Starting phenix.real_space_refine on Fri Aug 7 14:01:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/13dm_76994/08_2026/13dm_76994.cif Found real_map, /net/cci-nas-00/data/ceres_data/13dm_76994/08_2026/13dm_76994.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 { model { file = "/net/cci-nas-00/data/ceres_data/13dm_76994/08_2026/13dm_76994.cif" } default_model = "/net/cci-nas-00/data/ceres_data/13dm_76994/08_2026/13dm_76994.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/13dm_76994/08_2026/13dm_76994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/13dm_76994/08_2026/13dm_76994.map" } 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= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 13878 2.51 5 N 3707 2.21 5 O 4159 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 21854 Number of models: 1 Model: "" Number of chains: 3 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: 7293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 913, 7293 Classifications: {'peptide': 913} Link IDs: {'PTRANS': 52, 'TRANS': 860} Chain breaks: 3 Time building chain proxies: 4.29, per 1000 atoms: 0.20 Number of scatterers: 21854 At special positions: 0 Unit cell: (114.75, 115.6, 136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 110 16.00 O 4159 8.00 N 3707 7.00 C 13878 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: 1.33 Conformation dependent library (CDL) restraints added in 934.6 milliseconds 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5124 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 56 sheets defined 16.9% alpha, 26.1% 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: 3.562A pdb=" N SER A 11 " --> pdb=" O MET A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 24 removed outlier: 3.623A pdb=" N TYR A 23 " --> pdb=" O ASP A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 35 Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 319 through 325 removed outlier: 3.675A pdb=" N GLY A 324 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 3.742A 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 removed outlier: 3.500A pdb=" N GLY A 386 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'A' and resid 511 through 518 removed outlier: 3.604A pdb=" N ARG A 518 " --> pdb=" O TYR A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 526 removed outlier: 3.508A pdb=" N LEU A 524 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 525 " --> pdb=" O PRO A 522 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP A 526 " --> pdb=" O GLY A 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 521 through 526' Processing helix chain 'A' and resid 551 through 562 Processing helix chain 'A' and resid 634 through 646 Processing helix chain 'A' and resid 697 through 699 No H-bonds generated for 'chain 'A' and resid 697 through 699' Processing helix chain 'A' and resid 716 through 721 Processing helix chain 'A' and resid 774 through 786 Processing helix chain 'A' and resid 898 through 901 Processing helix chain 'A' and resid 902 through 907 removed outlier: 3.508A pdb=" N ASN A 907 " --> pdb=" O LEU A 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 24 removed outlier: 3.587A pdb=" N TYR B 23 " --> pdb=" O ASP B 19 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 19 through 24' 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 320 through 325 removed outlier: 3.567A pdb=" N GLY B 324 " --> pdb=" O VAL B 321 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 325 " --> pdb=" O MET B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 342 Processing helix chain 'B' and resid 374 through 386 Processing helix chain 'B' and resid 403 through 408 Processing helix chain 'B' and resid 475 through 488 Processing helix chain 'B' and resid 489 through 492 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: 3.747A pdb=" N ASP B 526 " --> pdb=" O GLY B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 removed outlier: 4.429A pdb=" N ASN B 542 " --> pdb=" O GLU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 562 Processing helix chain 'B' and resid 599 through 603 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 774 through 786 Processing helix chain 'B' and resid 897 through 901 Processing helix chain 'B' and resid 902 through 907 removed outlier: 3.936A pdb=" N ASN B 907 " --> pdb=" O LEU B 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 13 Processing helix chain 'C' and resid 19 through 24 removed outlier: 3.592A pdb=" N TYR C 23 " --> pdb=" O ASP C 19 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 19 through 24' Processing helix chain 'C' and resid 25 through 35 Processing helix chain 'C' and resid 41 through 45 removed outlier: 3.721A pdb=" N LYS C 44 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE C 45 " --> pdb=" O ASN C 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 41 through 45' Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 283 through 287 removed outlier: 4.265A pdb=" N ASN C 286 " --> pdb=" O ASN C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 325 removed outlier: 3.821A pdb=" N GLY C 324 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN C 325 " --> pdb=" O MET C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 342 Processing helix chain 'C' and resid 374 through 386 Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.547A pdb=" N ARG C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 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 removed outlier: 3.644A pdb=" N ARG C 518 " --> pdb=" O TYR C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 526 removed outlier: 3.632A pdb=" N LEU C 524 " --> pdb=" O ALA C 521 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 525 " --> pdb=" O PRO C 522 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP C 526 " --> pdb=" O GLY C 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 521 through 526' Processing helix chain 'C' and resid 551 through 562 Processing helix chain 'C' and resid 599 through 603 Processing helix chain 'C' and resid 634 through 646 Processing helix chain 'C' and resid 716 through 721 Processing helix chain 'C' and resid 774 through 786 Processing helix chain 'C' and resid 898 through 901 Processing helix chain 'C' and resid 902 through 908 removed outlier: 4.232A pdb=" N SER C 908 " --> pdb=" O LEU C 904 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 5.223A pdb=" N ILE A 619 " --> pdb=" O ASP A 108 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ASP A 108 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N PHE A 621 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL A 106 " --> pdb=" O PHE A 621 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 105 " --> pdb=" O PHE A 569 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 569 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 68 removed outlier: 5.223A pdb=" N ILE A 619 " --> pdb=" O ASP A 108 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ASP A 108 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N PHE A 621 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL A 106 " --> pdb=" O PHE A 621 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 75 removed outlier: 3.801A pdb=" N ASP A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 80 " --> pdb=" O PHE A 596 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP A 594 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 94 through 95 removed outlier: 3.599A pdb=" N LEU A 94 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 137 Processing sheet with id=AA6, first strand: chain 'A' and resid 174 through 175 Processing sheet with id=AA7, first strand: chain 'A' and resid 188 through 191 removed outlier: 3.687A pdb=" N GLY A 190 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 228 through 233 removed outlier: 12.869A pdb=" N MET A 272 " --> pdb=" O THR B 439 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N THR B 439 " --> pdb=" O MET A 272 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE A 274 " --> pdb=" O VAL B 437 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 246 through 247 Processing sheet with id=AB1, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.493A pdb=" N GLN A 326 " --> pdb=" O SER A 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 336 through 337 Processing sheet with id=AB3, first strand: chain 'A' and resid 409 through 410 Processing sheet with id=AB4, first strand: chain 'A' and resid 420 through 421 removed outlier: 3.739A pdb=" N ASN A 420 " --> pdb=" O ILE A 473 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 423 through 424 removed outlier: 3.751A pdb=" N ASN B 420 " --> pdb=" O ILE B 473 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 453 through 454 removed outlier: 3.558A pdb=" N LYS A 453 " --> pdb=" O LYS A 438 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP A 432 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N GLU A 462 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ALA C 175 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLY A 464 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS C 133 " --> pdb=" O TYR C 172 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 453 through 454 removed outlier: 3.558A pdb=" N LYS A 453 " --> pdb=" O LYS A 438 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N PHE C 274 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 652 through 655 removed outlier: 3.544A pdb=" N GLN A 652 " --> pdb=" O VAL A 939 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 660 through 667 removed outlier: 4.368A pdb=" N GLY A 688 " --> pdb=" O GLU A 932 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TRP A 882 " --> pdb=" O PHE A 691 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 673 through 681 removed outlier: 3.535A pdb=" N LEU A 912 " --> pdb=" O ILE A 678 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER A 680 " --> pdb=" O HIS A 910 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N HIS A 910 " --> pdb=" O SER A 680 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 673 through 681 removed outlier: 3.535A pdb=" N LEU A 912 " --> pdb=" O ILE A 678 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER A 680 " --> pdb=" O HIS A 910 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N HIS A 910 " --> pdb=" O SER A 680 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 766 through 767 removed outlier: 4.571A pdb=" N MET A 772 " --> pdb=" O VAL A 767 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 810 through 817 removed outlier: 3.508A pdb=" N GLN A 810 " --> pdb=" O LEU A 876 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 876 " --> pdb=" O GLN A 810 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.916A pdb=" N ARG B 104 " --> pdb=" O ASP B 622 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE B 624 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASP B 102 " --> pdb=" O ILE B 624 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LEU B 626 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N TYR B 100 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.916A pdb=" N ARG B 104 " --> pdb=" O ASP B 622 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE B 624 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASP B 102 " --> pdb=" O ILE B 624 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LEU B 626 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N TYR B 100 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 72 through 75 removed outlier: 3.763A pdb=" N ASP B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 94 through 95 removed outlier: 3.547A pdb=" N LEU B 94 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 177 through 178 removed outlier: 3.623A pdb=" N ALA B 173 " --> pdb=" O GLU C 462 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP C 432 " --> pdb=" O ILE C 463 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 177 through 178 removed outlier: 6.608A pdb=" N ALA B 228 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N TYR B 295 " --> pdb=" O ALA B 228 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY B 230 " --> pdb=" O TYR B 295 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N GLU B 297 " --> pdb=" O GLY B 230 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL B 232 " --> pdb=" O GLU B 297 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE B 274 " --> pdb=" O VAL C 437 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 188 through 191 removed outlier: 3.626A pdb=" N GLY B 190 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 246 through 247 Processing sheet with id=AD4, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.663A pdb=" N GLN B 326 " --> pdb=" O SER B 309 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 336 through 337 Processing sheet with id=AD6, first strand: chain 'B' and resid 409 through 410 removed outlier: 3.661A pdb=" N ILE B 409 " --> pdb=" O TRP B 535 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP B 535 " --> pdb=" O ILE B 409 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 652 through 655 removed outlier: 3.524A pdb=" N GLN B 652 " --> pdb=" O VAL B 939 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 660 through 667 removed outlier: 3.532A pdb=" N MET B 663 " --> pdb=" O VAL B 929 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY B 688 " --> pdb=" O GLU B 932 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE B 691 " --> pdb=" O TRP B 882 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 673 through 681 removed outlier: 4.407A pdb=" N SER B 680 " --> pdb=" O HIS B 910 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N HIS B 910 " --> pdb=" O SER B 680 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA B 911 " --> pdb=" O PHE B 736 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE B 736 " --> pdb=" O ALA B 911 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ASP B 913 " --> pdb=" O ILE B 734 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ILE B 734 " --> pdb=" O ASP B 913 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR B 915 " --> pdb=" O VAL B 732 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL B 732 " --> pdb=" O THR B 915 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLU B 917 " --> pdb=" O LYS B 730 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 673 through 681 removed outlier: 4.407A pdb=" N SER B 680 " --> pdb=" O HIS B 910 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N HIS B 910 " --> pdb=" O SER B 680 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA B 911 " --> pdb=" O PHE B 736 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE B 736 " --> pdb=" O ALA B 911 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ASP B 913 " --> pdb=" O ILE B 734 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ILE B 734 " --> pdb=" O ASP B 913 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR B 915 " --> pdb=" O VAL B 732 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL B 732 " --> pdb=" O THR B 915 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLU B 917 " --> pdb=" O LYS B 730 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 766 through 767 removed outlier: 4.673A pdb=" N MET B 772 " --> pdb=" O VAL B 767 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 810 through 817 removed outlier: 3.623A pdb=" N GLN B 810 " --> pdb=" O LEU B 876 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 876 " --> pdb=" O GLN B 810 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 65 through 68 removed outlier: 6.879A pdb=" N ARG C 104 " --> pdb=" O ASP C 622 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE C 624 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASP C 102 " --> pdb=" O ILE C 624 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU C 626 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TYR C 100 " --> pdb=" O LEU C 626 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 65 through 68 removed outlier: 6.879A pdb=" N ARG C 104 " --> pdb=" O ASP C 622 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE C 624 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASP C 102 " --> pdb=" O ILE C 624 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU C 626 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TYR C 100 " --> pdb=" O LEU C 626 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 72 through 75 removed outlier: 3.861A pdb=" N ASP C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 94 through 95 Processing sheet with id=AE8, first strand: chain 'C' and resid 190 through 191 Processing sheet with id=AE9, first strand: chain 'C' and resid 246 through 247 Processing sheet with id=AF1, first strand: chain 'C' and resid 261 through 262 Processing sheet with id=AF2, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.647A pdb=" N GLN C 326 " --> pdb=" O SER C 309 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 336 through 337 Processing sheet with id=AF4, first strand: chain 'C' and resid 409 through 410 Processing sheet with id=AF5, first strand: chain 'C' and resid 420 through 421 removed outlier: 3.715A pdb=" N ASN C 420 " --> pdb=" O ILE C 473 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 652 through 655 removed outlier: 3.502A pdb=" N GLN C 652 " --> pdb=" O VAL C 939 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 660 through 667 removed outlier: 4.164A pdb=" N GLY C 688 " --> pdb=" O GLU C 932 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TRP C 882 " --> pdb=" O PHE C 691 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 673 through 681 removed outlier: 4.430A pdb=" N SER C 680 " --> pdb=" O HIS C 910 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N HIS C 910 " --> pdb=" O SER C 680 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA C 911 " --> pdb=" O PHE C 736 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N PHE C 736 " --> pdb=" O ALA C 911 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ASP C 913 " --> pdb=" O ILE C 734 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ILE C 734 " --> pdb=" O ASP C 913 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR C 915 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL C 732 " --> pdb=" O THR C 915 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLU C 917 " --> pdb=" O LYS C 730 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 673 through 681 removed outlier: 4.430A pdb=" N SER C 680 " --> pdb=" O HIS C 910 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N HIS C 910 " --> pdb=" O SER C 680 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA C 911 " --> pdb=" O PHE C 736 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N PHE C 736 " --> pdb=" O ALA C 911 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ASP C 913 " --> pdb=" O ILE C 734 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ILE C 734 " --> pdb=" O ASP C 913 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR C 915 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL C 732 " --> pdb=" O THR C 915 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLU C 917 " --> pdb=" O LYS C 730 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 766 through 767 removed outlier: 4.613A pdb=" N MET C 772 " --> pdb=" O VAL C 767 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 810 through 817 removed outlier: 3.651A pdb=" N GLN C 810 " --> pdb=" O LEU C 876 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C 876 " --> pdb=" O GLN C 810 " (cutoff:3.500A) 610 hydrogen bonds defined for protein. 1599 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: 4.15 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7163 1.35 - 1.46: 5570 1.46 - 1.58: 9492 1.58 - 1.70: 0 1.70 - 1.82: 199 Bond restraints: 22424 Sorted by residual: bond pdb=" C CYS A 422 " pdb=" N PHE A 423 " ideal model delta sigma weight residual 1.330 1.350 -0.020 1.47e-02 4.63e+03 1.88e+00 bond pdb=" C THR C 699 " pdb=" O THR C 699 " ideal model delta sigma weight residual 1.249 1.239 0.010 8.50e-03 1.38e+04 1.44e+00 bond pdb=" C ILE A 189 " pdb=" O ILE A 189 " ideal model delta sigma weight residual 1.231 1.243 -0.011 1.02e-02 9.61e+03 1.25e+00 bond pdb=" N GLY A 216 " pdb=" CA GLY A 216 " ideal model delta sigma weight residual 1.458 1.449 0.009 9.20e-03 1.18e+04 9.36e-01 bond pdb=" C THR C 954 " pdb=" N PRO C 955 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.38e-01 ... (remaining 22419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 30067 1.45 - 2.91: 359 2.91 - 4.36: 51 4.36 - 5.82: 10 5.82 - 7.27: 3 Bond angle restraints: 30490 Sorted by residual: angle pdb=" C CYS A 422 " pdb=" N PHE A 423 " pdb=" CA PHE A 423 " ideal model delta sigma weight residual 120.68 127.95 -7.27 1.52e+00 4.33e-01 2.29e+01 angle pdb=" N ILE B 15 " pdb=" CA ILE B 15 " pdb=" C ILE B 15 " ideal model delta sigma weight residual 111.81 108.12 3.69 8.60e-01 1.35e+00 1.84e+01 angle pdb=" N GLY B 186 " pdb=" CA GLY B 186 " pdb=" C GLY B 186 " ideal model delta sigma weight residual 110.29 113.74 -3.45 1.28e+00 6.10e-01 7.27e+00 angle pdb=" N ASN A 287 " pdb=" CA ASN A 287 " pdb=" C ASN A 287 " ideal model delta sigma weight residual 110.97 113.90 -2.93 1.09e+00 8.42e-01 7.21e+00 angle pdb=" N GLY A 315 " pdb=" CA GLY A 315 " pdb=" C GLY A 315 " ideal model delta sigma weight residual 111.16 115.80 -4.64 1.76e+00 3.23e-01 6.94e+00 ... (remaining 30485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.13: 12805 16.13 - 32.25: 423 32.25 - 48.38: 63 48.38 - 64.50: 11 64.50 - 80.63: 2 Dihedral angle restraints: 13304 sinusoidal: 5294 harmonic: 8010 Sorted by residual: 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 -162.22 -17.78 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ALA C 223 " pdb=" C ALA C 223 " pdb=" N ASP C 224 " pdb=" CA ASP C 224 " ideal model delta harmonic sigma weight residual 180.00 -163.44 -16.56 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA SER B 455 " pdb=" C SER B 455 " pdb=" N THR B 456 " pdb=" CA THR B 456 " ideal model delta harmonic sigma weight residual -180.00 -164.45 -15.55 0 5.00e+00 4.00e-02 9.68e+00 ... (remaining 13301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2018 0.030 - 0.059: 786 0.059 - 0.089: 225 0.089 - 0.118: 204 0.118 - 0.148: 11 Chirality restraints: 3244 Sorted by residual: chirality pdb=" CA THR A 954 " pdb=" N THR A 954 " pdb=" C THR A 954 " pdb=" CB THR A 954 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA ILE B 678 " pdb=" N ILE B 678 " pdb=" C ILE B 678 " pdb=" CB ILE B 678 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA ILE C 203 " pdb=" N ILE C 203 " pdb=" C ILE C 203 " pdb=" CB ILE C 203 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 3241 not shown) Planarity restraints: 4012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 418 " 0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO C 419 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 419 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 419 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 418 " 0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO B 419 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 419 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 419 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 665 " 0.019 5.00e-02 4.00e+02 2.91e-02 1.35e+00 pdb=" N PRO A 666 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 666 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 666 " 0.016 5.00e-02 4.00e+02 ... (remaining 4009 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1940 2.75 - 3.29: 20406 3.29 - 3.82: 34156 3.82 - 4.36: 41127 4.36 - 4.90: 73435 Nonbonded interactions: 171064 Sorted by model distance: nonbonded pdb=" OD1 ASN C 662 " pdb=" OH TYR C 928 " model vdw 2.211 3.040 nonbonded pdb=" OG SER B 278 " pdb=" O THR C 433 " model vdw 2.212 3.040 nonbonded pdb=" OD1 ASN A 662 " pdb=" OH TYR A 928 " model vdw 2.218 3.040 nonbonded pdb=" OD1 ASP A 55 " pdb=" OG1 THR A 637 " model vdw 2.239 3.040 nonbonded pdb=" OD1 ASN B 662 " pdb=" OH TYR B 928 " model vdw 2.240 3.040 ... (remaining 171059 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: 1.040 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: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.940 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 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 : 0.002 0.044 22424 Z= 0.088 Angle : 0.441 7.274 30490 Z= 0.250 Chirality : 0.041 0.148 3244 Planarity : 0.003 0.032 4012 Dihedral : 8.165 80.627 8180 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.13 % Favored : 95.83 % Rotamer: Outliers : 1.77 % Allowed : 4.76 % Favored : 93.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.16), residues: 2712 helix: 1.68 (0.32), residues: 310 sheet: 1.03 (0.23), residues: 561 loop : -0.99 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 687 TYR 0.009 0.001 TYR C 23 PHE 0.006 0.001 PHE A 886 TRP 0.011 0.001 TRP C 220 HIS 0.002 0.000 HIS B 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00160 / 0.09 (22424) covalent geometry : angle 0.44077 / 0.25 (30490) hydrogen bonds : bond 0.25708 / 17.22 ( 552) hydrogen bonds : angle 9.30440 / 6.34 ( 1599) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 805 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.8229 (t80) cc_final: 0.7984 (t80) REVERT: A 258 VAL cc_start: 0.6189 (t) cc_final: 0.5900 (m) REVERT: A 272 MET cc_start: 0.7551 (mtm) cc_final: 0.7319 (mtm) REVERT: A 471 MET cc_start: 0.7184 (mtp) cc_final: 0.6971 (mtm) REVERT: A 618 SER cc_start: 0.8312 (t) cc_final: 0.8034 (p) REVERT: A 753 GLU cc_start: 0.7887 (pt0) cc_final: 0.7634 (pt0) REVERT: A 830 ILE cc_start: 0.7601 (mp) cc_final: 0.7153 (tt) REVERT: A 870 ILE cc_start: 0.6981 (tt) cc_final: 0.6750 (pt) REVERT: A 912 LEU cc_start: 0.8304 (tp) cc_final: 0.8073 (tt) REVERT: A 947 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7771 (tt) REVERT: B 31 PHE cc_start: 0.8221 (t80) cc_final: 0.7841 (t80) REVERT: B 33 ARG cc_start: 0.8416 (ttp-170) cc_final: 0.8191 (ttp-170) REVERT: B 42 ASN cc_start: 0.7988 (p0) cc_final: 0.7757 (m110) REVERT: B 168 LYS cc_start: 0.5758 (mtpt) cc_final: 0.3301 (mtpp) REVERT: B 171 VAL cc_start: 0.7670 (t) cc_final: 0.7420 (p) REVERT: B 182 ILE cc_start: 0.7953 (mt) cc_final: 0.7662 (mt) REVERT: B 272 MET cc_start: 0.7690 (mtm) cc_final: 0.7394 (mtt) REVERT: B 290 PRO cc_start: 0.7719 (Cg_exo) cc_final: 0.7420 (Cg_endo) REVERT: B 292 VAL cc_start: 0.7331 (t) cc_final: 0.7034 (p) REVERT: B 355 VAL cc_start: 0.8295 (t) cc_final: 0.7983 (p) REVERT: B 498 TYR cc_start: 0.7256 (p90) cc_final: 0.6932 (p90) REVERT: B 600 VAL cc_start: 0.8313 (t) cc_final: 0.7980 (m) REVERT: B 606 SER cc_start: 0.7918 (t) cc_final: 0.7355 (p) REVERT: B 608 LEU cc_start: 0.8488 (mp) cc_final: 0.8264 (mt) REVERT: B 623 SER cc_start: 0.8518 (m) cc_final: 0.8191 (p) REVERT: B 732 VAL cc_start: 0.8437 (t) cc_final: 0.8042 (p) REVERT: B 765 TYR cc_start: 0.7528 (m-10) cc_final: 0.7128 (m-10) REVERT: B 817 VAL cc_start: 0.7108 (t) cc_final: 0.6811 (p) REVERT: B 830 ILE cc_start: 0.7524 (mp) cc_final: 0.7128 (tp) REVERT: B 889 ASN cc_start: 0.8041 (p0) cc_final: 0.7715 (p0) REVERT: B 912 LEU cc_start: 0.8160 (tp) cc_final: 0.7960 (tt) REVERT: B 947 ILE cc_start: 0.8182 (mm) cc_final: 0.7642 (tt) REVERT: C 24 LEU cc_start: 0.8638 (mt) cc_final: 0.8427 (mt) REVERT: C 104 ARG cc_start: 0.7870 (mtm180) cc_final: 0.7558 (mtm-85) REVERT: C 169 THR cc_start: 0.6019 (p) cc_final: 0.5677 (p) REVERT: C 231 ARG cc_start: 0.7915 (mtp180) cc_final: 0.7681 (mtp85) REVERT: C 267 GLU cc_start: 0.5314 (pt0) cc_final: 0.4388 (pt0) REVERT: C 434 PHE cc_start: 0.6494 (m-80) cc_final: 0.6252 (m-80) REVERT: C 600 VAL cc_start: 0.8241 (t) cc_final: 0.8015 (m) REVERT: C 701 SER cc_start: 0.6466 (m) cc_final: 0.6209 (t) REVERT: C 754 PHE cc_start: 0.7736 (m-80) cc_final: 0.7369 (m-80) REVERT: C 818 ASP cc_start: 0.7323 (t0) cc_final: 0.6841 (t70) REVERT: C 821 LYS cc_start: 0.6992 (mttt) cc_final: 0.6685 (mttp) outliers start: 42 outliers final: 15 residues processed: 828 average time/residue: 0.1567 time to fit residues: 198.4661 Evaluate side-chains 685 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 669 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 848 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN A 326 GLN ** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 ASN A 572 GLN A 650 ASN A 851 GLN B 256 GLN B 273 GLN B 300 ASN B 348 ASN B 575 GLN B 647 ASN B 673 ASN B 790 GLN B 851 GLN C 256 GLN C 263 ASN C 269 GLN C 370 GLN C 412 HIS C 420 ASN C 548 HIS C 570 HIS C 682 ASN C 836 ASN C 851 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.103164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.090354 restraints weight = 32346.896| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.82 r_work: 0.2890 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22424 Z= 0.149 Angle : 0.537 6.560 30490 Z= 0.287 Chirality : 0.045 0.183 3244 Planarity : 0.004 0.048 4012 Dihedral : 5.043 56.858 3050 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.42 % Favored : 94.54 % Rotamer: Outliers : 2.57 % Allowed : 11.42 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.16), residues: 2712 helix: 1.58 (0.32), residues: 310 sheet: 0.99 (0.22), residues: 580 loop : -1.18 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 518 TYR 0.015 0.001 TYR C 710 PHE 0.017 0.002 PHE C 31 TRP 0.016 0.001 TRP C 220 HIS 0.005 0.001 HIS C 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (22424) covalent geometry : angle 0.53679 / 0.29 (30490) hydrogen bonds : bond 0.04703 / 3.10 ( 552) hydrogen bonds : angle 6.12060 / 4.22 ( 1599) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 682 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7979 (ttp-170) cc_final: 0.7758 (ttp-170) REVERT: A 74 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7691 (mm-30) REVERT: A 138 ASN cc_start: 0.7554 (m-40) cc_final: 0.7281 (m-40) REVERT: A 218 SER cc_start: 0.8159 (m) cc_final: 0.7697 (p) REVERT: A 591 THR cc_start: 0.8530 (t) cc_final: 0.8195 (m) REVERT: A 651 ASP cc_start: 0.7702 (m-30) cc_final: 0.7437 (m-30) REVERT: A 710 TYR cc_start: 0.8471 (t80) cc_final: 0.8148 (t80) REVERT: A 753 GLU cc_start: 0.7514 (pt0) cc_final: 0.6954 (pt0) REVERT: A 806 PHE cc_start: 0.8690 (t80) cc_final: 0.8365 (t80) REVERT: A 823 LYS cc_start: 0.7668 (mmtt) cc_final: 0.7415 (mmtt) REVERT: A 881 LEU cc_start: 0.8586 (mp) cc_final: 0.8358 (mt) REVERT: A 912 LEU cc_start: 0.8477 (tp) cc_final: 0.8267 (tt) REVERT: A 926 LEU cc_start: 0.8537 (mt) cc_final: 0.8304 (mt) REVERT: B 24 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8305 (mt) REVERT: B 31 PHE cc_start: 0.8280 (t80) cc_final: 0.7664 (t80) REVERT: B 42 ASN cc_start: 0.8114 (p0) cc_final: 0.7900 (m110) REVERT: B 43 ASN cc_start: 0.7794 (t0) cc_final: 0.7592 (t0) REVERT: B 61 SER cc_start: 0.8368 (m) cc_final: 0.8068 (t) REVERT: B 272 MET cc_start: 0.8581 (mtm) cc_final: 0.8328 (mtt) REVERT: B 292 VAL cc_start: 0.8386 (t) cc_final: 0.7946 (p) REVERT: B 600 VAL cc_start: 0.8544 (t) cc_final: 0.8277 (m) REVERT: B 606 SER cc_start: 0.8608 (t) cc_final: 0.8277 (p) REVERT: B 623 SER cc_start: 0.8547 (m) cc_final: 0.8182 (p) REVERT: B 731 LYS cc_start: 0.8735 (pttt) cc_final: 0.8520 (pttt) REVERT: B 740 VAL cc_start: 0.7941 (t) cc_final: 0.7586 (m) REVERT: B 753 GLU cc_start: 0.7628 (pm20) cc_final: 0.7130 (pm20) REVERT: B 755 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7639 (mm-30) REVERT: B 821 LYS cc_start: 0.8608 (mmtt) cc_final: 0.8319 (mmtp) REVERT: B 823 LYS cc_start: 0.7844 (mmtt) cc_final: 0.7526 (mmtt) REVERT: B 883 ARG cc_start: 0.8286 (mmt90) cc_final: 0.8024 (mmt180) REVERT: B 912 LEU cc_start: 0.8292 (tp) cc_final: 0.8069 (tt) REVERT: B 917 GLU cc_start: 0.7876 (tt0) cc_final: 0.7572 (tt0) REVERT: B 935 ASP cc_start: 0.8208 (t0) cc_final: 0.7916 (t0) REVERT: B 947 ILE cc_start: 0.8309 (mm) cc_final: 0.8000 (tt) REVERT: C 14 HIS cc_start: 0.8509 (m-70) cc_final: 0.8277 (m90) REVERT: C 24 LEU cc_start: 0.8552 (mt) cc_final: 0.8308 (mt) REVERT: C 134 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7936 (mt-10) REVERT: C 167 LYS cc_start: 0.8101 (ptpt) cc_final: 0.7804 (ptpt) REVERT: C 291 THR cc_start: 0.8359 (p) cc_final: 0.8094 (m) REVERT: C 454 ASP cc_start: 0.6963 (t70) cc_final: 0.6697 (t0) REVERT: C 471 MET cc_start: 0.8600 (mtp) cc_final: 0.8339 (mtt) REVERT: C 586 LEU cc_start: 0.8482 (mm) cc_final: 0.8241 (mt) REVERT: C 686 PHE cc_start: 0.8457 (t80) cc_final: 0.8250 (t80) REVERT: C 701 SER cc_start: 0.7712 (m) cc_final: 0.7393 (t) REVERT: C 730 LYS cc_start: 0.8516 (mttm) cc_final: 0.8307 (mttm) REVERT: C 740 VAL cc_start: 0.7930 (t) cc_final: 0.7669 (m) REVERT: C 752 ASN cc_start: 0.8316 (m-40) cc_final: 0.8101 (m110) REVERT: C 754 PHE cc_start: 0.8213 (m-80) cc_final: 0.7410 (m-80) REVERT: C 777 PHE cc_start: 0.8425 (t80) cc_final: 0.8098 (t80) REVERT: C 821 LYS cc_start: 0.8624 (mttt) cc_final: 0.8162 (mttt) REVERT: C 836 ASN cc_start: 0.8409 (m110) cc_final: 0.8089 (m-40) outliers start: 61 outliers final: 43 residues processed: 710 average time/residue: 0.1482 time to fit residues: 162.0402 Evaluate side-chains 677 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 633 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 495 LYS Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 840 VAL Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 903 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 1 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 26 optimal weight: 0.0370 chunk 85 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 69 optimal weight: 0.1980 chunk 38 optimal weight: 3.9990 chunk 214 optimal weight: 0.0070 chunk 216 optimal weight: 4.9990 chunk 265 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 overall best weight: 1.0480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 379 GLN A 487 ASN A 572 GLN A 650 ASN B 273 GLN B 502 ASN B 570 HIS B 647 ASN B 790 GLN C 137 GLN C 370 GLN C 548 HIS C 572 GLN C 650 ASN C 673 ASN C 682 ASN C 769 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.102932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.090147 restraints weight = 32556.581| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.83 r_work: 0.2869 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22424 Z= 0.119 Angle : 0.508 6.012 30490 Z= 0.270 Chirality : 0.044 0.184 3244 Planarity : 0.004 0.059 4012 Dihedral : 4.834 55.213 3040 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.35 % Favored : 94.62 % Rotamer: Outliers : 2.91 % Allowed : 12.44 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.16), residues: 2712 helix: 1.48 (0.31), residues: 316 sheet: 0.88 (0.22), residues: 580 loop : -1.19 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 518 TYR 0.016 0.001 TYR B 798 PHE 0.014 0.001 PHE C 31 TRP 0.014 0.001 TRP C 220 HIS 0.005 0.001 HIS C 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (22424) covalent geometry : angle 0.50792 / 0.27 (30490) hydrogen bonds : bond 0.03878 / 2.55 ( 552) hydrogen bonds : angle 5.64854 / 3.90 ( 1599) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 640 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.7931 (pt0) cc_final: 0.7662 (mt-10) REVERT: A 167 LYS cc_start: 0.7868 (mmmt) cc_final: 0.7418 (mmmt) REVERT: A 207 LYS cc_start: 0.8600 (ttpp) cc_final: 0.8394 (ttpp) REVERT: A 218 SER cc_start: 0.8131 (m) cc_final: 0.7682 (p) REVERT: A 297 GLU cc_start: 0.7229 (pt0) cc_final: 0.6967 (pt0) REVERT: A 484 LEU cc_start: 0.8325 (mt) cc_final: 0.8123 (mp) REVERT: A 591 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8223 (m) REVERT: A 651 ASP cc_start: 0.7704 (m-30) cc_final: 0.7390 (m-30) REVERT: A 710 TYR cc_start: 0.8454 (t80) cc_final: 0.8212 (t80) REVERT: A 753 GLU cc_start: 0.7516 (pt0) cc_final: 0.6943 (pt0) REVERT: A 786 ASN cc_start: 0.8340 (m-40) cc_final: 0.8089 (m-40) REVERT: A 823 LYS cc_start: 0.7672 (mmtt) cc_final: 0.7368 (mmtt) REVERT: A 851 GLN cc_start: 0.8187 (pt0) cc_final: 0.7931 (pt0) REVERT: A 881 LEU cc_start: 0.8562 (mp) cc_final: 0.8320 (mt) REVERT: A 912 LEU cc_start: 0.8469 (tp) cc_final: 0.8264 (tt) REVERT: A 926 LEU cc_start: 0.8537 (mt) cc_final: 0.8315 (mt) REVERT: A 948 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7529 (mp0) REVERT: B 24 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8304 (mt) REVERT: B 31 PHE cc_start: 0.8292 (t80) cc_final: 0.7639 (t80) REVERT: B 42 ASN cc_start: 0.8157 (p0) cc_final: 0.7872 (m110) REVERT: B 43 ASN cc_start: 0.7886 (t0) cc_final: 0.7641 (t0) REVERT: B 61 SER cc_start: 0.8373 (m) cc_final: 0.8059 (t) REVERT: B 63 ARG cc_start: 0.8236 (mtt180) cc_final: 0.8032 (mtt90) REVERT: B 218 SER cc_start: 0.8464 (m) cc_final: 0.8088 (p) REVERT: B 272 MET cc_start: 0.8539 (mtm) cc_final: 0.8275 (mtt) REVERT: B 292 VAL cc_start: 0.8402 (t) cc_final: 0.7922 (p) REVERT: B 320 LYS cc_start: 0.8571 (tttp) cc_final: 0.8347 (tttm) REVERT: B 498 TYR cc_start: 0.8544 (p90) cc_final: 0.8149 (p90) REVERT: B 600 VAL cc_start: 0.8549 (t) cc_final: 0.8265 (m) REVERT: B 606 SER cc_start: 0.8599 (t) cc_final: 0.8313 (p) REVERT: B 623 SER cc_start: 0.8529 (m) cc_final: 0.8172 (p) REVERT: B 663 MET cc_start: 0.8187 (mmm) cc_final: 0.7830 (mmm) REVERT: B 730 LYS cc_start: 0.8478 (mttp) cc_final: 0.8195 (mttp) REVERT: B 753 GLU cc_start: 0.7644 (pm20) cc_final: 0.7121 (pm20) REVERT: B 755 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7624 (mm-30) REVERT: B 821 LYS cc_start: 0.8589 (mmtt) cc_final: 0.8254 (mmtp) REVERT: B 823 LYS cc_start: 0.7832 (mmtt) cc_final: 0.7537 (mmtt) REVERT: B 912 LEU cc_start: 0.8280 (tp) cc_final: 0.8058 (tt) REVERT: B 935 ASP cc_start: 0.8231 (t0) cc_final: 0.7914 (t0) REVERT: B 944 ARG cc_start: 0.7878 (ptm160) cc_final: 0.7630 (ptm160) REVERT: B 947 ILE cc_start: 0.8297 (mm) cc_final: 0.8037 (tt) REVERT: C 14 HIS cc_start: 0.8518 (m-70) cc_final: 0.8275 (m90) REVERT: C 134 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7905 (mt-10) REVERT: C 233 LEU cc_start: 0.8219 (mt) cc_final: 0.7858 (mt) REVERT: C 454 ASP cc_start: 0.6955 (t70) cc_final: 0.6695 (t0) REVERT: C 498 TYR cc_start: 0.8572 (p90) cc_final: 0.8161 (p90) REVERT: C 586 LEU cc_start: 0.8497 (mm) cc_final: 0.8213 (mt) REVERT: C 642 GLU cc_start: 0.7599 (tp30) cc_final: 0.7202 (tp30) REVERT: C 686 PHE cc_start: 0.8464 (t80) cc_final: 0.8248 (t80) REVERT: C 701 SER cc_start: 0.7729 (m) cc_final: 0.7382 (t) REVERT: C 730 LYS cc_start: 0.8480 (mttm) cc_final: 0.8237 (mttm) REVERT: C 740 VAL cc_start: 0.7921 (t) cc_final: 0.7605 (m) REVERT: C 752 ASN cc_start: 0.8382 (m-40) cc_final: 0.8163 (m110) REVERT: C 754 PHE cc_start: 0.8279 (m-80) cc_final: 0.7553 (m-80) REVERT: C 777 PHE cc_start: 0.8372 (t80) cc_final: 0.8129 (t80) REVERT: C 800 ASP cc_start: 0.7996 (t0) cc_final: 0.7574 (t0) REVERT: C 821 LYS cc_start: 0.8405 (mttt) cc_final: 0.8162 (mtpm) REVERT: C 935 ASP cc_start: 0.8244 (t0) cc_final: 0.8042 (t0) REVERT: C 952 LEU cc_start: 0.8641 (tp) cc_final: 0.8367 (tt) outliers start: 69 outliers final: 44 residues processed: 671 average time/residue: 0.1529 time to fit residues: 158.4247 Evaluate side-chains 669 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 623 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 495 LYS Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 897 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 840 VAL Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 903 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 102 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 5 optimal weight: 0.0370 chunk 217 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 109 optimal weight: 0.0070 chunk 114 optimal weight: 6.9990 chunk 246 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 overall best weight: 2.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 ASN A 502 ASN A 572 GLN A 650 ASN ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN B 273 GLN B 790 GLN C 370 GLN ** C 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 ASN C 682 ASN C 836 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.099703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.087075 restraints weight = 32762.383| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.82 r_work: 0.2824 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 22424 Z= 0.251 Angle : 0.602 6.650 30490 Z= 0.324 Chirality : 0.048 0.194 3244 Planarity : 0.005 0.069 4012 Dihedral : 5.426 56.013 3038 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.12 % Favored : 92.85 % Rotamer: Outliers : 3.33 % Allowed : 13.41 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.16), residues: 2712 helix: 1.11 (0.30), residues: 322 sheet: 0.80 (0.22), residues: 562 loop : -1.40 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 92 TYR 0.020 0.002 TYR C 710 PHE 0.018 0.002 PHE A 754 TRP 0.014 0.002 TRP A 882 HIS 0.008 0.002 HIS C 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.25 (22424) covalent geometry : angle 0.60210 / 0.32 (30490) hydrogen bonds : bond 0.05074 / 3.37 ( 552) hydrogen bonds : angle 5.66351 / 3.93 ( 1599) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 648 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 TYR cc_start: 0.7834 (p90) cc_final: 0.7432 (p90) REVERT: A 92 ARG cc_start: 0.8496 (mtt-85) cc_final: 0.8243 (mtt90) REVERT: A 104 ARG cc_start: 0.8314 (ptt180) cc_final: 0.8079 (ptt180) REVERT: A 134 GLU cc_start: 0.7956 (pt0) cc_final: 0.7657 (mt-10) REVERT: A 167 LYS cc_start: 0.7971 (mmmt) cc_final: 0.7495 (mmmt) REVERT: A 207 LYS cc_start: 0.8710 (ttpp) cc_final: 0.8420 (ttpp) REVERT: A 217 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6760 (mt-10) REVERT: A 218 SER cc_start: 0.8248 (m) cc_final: 0.7759 (p) REVERT: A 231 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7468 (ptm160) REVERT: A 297 GLU cc_start: 0.7273 (pt0) cc_final: 0.6521 (pt0) REVERT: A 591 THR cc_start: 0.8547 (t) cc_final: 0.8222 (m) REVERT: A 651 ASP cc_start: 0.7628 (m-30) cc_final: 0.7311 (m-30) REVERT: A 753 GLU cc_start: 0.7562 (pt0) cc_final: 0.7013 (pt0) REVERT: A 786 ASN cc_start: 0.8405 (m-40) cc_final: 0.8142 (m-40) REVERT: A 823 LYS cc_start: 0.7762 (mmtt) cc_final: 0.7449 (mmtt) REVERT: A 851 GLN cc_start: 0.8220 (pt0) cc_final: 0.7970 (pt0) REVERT: A 881 LEU cc_start: 0.8563 (mp) cc_final: 0.8298 (mt) REVERT: A 912 LEU cc_start: 0.8452 (tp) cc_final: 0.8250 (tt) REVERT: B 31 PHE cc_start: 0.8367 (t80) cc_final: 0.8078 (t80) REVERT: B 38 TYR cc_start: 0.7829 (p90) cc_final: 0.7619 (p90) REVERT: B 61 SER cc_start: 0.8556 (m) cc_final: 0.8252 (t) REVERT: B 181 LYS cc_start: 0.8067 (ttpp) cc_final: 0.7651 (pttm) REVERT: B 320 LYS cc_start: 0.8589 (tttp) cc_final: 0.8187 (tttm) REVERT: B 370 GLN cc_start: 0.8258 (tp40) cc_final: 0.8057 (tp40) REVERT: B 417 GLU cc_start: 0.8008 (mp0) cc_final: 0.7787 (mp0) REVERT: B 555 ARG cc_start: 0.8392 (ttp-170) cc_final: 0.8163 (mtp180) REVERT: B 600 VAL cc_start: 0.8561 (t) cc_final: 0.8266 (m) REVERT: B 606 SER cc_start: 0.8582 (t) cc_final: 0.8320 (p) REVERT: B 623 SER cc_start: 0.8524 (m) cc_final: 0.8191 (p) REVERT: B 639 SER cc_start: 0.8010 (t) cc_final: 0.7765 (m) REVERT: B 663 MET cc_start: 0.8195 (mmm) cc_final: 0.7898 (mmm) REVERT: B 753 GLU cc_start: 0.7604 (pm20) cc_final: 0.7132 (pm20) REVERT: B 755 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7618 (mm-30) REVERT: B 821 LYS cc_start: 0.8630 (mmtt) cc_final: 0.8259 (mmtp) REVERT: B 823 LYS cc_start: 0.7914 (mmtt) cc_final: 0.7569 (mmtt) REVERT: B 935 ASP cc_start: 0.8300 (t0) cc_final: 0.8045 (t0) REVERT: C 14 HIS cc_start: 0.8537 (m-70) cc_final: 0.8291 (m90) REVERT: C 64 LEU cc_start: 0.8278 (mt) cc_final: 0.8058 (mp) REVERT: C 92 ARG cc_start: 0.8172 (mtt90) cc_final: 0.7879 (mtt90) REVERT: C 212 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6944 (mm-30) REVERT: C 233 LEU cc_start: 0.8177 (mt) cc_final: 0.7906 (mt) REVERT: C 350 THR cc_start: 0.8525 (m) cc_final: 0.8237 (p) REVERT: C 501 THR cc_start: 0.8150 (m) cc_final: 0.7916 (t) REVERT: C 586 LEU cc_start: 0.8623 (mm) cc_final: 0.8354 (mt) REVERT: C 642 GLU cc_start: 0.7600 (tp30) cc_final: 0.7079 (tp30) REVERT: C 686 PHE cc_start: 0.8497 (t80) cc_final: 0.8212 (t80) REVERT: C 701 SER cc_start: 0.7802 (m) cc_final: 0.7480 (t) REVERT: C 740 VAL cc_start: 0.7979 (t) cc_final: 0.7592 (m) REVERT: C 746 ASP cc_start: 0.7181 (OUTLIER) cc_final: 0.6958 (t70) REVERT: C 797 SER cc_start: 0.8384 (m) cc_final: 0.8074 (p) REVERT: C 800 ASP cc_start: 0.8001 (t0) cc_final: 0.7650 (t0) REVERT: C 821 LYS cc_start: 0.8483 (mttt) cc_final: 0.8128 (mtpp) outliers start: 79 outliers final: 54 residues processed: 685 average time/residue: 0.1439 time to fit residues: 153.1750 Evaluate side-chains 680 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 623 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 495 LYS Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 897 THR Chi-restraints excluded: chain B residue 917 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 167 LYS Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 541 ASP Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 746 ASP Chi-restraints excluded: chain C residue 840 VAL Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 903 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 143 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 131 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 238 optimal weight: 0.0000 chunk 29 optimal weight: 0.7980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A 502 ASN A 572 GLN A 650 ASN ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 ASN B 572 GLN C 370 GLN C 548 HIS C 650 ASN C 682 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.102132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.089438 restraints weight = 32441.289| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.83 r_work: 0.2883 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22424 Z= 0.096 Angle : 0.495 6.528 30490 Z= 0.262 Chirality : 0.043 0.191 3244 Planarity : 0.004 0.057 4012 Dihedral : 4.970 56.080 3038 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.09 % Favored : 94.87 % Rotamer: Outliers : 3.08 % Allowed : 15.35 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.16), residues: 2712 helix: 1.48 (0.31), residues: 315 sheet: 0.61 (0.22), residues: 571 loop : -1.31 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 92 TYR 0.022 0.001 TYR B 498 PHE 0.012 0.001 PHE A 654 TRP 0.012 0.001 TRP C 220 HIS 0.003 0.001 HIS C 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (22424) covalent geometry : angle 0.49496 / 0.26 (30490) hydrogen bonds : bond 0.03191 / 2.11 ( 552) hydrogen bonds : angle 5.37578 / 3.70 ( 1599) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 634 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TYR cc_start: 0.7829 (p90) cc_final: 0.7409 (p90) REVERT: A 53 THR cc_start: 0.8443 (t) cc_final: 0.8136 (m) REVERT: A 167 LYS cc_start: 0.7996 (mmmt) cc_final: 0.7566 (mmmt) REVERT: A 207 LYS cc_start: 0.8580 (ttpp) cc_final: 0.8275 (ttpp) REVERT: A 218 SER cc_start: 0.8207 (m) cc_final: 0.7755 (p) REVERT: A 297 GLU cc_start: 0.7208 (pt0) cc_final: 0.6920 (pt0) REVERT: A 392 PHE cc_start: 0.8512 (t80) cc_final: 0.8173 (t80) REVERT: A 591 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8210 (m) REVERT: A 651 ASP cc_start: 0.7576 (m-30) cc_final: 0.7231 (m-30) REVERT: A 662 ASN cc_start: 0.7965 (m110) cc_final: 0.7645 (m-40) REVERT: A 730 LYS cc_start: 0.8694 (ttmm) cc_final: 0.8439 (ttmm) REVERT: A 753 GLU cc_start: 0.7505 (pt0) cc_final: 0.6965 (pt0) REVERT: A 786 ASN cc_start: 0.8340 (m-40) cc_final: 0.8079 (m-40) REVERT: A 823 LYS cc_start: 0.7740 (mmtt) cc_final: 0.7440 (mmtt) REVERT: A 851 GLN cc_start: 0.8184 (pt0) cc_final: 0.7918 (pt0) REVERT: A 881 LEU cc_start: 0.8574 (mp) cc_final: 0.8293 (mt) REVERT: A 912 LEU cc_start: 0.8452 (tp) cc_final: 0.8239 (tt) REVERT: A 928 TYR cc_start: 0.8571 (t80) cc_final: 0.8262 (t80) REVERT: A 948 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7434 (mp0) REVERT: B 31 PHE cc_start: 0.8354 (t80) cc_final: 0.7768 (t80) REVERT: B 38 TYR cc_start: 0.7789 (p90) cc_final: 0.7513 (p90) REVERT: B 61 SER cc_start: 0.8403 (m) cc_final: 0.8118 (t) REVERT: B 181 LYS cc_start: 0.8100 (ttpp) cc_final: 0.7652 (pttm) REVERT: B 218 SER cc_start: 0.8483 (m) cc_final: 0.8062 (p) REVERT: B 273 GLN cc_start: 0.8492 (mt0) cc_final: 0.8239 (mt0) REVERT: B 320 LYS cc_start: 0.8585 (tttp) cc_final: 0.8369 (tttm) REVERT: B 572 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7462 (mt0) REVERT: B 600 VAL cc_start: 0.8534 (t) cc_final: 0.8270 (m) REVERT: B 606 SER cc_start: 0.8580 (t) cc_final: 0.8315 (p) REVERT: B 623 SER cc_start: 0.8505 (m) cc_final: 0.8169 (p) REVERT: B 753 GLU cc_start: 0.7641 (pm20) cc_final: 0.7146 (pm20) REVERT: B 755 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7572 (mm-30) REVERT: B 821 LYS cc_start: 0.8650 (mmtt) cc_final: 0.8249 (mmtp) REVERT: B 823 LYS cc_start: 0.7870 (mmtt) cc_final: 0.7529 (mmtt) REVERT: B 935 ASP cc_start: 0.8260 (t0) cc_final: 0.7959 (t0) REVERT: C 14 HIS cc_start: 0.8523 (m-70) cc_final: 0.8271 (m90) REVERT: C 80 TYR cc_start: 0.8505 (p90) cc_final: 0.8220 (p90) REVERT: C 92 ARG cc_start: 0.8166 (mtt90) cc_final: 0.7888 (mtt90) REVERT: C 212 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6864 (mm-30) REVERT: C 233 LEU cc_start: 0.8168 (mt) cc_final: 0.7800 (mt) REVERT: C 236 THR cc_start: 0.8364 (m) cc_final: 0.8136 (p) REVERT: C 454 ASP cc_start: 0.6937 (t70) cc_final: 0.6673 (t0) REVERT: C 498 TYR cc_start: 0.8604 (p90) cc_final: 0.8281 (p90) REVERT: C 501 THR cc_start: 0.8063 (m) cc_final: 0.7791 (t) REVERT: C 586 LEU cc_start: 0.8542 (mm) cc_final: 0.8139 (mt) REVERT: C 642 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7055 (tp30) REVERT: C 686 PHE cc_start: 0.8470 (t80) cc_final: 0.8269 (t80) REVERT: C 698 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7889 (mt-10) REVERT: C 701 SER cc_start: 0.7816 (m) cc_final: 0.7426 (t) REVERT: C 740 VAL cc_start: 0.7951 (t) cc_final: 0.7576 (m) REVERT: C 746 ASP cc_start: 0.7095 (OUTLIER) cc_final: 0.6861 (t70) REVERT: C 777 PHE cc_start: 0.8401 (t80) cc_final: 0.8113 (t80) REVERT: C 797 SER cc_start: 0.8387 (m) cc_final: 0.8044 (p) REVERT: C 800 ASP cc_start: 0.7925 (t0) cc_final: 0.7637 (t0) REVERT: C 952 LEU cc_start: 0.8665 (tp) cc_final: 0.8410 (tt) outliers start: 73 outliers final: 48 residues processed: 666 average time/residue: 0.1647 time to fit residues: 169.3627 Evaluate side-chains 675 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 623 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 745 ASN Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 897 THR Chi-restraints excluded: chain B residue 917 GLU Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 642 GLU Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 746 ASP Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 903 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 241 optimal weight: 7.9990 chunk 172 optimal weight: 0.0970 chunk 57 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 218 optimal weight: 0.0000 chunk 164 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 181 optimal weight: 0.0770 chunk 208 optimal weight: 4.9990 chunk 254 optimal weight: 0.9980 chunk 239 optimal weight: 7.9990 overall best weight: 0.3940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 ASN A 572 GLN A 635 HIS A 650 ASN ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 ASN B 572 GLN C 131 ASN C 548 HIS C 650 ASN C 682 ASN C 752 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.104158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.091342 restraints weight = 32698.172| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.84 r_work: 0.2905 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22424 Z= 0.083 Angle : 0.475 7.963 30490 Z= 0.249 Chirality : 0.043 0.180 3244 Planarity : 0.004 0.058 4012 Dihedral : 4.736 56.070 3038 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.49 % Favored : 94.47 % Rotamer: Outliers : 2.95 % Allowed : 15.89 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.16), residues: 2712 helix: 1.43 (0.31), residues: 328 sheet: 0.60 (0.22), residues: 572 loop : -1.22 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 92 TYR 0.021 0.001 TYR B 498 PHE 0.014 0.001 PHE A 654 TRP 0.011 0.001 TRP A 220 HIS 0.005 0.001 HIS C 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.08 (22424) covalent geometry : angle 0.47525 / 0.25 (30490) hydrogen bonds : bond 0.02856 / 1.89 ( 552) hydrogen bonds : angle 5.19650 / 3.56 ( 1599) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 627 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TYR cc_start: 0.7801 (p90) cc_final: 0.7320 (p90) REVERT: A 53 THR cc_start: 0.8438 (t) cc_final: 0.8113 (m) REVERT: A 167 LYS cc_start: 0.8004 (mmmt) cc_final: 0.7678 (mmmt) REVERT: A 207 LYS cc_start: 0.8548 (ttpp) cc_final: 0.8240 (ttpp) REVERT: A 218 SER cc_start: 0.8189 (m) cc_final: 0.7731 (p) REVERT: A 297 GLU cc_start: 0.7208 (pt0) cc_final: 0.6936 (pt0) REVERT: A 392 PHE cc_start: 0.8505 (t80) cc_final: 0.8168 (t80) REVERT: A 591 THR cc_start: 0.8460 (OUTLIER) cc_final: 0.8202 (m) REVERT: A 651 ASP cc_start: 0.7587 (m-30) cc_final: 0.7223 (m-30) REVERT: A 662 ASN cc_start: 0.7998 (m110) cc_final: 0.7694 (m-40) REVERT: A 753 GLU cc_start: 0.7440 (pt0) cc_final: 0.6918 (pt0) REVERT: A 786 ASN cc_start: 0.8339 (m-40) cc_final: 0.8071 (m-40) REVERT: A 823 LYS cc_start: 0.7700 (mmtt) cc_final: 0.7411 (mmtt) REVERT: A 851 GLN cc_start: 0.8181 (pt0) cc_final: 0.7917 (pt0) REVERT: A 881 LEU cc_start: 0.8586 (mp) cc_final: 0.8297 (mt) REVERT: A 912 LEU cc_start: 0.8469 (tp) cc_final: 0.8257 (tt) REVERT: A 928 TYR cc_start: 0.8562 (t80) cc_final: 0.8284 (t80) REVERT: A 948 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7470 (mp0) REVERT: B 31 PHE cc_start: 0.8309 (t80) cc_final: 0.7683 (t80) REVERT: B 38 TYR cc_start: 0.7774 (p90) cc_final: 0.7446 (p90) REVERT: B 61 SER cc_start: 0.8377 (m) cc_final: 0.8092 (t) REVERT: B 99 THR cc_start: 0.8421 (m) cc_final: 0.8123 (p) REVERT: B 181 LYS cc_start: 0.8140 (ttpp) cc_final: 0.7707 (pttm) REVERT: B 462 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6829 (mm-30) REVERT: B 555 ARG cc_start: 0.8331 (ttp-170) cc_final: 0.8120 (mtp180) REVERT: B 572 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7444 (mt0) REVERT: B 600 VAL cc_start: 0.8521 (t) cc_final: 0.8277 (m) REVERT: B 606 SER cc_start: 0.8585 (t) cc_final: 0.8300 (p) REVERT: B 623 SER cc_start: 0.8500 (m) cc_final: 0.8163 (p) REVERT: B 753 GLU cc_start: 0.7640 (pm20) cc_final: 0.7175 (pm20) REVERT: B 821 LYS cc_start: 0.8657 (mmtt) cc_final: 0.8260 (mmtp) REVERT: B 823 LYS cc_start: 0.7819 (mmtt) cc_final: 0.7489 (mmtt) REVERT: B 935 ASP cc_start: 0.8209 (t0) cc_final: 0.7962 (t0) REVERT: C 14 HIS cc_start: 0.8506 (m-70) cc_final: 0.8221 (m90) REVERT: C 31 PHE cc_start: 0.8232 (t80) cc_final: 0.7498 (t80) REVERT: C 92 ARG cc_start: 0.8177 (mtt90) cc_final: 0.7843 (mtt90) REVERT: C 350 THR cc_start: 0.8488 (m) cc_final: 0.8193 (p) REVERT: C 498 TYR cc_start: 0.8580 (p90) cc_final: 0.8268 (p90) REVERT: C 501 THR cc_start: 0.8080 (m) cc_final: 0.7794 (t) REVERT: C 701 SER cc_start: 0.7804 (m) cc_final: 0.7369 (t) REVERT: C 740 VAL cc_start: 0.7972 (t) cc_final: 0.7610 (m) REVERT: C 777 PHE cc_start: 0.8387 (t80) cc_final: 0.8053 (t80) REVERT: C 797 SER cc_start: 0.8391 (m) cc_final: 0.8040 (p) REVERT: C 800 ASP cc_start: 0.7891 (t0) cc_final: 0.7596 (t0) REVERT: C 952 LEU cc_start: 0.8641 (tp) cc_final: 0.8391 (tt) outliers start: 70 outliers final: 53 residues processed: 659 average time/residue: 0.1632 time to fit residues: 166.5212 Evaluate side-chains 666 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 611 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 864 LYS Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 745 ASN Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 917 GLU Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 840 VAL Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 936 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 170 optimal weight: 0.4980 chunk 74 optimal weight: 0.7980 chunk 154 optimal weight: 0.0970 chunk 209 optimal weight: 5.9990 chunk 259 optimal weight: 3.9990 chunk 187 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 243 optimal weight: 5.9990 chunk 221 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 250 optimal weight: 3.9990 overall best weight: 1.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 HIS ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 ASN A 572 GLN A 650 ASN ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN B 412 HIS B 502 ASN B 572 GLN C 411 ASN C 412 HIS C 548 HIS C 650 ASN C 682 ASN C 752 ASN C 836 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.102391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.089593 restraints weight = 32572.840| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.86 r_work: 0.2854 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22424 Z= 0.132 Angle : 0.523 7.612 30490 Z= 0.275 Chirality : 0.045 0.221 3244 Planarity : 0.004 0.056 4012 Dihedral : 4.949 55.815 3038 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.12 % Favored : 93.84 % Rotamer: Outliers : 2.95 % Allowed : 16.82 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.16), residues: 2712 helix: 1.59 (0.31), residues: 310 sheet: 0.57 (0.22), residues: 571 loop : -1.23 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 92 TYR 0.026 0.001 TYR B 498 PHE 0.013 0.001 PHE B 569 TRP 0.012 0.001 TRP C 220 HIS 0.005 0.001 HIS C 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (22424) covalent geometry : angle 0.52253 / 0.27 (30490) hydrogen bonds : bond 0.03637 / 2.41 ( 552) hydrogen bonds : angle 5.21010 / 3.60 ( 1599) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 623 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 TYR cc_start: 0.8402 (p90) cc_final: 0.7931 (p90) REVERT: A 38 TYR cc_start: 0.7800 (p90) cc_final: 0.7298 (p90) REVERT: A 167 LYS cc_start: 0.8044 (mmmt) cc_final: 0.7671 (mmmt) REVERT: A 218 SER cc_start: 0.8213 (m) cc_final: 0.7743 (p) REVERT: A 297 GLU cc_start: 0.7270 (pt0) cc_final: 0.7005 (pt0) REVERT: A 392 PHE cc_start: 0.8516 (t80) cc_final: 0.8230 (t80) REVERT: A 591 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8214 (m) REVERT: A 651 ASP cc_start: 0.7641 (m-30) cc_final: 0.7280 (m-30) REVERT: A 662 ASN cc_start: 0.8015 (m110) cc_final: 0.7664 (m-40) REVERT: A 753 GLU cc_start: 0.7486 (pt0) cc_final: 0.6981 (pt0) REVERT: A 786 ASN cc_start: 0.8359 (m-40) cc_final: 0.8090 (m-40) REVERT: A 823 LYS cc_start: 0.7719 (mmtt) cc_final: 0.7412 (mmtt) REVERT: A 851 GLN cc_start: 0.8210 (pt0) cc_final: 0.7938 (pt0) REVERT: A 881 LEU cc_start: 0.8548 (mp) cc_final: 0.8288 (mt) REVERT: A 912 LEU cc_start: 0.8410 (tp) cc_final: 0.8208 (tt) REVERT: A 928 TYR cc_start: 0.8610 (t80) cc_final: 0.8393 (t80) REVERT: B 31 PHE cc_start: 0.8328 (t80) cc_final: 0.8055 (t80) REVERT: B 38 TYR cc_start: 0.7770 (p90) cc_final: 0.7414 (p90) REVERT: B 61 SER cc_start: 0.8397 (m) cc_final: 0.8096 (t) REVERT: B 181 LYS cc_start: 0.8100 (ttpp) cc_final: 0.7662 (ptpp) REVERT: B 292 VAL cc_start: 0.8377 (t) cc_final: 0.7917 (p) REVERT: B 462 GLU cc_start: 0.7331 (mm-30) cc_final: 0.6896 (mm-30) REVERT: B 555 ARG cc_start: 0.8352 (ttp-170) cc_final: 0.8124 (mtp180) REVERT: B 572 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7509 (mt0) REVERT: B 600 VAL cc_start: 0.8518 (t) cc_final: 0.8257 (m) REVERT: B 606 SER cc_start: 0.8578 (t) cc_final: 0.8283 (p) REVERT: B 608 LEU cc_start: 0.8346 (mt) cc_final: 0.8137 (mp) REVERT: B 623 SER cc_start: 0.8529 (m) cc_final: 0.8167 (p) REVERT: B 753 GLU cc_start: 0.7630 (pm20) cc_final: 0.7117 (pm20) REVERT: B 755 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7609 (mm-30) REVERT: B 821 LYS cc_start: 0.8632 (mmtt) cc_final: 0.8200 (mmtp) REVERT: B 823 LYS cc_start: 0.7838 (mmtt) cc_final: 0.7537 (mmtt) REVERT: B 935 ASP cc_start: 0.8238 (t0) cc_final: 0.7966 (t0) REVERT: C 12 TYR cc_start: 0.8346 (t80) cc_final: 0.8123 (t80) REVERT: C 14 HIS cc_start: 0.8526 (m-70) cc_final: 0.8247 (m90) REVERT: C 31 PHE cc_start: 0.8312 (t80) cc_final: 0.7595 (t80) REVERT: C 64 LEU cc_start: 0.8229 (mt) cc_final: 0.8010 (mp) REVERT: C 80 TYR cc_start: 0.8495 (p90) cc_final: 0.8213 (p90) REVERT: C 92 ARG cc_start: 0.8238 (mtt90) cc_final: 0.7862 (mtt90) REVERT: C 212 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6883 (mm-30) REVERT: C 233 LEU cc_start: 0.8040 (mt) cc_final: 0.7743 (mt) REVERT: C 350 THR cc_start: 0.8486 (m) cc_final: 0.8201 (p) REVERT: C 454 ASP cc_start: 0.6976 (t70) cc_final: 0.6710 (t0) REVERT: C 498 TYR cc_start: 0.8630 (p90) cc_final: 0.8308 (p90) REVERT: C 501 THR cc_start: 0.8111 (m) cc_final: 0.7836 (t) REVERT: C 608 LEU cc_start: 0.8405 (mt) cc_final: 0.8132 (mp) REVERT: C 642 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7451 (tt0) REVERT: C 698 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7942 (mt-10) REVERT: C 701 SER cc_start: 0.7795 (m) cc_final: 0.7396 (t) REVERT: C 740 VAL cc_start: 0.7975 (t) cc_final: 0.7582 (m) REVERT: C 797 SER cc_start: 0.8397 (m) cc_final: 0.8044 (p) REVERT: C 800 ASP cc_start: 0.7951 (t0) cc_final: 0.7698 (t0) REVERT: C 893 MET cc_start: 0.7970 (mtm) cc_final: 0.7533 (mtm) REVERT: C 952 LEU cc_start: 0.8651 (tp) cc_final: 0.8408 (tt) outliers start: 70 outliers final: 55 residues processed: 654 average time/residue: 0.1638 time to fit residues: 165.6409 Evaluate side-chains 673 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 615 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 495 LYS Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 745 ASN Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 897 THR Chi-restraints excluded: chain B residue 936 VAL Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 642 GLU Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 840 VAL Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 936 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 114 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 155 optimal weight: 0.7980 chunk 238 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 chunk 242 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 188 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 ASN A 572 GLN A 650 ASN ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN B 300 ASN B 572 GLN C 370 GLN ** C 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 ASN C 682 ASN C 836 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.100272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.087471 restraints weight = 32562.392| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.87 r_work: 0.2828 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 22424 Z= 0.191 Angle : 0.566 7.273 30490 Z= 0.301 Chirality : 0.047 0.193 3244 Planarity : 0.004 0.058 4012 Dihedral : 5.259 56.274 3038 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.64 % Favored : 93.33 % Rotamer: Outliers : 3.37 % Allowed : 16.02 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.16), residues: 2712 helix: 1.30 (0.31), residues: 316 sheet: 0.57 (0.21), residues: 568 loop : -1.35 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 92 TYR 0.028 0.002 TYR B 498 PHE 0.015 0.002 PHE B 569 TRP 0.011 0.002 TRP A 882 HIS 0.007 0.001 HIS B 570 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 (22424) covalent geometry : angle 0.56563 / 0.30 (30490) hydrogen bonds : bond 0.04314 / 2.86 ( 552) hydrogen bonds : angle 5.32376 / 3.69 ( 1599) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 620 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 TYR cc_start: 0.7789 (p90) cc_final: 0.7292 (p90) REVERT: A 92 ARG cc_start: 0.8493 (mtt90) cc_final: 0.8263 (mtt90) REVERT: A 134 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8079 (mt-10) REVERT: A 137 GLN cc_start: 0.8044 (tt0) cc_final: 0.7287 (tt0) REVERT: A 167 LYS cc_start: 0.8082 (mmmt) cc_final: 0.7631 (mmmt) REVERT: A 218 SER cc_start: 0.8269 (m) cc_final: 0.7794 (p) REVERT: A 297 GLU cc_start: 0.7332 (pt0) cc_final: 0.7028 (pt0) REVERT: A 591 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8214 (m) REVERT: A 651 ASP cc_start: 0.7665 (m-30) cc_final: 0.7298 (m-30) REVERT: A 662 ASN cc_start: 0.7994 (m110) cc_final: 0.7695 (m-40) REVERT: A 753 GLU cc_start: 0.7490 (pt0) cc_final: 0.6947 (pt0) REVERT: A 786 ASN cc_start: 0.8412 (m-40) cc_final: 0.8147 (m-40) REVERT: A 800 ASP cc_start: 0.8004 (t0) cc_final: 0.7579 (t0) REVERT: A 817 VAL cc_start: 0.8138 (OUTLIER) cc_final: 0.7925 (p) REVERT: A 823 LYS cc_start: 0.7743 (mmtt) cc_final: 0.7437 (mmtt) REVERT: A 851 GLN cc_start: 0.8222 (pt0) cc_final: 0.7943 (pt0) REVERT: A 881 LEU cc_start: 0.8535 (mp) cc_final: 0.8301 (mt) REVERT: B 31 PHE cc_start: 0.8369 (t80) cc_final: 0.8100 (t80) REVERT: B 38 TYR cc_start: 0.7783 (p90) cc_final: 0.7460 (p90) REVERT: B 47 ASN cc_start: 0.7819 (p0) cc_final: 0.7532 (p0) REVERT: B 61 SER cc_start: 0.8465 (m) cc_final: 0.8162 (t) REVERT: B 181 LYS cc_start: 0.8079 (ttpp) cc_final: 0.7689 (pttm) REVERT: B 273 GLN cc_start: 0.8540 (mt0) cc_final: 0.8295 (mt0) REVERT: B 292 VAL cc_start: 0.8403 (t) cc_final: 0.7950 (p) REVERT: B 462 GLU cc_start: 0.7397 (mm-30) cc_final: 0.6960 (mm-30) REVERT: B 540 MET cc_start: 0.8250 (mmm) cc_final: 0.8029 (mmm) REVERT: B 555 ARG cc_start: 0.8373 (ttp-170) cc_final: 0.8142 (mtp180) REVERT: B 572 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7689 (mt0) REVERT: B 600 VAL cc_start: 0.8527 (t) cc_final: 0.8254 (m) REVERT: B 606 SER cc_start: 0.8553 (t) cc_final: 0.8279 (p) REVERT: B 623 SER cc_start: 0.8541 (m) cc_final: 0.8173 (p) REVERT: B 753 GLU cc_start: 0.7616 (pm20) cc_final: 0.7142 (pm20) REVERT: B 755 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7646 (mm-30) REVERT: B 823 LYS cc_start: 0.7860 (mmtt) cc_final: 0.7564 (mmtt) REVERT: B 893 MET cc_start: 0.8312 (mtm) cc_final: 0.7987 (mtm) REVERT: B 935 ASP cc_start: 0.8306 (t0) cc_final: 0.8055 (t0) REVERT: C 14 HIS cc_start: 0.8528 (m-70) cc_final: 0.8231 (m90) REVERT: C 63 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7131 (ptm160) REVERT: C 80 TYR cc_start: 0.8465 (p90) cc_final: 0.8178 (p90) REVERT: C 233 LEU cc_start: 0.8047 (mt) cc_final: 0.7825 (mt) REVERT: C 498 TYR cc_start: 0.8643 (p90) cc_final: 0.8365 (p90) REVERT: C 501 THR cc_start: 0.8138 (m) cc_final: 0.7877 (t) REVERT: C 608 LEU cc_start: 0.8411 (mt) cc_final: 0.8081 (mp) REVERT: C 642 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7443 (tt0) REVERT: C 701 SER cc_start: 0.7821 (m) cc_final: 0.7425 (t) REVERT: C 797 SER cc_start: 0.8357 (m) cc_final: 0.8018 (p) REVERT: C 800 ASP cc_start: 0.7957 (t0) cc_final: 0.7747 (t0) REVERT: C 893 MET cc_start: 0.8061 (mtm) cc_final: 0.7673 (mtt) outliers start: 80 outliers final: 58 residues processed: 659 average time/residue: 0.1537 time to fit residues: 156.3557 Evaluate side-chains 672 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 609 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 495 LYS Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 745 ASN Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 897 THR Chi-restraints excluded: chain B residue 936 VAL Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 167 LYS Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 642 GLU Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 840 VAL Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 888 SER Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 936 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 122 optimal weight: 8.9990 chunk 251 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 190 optimal weight: 10.0000 chunk 134 optimal weight: 0.5980 chunk 245 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 229 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 ASN A 572 GLN A 650 ASN ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 ASN B 412 HIS B 572 GLN C 131 ASN C 370 GLN C 411 ASN C 548 HIS C 650 ASN C 836 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.100643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.087928 restraints weight = 32569.427| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.86 r_work: 0.2832 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22424 Z= 0.224 Angle : 0.596 9.331 30490 Z= 0.317 Chirality : 0.048 0.211 3244 Planarity : 0.005 0.057 4012 Dihedral : 5.475 57.445 3038 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.86 % Favored : 93.10 % Rotamer: Outliers : 3.20 % Allowed : 16.86 % 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: -0.99 (0.15), residues: 2712 helix: 1.19 (0.31), residues: 310 sheet: 0.53 (0.21), residues: 567 loop : -1.48 (0.14), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 92 TYR 0.028 0.002 TYR B 498 PHE 0.016 0.002 PHE A 754 TRP 0.015 0.002 TRP A 451 HIS 0.007 0.002 HIS C 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.22 (22424) covalent geometry : angle 0.59627 / 0.32 (30490) hydrogen bonds : bond 0.04613 / 3.06 ( 552) hydrogen bonds : angle 5.40014 / 3.75 ( 1599) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 618 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 TYR cc_start: 0.7783 (p90) cc_final: 0.7271 (p90) REVERT: A 137 GLN cc_start: 0.8029 (tt0) cc_final: 0.7298 (tt0) REVERT: A 167 LYS cc_start: 0.8093 (mmmt) cc_final: 0.7627 (mmmt) REVERT: A 177 LEU cc_start: 0.8607 (tp) cc_final: 0.8375 (tp) REVERT: A 217 GLU cc_start: 0.7157 (pt0) cc_final: 0.6953 (mt-10) REVERT: A 218 SER cc_start: 0.8263 (m) cc_final: 0.7809 (p) REVERT: A 297 GLU cc_start: 0.7356 (pt0) cc_final: 0.7043 (pt0) REVERT: A 591 THR cc_start: 0.8508 (OUTLIER) cc_final: 0.8205 (m) REVERT: A 651 ASP cc_start: 0.7693 (m-30) cc_final: 0.7323 (m-30) REVERT: A 730 LYS cc_start: 0.8681 (ttmm) cc_final: 0.8438 (ttmm) REVERT: A 753 GLU cc_start: 0.7463 (pt0) cc_final: 0.6940 (pt0) REVERT: A 786 ASN cc_start: 0.8404 (m-40) cc_final: 0.8141 (m-40) REVERT: A 800 ASP cc_start: 0.8032 (t0) cc_final: 0.7612 (t0) REVERT: A 817 VAL cc_start: 0.8154 (OUTLIER) cc_final: 0.7920 (p) REVERT: A 823 LYS cc_start: 0.7760 (mmtt) cc_final: 0.7469 (mmtt) REVERT: A 851 GLN cc_start: 0.8222 (pt0) cc_final: 0.7950 (pt0) REVERT: A 881 LEU cc_start: 0.8506 (mp) cc_final: 0.8292 (mt) REVERT: B 31 PHE cc_start: 0.8328 (t80) cc_final: 0.8068 (t80) REVERT: B 38 TYR cc_start: 0.7789 (p90) cc_final: 0.7427 (p90) REVERT: B 47 ASN cc_start: 0.7938 (p0) cc_final: 0.7679 (p0) REVERT: B 61 SER cc_start: 0.8471 (m) cc_final: 0.8117 (p) REVERT: B 292 VAL cc_start: 0.8398 (t) cc_final: 0.7930 (p) REVERT: B 350 THR cc_start: 0.8644 (p) cc_final: 0.8425 (p) REVERT: B 555 ARG cc_start: 0.8381 (ttp-170) cc_final: 0.8152 (mtp180) REVERT: B 572 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7741 (mt0) REVERT: B 600 VAL cc_start: 0.8493 (t) cc_final: 0.8225 (m) REVERT: B 606 SER cc_start: 0.8571 (t) cc_final: 0.8274 (p) REVERT: B 608 LEU cc_start: 0.8366 (mt) cc_final: 0.8142 (mp) REVERT: B 623 SER cc_start: 0.8550 (m) cc_final: 0.8155 (p) REVERT: B 639 SER cc_start: 0.7975 (t) cc_final: 0.7713 (m) REVERT: B 753 GLU cc_start: 0.7605 (pm20) cc_final: 0.7113 (pm20) REVERT: B 755 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7593 (mm-30) REVERT: B 823 LYS cc_start: 0.7861 (mmtt) cc_final: 0.7568 (mmtt) REVERT: B 893 MET cc_start: 0.8295 (mtm) cc_final: 0.7997 (mtt) REVERT: B 935 ASP cc_start: 0.8324 (t0) cc_final: 0.8048 (t0) REVERT: C 14 HIS cc_start: 0.8505 (m-70) cc_final: 0.8232 (m90) REVERT: C 38 TYR cc_start: 0.7382 (p90) cc_final: 0.7166 (p90) REVERT: C 80 TYR cc_start: 0.8455 (p90) cc_final: 0.8152 (p90) REVERT: C 102 ASP cc_start: 0.7833 (t0) cc_final: 0.7615 (t0) REVERT: C 233 LEU cc_start: 0.8055 (mt) cc_final: 0.7839 (mt) REVERT: C 498 TYR cc_start: 0.8635 (p90) cc_final: 0.8369 (p90) REVERT: C 501 THR cc_start: 0.8199 (m) cc_final: 0.7947 (t) REVERT: C 539 TYR cc_start: 0.8480 (m-80) cc_final: 0.8267 (m-80) REVERT: C 608 LEU cc_start: 0.8413 (mt) cc_final: 0.8085 (mp) REVERT: C 614 VAL cc_start: 0.8629 (m) cc_final: 0.8334 (p) REVERT: C 642 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7426 (tt0) REVERT: C 701 SER cc_start: 0.7812 (m) cc_final: 0.7377 (t) REVERT: C 797 SER cc_start: 0.8331 (m) cc_final: 0.7998 (p) REVERT: C 800 ASP cc_start: 0.7981 (t0) cc_final: 0.7773 (t0) REVERT: C 893 MET cc_start: 0.8078 (mtm) cc_final: 0.7705 (mtt) outliers start: 76 outliers final: 65 residues processed: 655 average time/residue: 0.1470 time to fit residues: 149.0425 Evaluate side-chains 677 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 608 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 673 ASN Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 802 MET Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 495 LYS Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 745 ASN Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 897 THR Chi-restraints excluded: chain B residue 936 VAL Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 167 LYS Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 541 ASP Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 642 GLU Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 840 VAL Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 888 SER Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 936 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 235 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 ASN A 572 GLN A 650 ASN ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 ASN B 412 HIS B 502 ASN B 572 GLN ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 HIS C 650 ASN C 752 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.101782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.088974 restraints weight = 32590.305| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.87 r_work: 0.2851 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22424 Z= 0.145 Angle : 0.550 8.392 30490 Z= 0.291 Chirality : 0.046 0.202 3244 Planarity : 0.004 0.056 4012 Dihedral : 5.302 57.352 3038 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.01 % Favored : 93.95 % Rotamer: Outliers : 2.91 % Allowed : 17.33 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.16), residues: 2712 helix: 1.44 (0.31), residues: 304 sheet: 0.47 (0.21), residues: 576 loop : -1.43 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 92 TYR 0.026 0.001 TYR B 498 PHE 0.012 0.001 PHE B 569 TRP 0.012 0.001 TRP A 220 HIS 0.005 0.001 HIS C 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (22424) covalent geometry : angle 0.55037 / 0.29 (30490) hydrogen bonds : bond 0.03823 / 2.53 ( 552) hydrogen bonds : angle 5.31011 / 3.68 ( 1599) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 617 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.8367 (t80) cc_final: 0.8053 (t80) REVERT: A 38 TYR cc_start: 0.7775 (p90) cc_final: 0.7294 (p90) REVERT: A 53 THR cc_start: 0.8445 (t) cc_final: 0.8173 (m) REVERT: A 137 GLN cc_start: 0.8028 (tt0) cc_final: 0.7287 (tt0) REVERT: A 167 LYS cc_start: 0.8064 (mmmt) cc_final: 0.7598 (mmmt) REVERT: A 207 LYS cc_start: 0.8648 (ttpp) cc_final: 0.8379 (pttp) REVERT: A 217 GLU cc_start: 0.7224 (pt0) cc_final: 0.6876 (mt-10) REVERT: A 218 SER cc_start: 0.8273 (m) cc_final: 0.7765 (p) REVERT: A 297 GLU cc_start: 0.7369 (pt0) cc_final: 0.7050 (pt0) REVERT: A 591 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8189 (m) REVERT: A 662 ASN cc_start: 0.7985 (m110) cc_final: 0.7730 (m-40) REVERT: A 753 GLU cc_start: 0.7435 (pt0) cc_final: 0.6883 (pt0) REVERT: A 786 ASN cc_start: 0.8350 (m-40) cc_final: 0.8091 (m-40) REVERT: A 799 LYS cc_start: 0.8494 (mtmt) cc_final: 0.8293 (mtmm) REVERT: A 800 ASP cc_start: 0.8047 (t0) cc_final: 0.7631 (t0) REVERT: A 817 VAL cc_start: 0.8147 (OUTLIER) cc_final: 0.7903 (p) REVERT: A 823 LYS cc_start: 0.7724 (mmtt) cc_final: 0.7443 (mmtt) REVERT: A 851 GLN cc_start: 0.8172 (pt0) cc_final: 0.7875 (pt0) REVERT: A 881 LEU cc_start: 0.8470 (mp) cc_final: 0.8258 (mt) REVERT: B 31 PHE cc_start: 0.8225 (t80) cc_final: 0.7997 (t80) REVERT: B 38 TYR cc_start: 0.7775 (p90) cc_final: 0.7400 (p90) REVERT: B 47 ASN cc_start: 0.7911 (p0) cc_final: 0.7643 (p0) REVERT: B 61 SER cc_start: 0.8425 (m) cc_final: 0.8099 (p) REVERT: B 181 LYS cc_start: 0.8090 (ttpp) cc_final: 0.7573 (ptpp) REVERT: B 273 GLN cc_start: 0.8517 (mt0) cc_final: 0.8255 (mt0) REVERT: B 292 VAL cc_start: 0.8341 (t) cc_final: 0.7862 (p) REVERT: B 301 MET cc_start: 0.8326 (ttm) cc_final: 0.8117 (ttp) REVERT: B 350 THR cc_start: 0.8625 (p) cc_final: 0.8396 (p) REVERT: B 368 ASP cc_start: 0.7510 (t0) cc_final: 0.7213 (t0) REVERT: B 462 GLU cc_start: 0.7404 (mm-30) cc_final: 0.6928 (mm-30) REVERT: B 555 ARG cc_start: 0.8357 (ttp-170) cc_final: 0.8125 (mtp180) REVERT: B 572 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7537 (mt0) REVERT: B 600 VAL cc_start: 0.8441 (t) cc_final: 0.8186 (m) REVERT: B 606 SER cc_start: 0.8578 (t) cc_final: 0.8276 (p) REVERT: B 623 SER cc_start: 0.8553 (m) cc_final: 0.8148 (p) REVERT: B 753 GLU cc_start: 0.7606 (pm20) cc_final: 0.7090 (pm20) REVERT: B 755 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7550 (mm-30) REVERT: B 816 VAL cc_start: 0.8160 (p) cc_final: 0.7927 (m) REVERT: B 823 LYS cc_start: 0.7838 (mmtt) cc_final: 0.7558 (mmtt) REVERT: B 893 MET cc_start: 0.8302 (mtm) cc_final: 0.8013 (mtt) REVERT: B 935 ASP cc_start: 0.8314 (t0) cc_final: 0.8065 (t0) REVERT: C 14 HIS cc_start: 0.8471 (m-70) cc_final: 0.8191 (m90) REVERT: C 80 TYR cc_start: 0.8460 (p90) cc_final: 0.8139 (p90) REVERT: C 233 LEU cc_start: 0.8023 (mt) cc_final: 0.7809 (mt) REVERT: C 370 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7963 (mm-40) REVERT: C 454 ASP cc_start: 0.7089 (t70) cc_final: 0.6839 (t0) REVERT: C 498 TYR cc_start: 0.8626 (p90) cc_final: 0.8363 (p90) REVERT: C 501 THR cc_start: 0.8203 (m) cc_final: 0.7936 (t) REVERT: C 539 TYR cc_start: 0.8479 (m-80) cc_final: 0.8260 (m-80) REVERT: C 608 LEU cc_start: 0.8398 (mt) cc_final: 0.8110 (mp) REVERT: C 614 VAL cc_start: 0.8578 (m) cc_final: 0.8287 (p) REVERT: C 701 SER cc_start: 0.7795 (m) cc_final: 0.7321 (t) REVERT: C 797 SER cc_start: 0.8305 (m) cc_final: 0.7954 (p) REVERT: C 800 ASP cc_start: 0.7976 (t0) cc_final: 0.7774 (t0) REVERT: C 893 MET cc_start: 0.8073 (mtm) cc_final: 0.7703 (mtt) outliers start: 69 outliers final: 61 residues processed: 649 average time/residue: 0.1487 time to fit residues: 149.4962 Evaluate side-chains 677 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 612 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 673 ASN Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 495 LYS Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 745 ASN Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 897 THR Chi-restraints excluded: chain B residue 917 GLU Chi-restraints excluded: chain B residue 936 VAL Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 167 LYS Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 541 ASP Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 840 VAL Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 936 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 127 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 201 optimal weight: 0.9990 chunk 123 optimal weight: 0.2980 chunk 51 optimal weight: 0.0000 chunk 211 optimal weight: 0.3980 chunk 57 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 199 optimal weight: 0.8980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 ASN A 572 GLN A 650 ASN B 289 GLN B 300 ASN B 502 ASN B 572 GLN C 131 ASN C 548 HIS C 650 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.102717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.089970 restraints weight = 32459.367| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.83 r_work: 0.2896 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22424 Z= 0.091 Angle : 0.505 8.796 30490 Z= 0.264 Chirality : 0.044 0.182 3244 Planarity : 0.004 0.054 4012 Dihedral : 4.982 57.311 3038 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.49 % Allowed : 17.83 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.16), residues: 2712 helix: 1.69 (0.32), residues: 298 sheet: 0.37 (0.21), residues: 598 loop : -1.30 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 92 TYR 0.023 0.001 TYR B 498 PHE 0.010 0.001 PHE B 691 TRP 0.013 0.001 TRP A 220 HIS 0.009 0.001 HIS B 570 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 (22424) covalent geometry : angle 0.50507 / 0.26 (30490) hydrogen bonds : bond 0.02915 / 1.93 ( 552) hydrogen bonds : angle 5.17332 / 3.57 ( 1599) =============================================================================== Job complete usr+sys time: 5517.10 seconds wall clock time: 95 minutes 6.87 seconds (5706.87 seconds total)