (mm-30) REVERT: C 184 LYS cc_start: 0.8557 (ttmt) cc_final: 0.8252 (mmtt) REVERT: C 185 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7503 (mp0) REVERT: C 235 LYS cc_start: 0.8205 (pttt) cc_final: 0.7874 (ptpp) REVERT: C 273 GLN cc_start: 0.7426 (mp10) cc_final: 0.6034 (mp10) REVERT: C 276 SER cc_start: 0.8323 (t) cc_final: 0.7892 (p) REVERT: C 302 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7052 (pt0) REVERT: C 317 LYS cc_start: 0.8175 (mttt) cc_final: 0.7866 (mttt) REVERT: C 494 ASP cc_start: 0.7304 (t0) cc_final: 0.7021 (t0) REVERT: C 495 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8115 (ptmm) REVERT: C 664 LEU cc_start: 0.8567 (mp) cc_final: 0.8283 (mt) REVERT: C 678 ILE cc_start: 0.8542 (mm) cc_final: 0.8293 (mm) REVERT: C 701 SER cc_start: 0.8082 (m) cc_final: 0.7812 (p) REVERT: C 731 LYS cc_start: 0.8483 (ptpt) cc_final: 0.8265 (ptpp) REVERT: C 758 ARG cc_start: 0.8438 (mtp85) cc_final: 0.8055 (mtp85) REVERT: C 821 LYS cc_start: 0.8423 (mttt) cc_final: 0.8056 (mttt) REVERT: C 848 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8036 (ppt170) REVERT: C 873 LYS cc_start: 0.8188 (mttt) cc_final: 0.7938 (mttm) REVERT: C 930 LEU cc_start: 0.8307 (mm) cc_final: 0.7989 (mt) REVERT: C 944 ARG cc_start: 0.7318 (ttt90) cc_final: 0.6827 (ttt90) outliers start: 103 outliers final: 83 residues processed: 685 average time/residue: 0.1482 time to fit residues: 155.7529 Evaluate side-chains 718 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 625 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 707 ASP Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 873 LYS Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 810 GLN Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 913 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 38 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 352 ASN Chi-restraints excluded: chain C residue 476 ASN Chi-restraints excluded: chain C residue 495 LYS Chi-restraints excluded: chain C residue 513 ASP Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 667 ILE Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 804 SER Chi-restraints excluded: chain C residue 830 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 888 SER Chi-restraints excluded: chain C residue 892 SER Chi-restraints excluded: chain C residue 914 MET Chi-restraints excluded: chain C residue 923 GLU Chi-restraints excluded: chain C residue 929 VAL Chi-restraints excluded: chain G residue 8 MET Chi-restraints excluded: chain G residue 43 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 49 optimal weight: 0.0570 chunk 82 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 213 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 197 optimal weight: 4.9990 chunk 107 optimal weight: 0.0030 chunk 44 optimal weight: 0.8980 chunk 253 optimal weight: 1.9990 overall best weight: 0.5708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN A 516 ASN A 808 ASN B 14 HIS B 370 GLN B 510 ASN B 563 ASN ** B 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 771 ASN C 940 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.119301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.105469 restraints weight = 30811.478| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.97 r_work: 0.3211 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 22831 Z= 0.103 Angle : 0.545 9.744 31043 Z= 0.285 Chirality : 0.044 0.221 3291 Planarity : 0.004 0.059 4089 Dihedral : 6.209 55.815 3147 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.62 % Allowed : 19.37 % Favored : 77.01 % 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: -1.59 (0.16), residues: 2727 helix: 0.43 (0.30), residues: 344 sheet: -0.28 (0.22), residues: 568 loop : -1.72 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 646 TYR 0.024 0.001 TYR B 724 PHE 0.032 0.001 PHE B 875 TRP 0.031 0.002 TRP B 135 HIS 0.012 0.001 HIS C 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (22831) covalent geometry : angle 0.54518 / 0.29 (31043) hydrogen bonds : bond 0.03171 / 2.13 ( 522) hydrogen bonds : angle 5.50078 / 3.78 ( 1440) =============================================================================== Job complete usr+sys time: 5421.15 seconds wall clock time: 93 minutes 23.46 seconds (5603.46 seconds total)