Starting phenix.real_space_refine on Thu Nov 20 03:59:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bco_7083/11_2025/6bco_7083.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bco_7083/11_2025/6bco_7083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6bco_7083/11_2025/6bco_7083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bco_7083/11_2025/6bco_7083.map" model { file = "/net/cci-nas-00/data/ceres_data/6bco_7083/11_2025/6bco_7083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bco_7083/11_2025/6bco_7083.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 140 5.16 5 C 19576 2.51 5 N 5308 2.21 5 O 5396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 97 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30432 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 7577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 952, 7577 Classifications: {'peptide': 952} Link IDs: {'PTRANS': 38, 'TRANS': 913} Chain breaks: 7 Chain: "A" Number of atoms: 7577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 952, 7577 Classifications: {'peptide': 952} Link IDs: {'PTRANS': 38, 'TRANS': 913} Chain breaks: 7 Chain: "C" Number of atoms: 7577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 952, 7577 Classifications: {'peptide': 952} Link IDs: {'PTRANS': 38, 'TRANS': 913} Chain breaks: 7 Chain: "D" Number of atoms: 7577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 952, 7577 Classifications: {'peptide': 952} Link IDs: {'PTRANS': 38, 'TRANS': 913} Chain breaks: 7 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.12, per 1000 atoms: 0.23 Number of scatterers: 30432 At special positions: 0 Unit cell: (153.01, 153.01, 165.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 140 16.00 P 12 15.00 O 5396 8.00 N 5308 7.00 C 19576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 989 " - pdb=" SG CYS B1007 " distance=2.05 Simple disulfide: pdb=" SG CYS A 989 " - pdb=" SG CYS A1007 " distance=2.05 Simple disulfide: pdb=" SG CYS C 989 " - pdb=" SG CYS C1007 " distance=2.05 Simple disulfide: pdb=" SG CYS D 989 " - pdb=" SG CYS D1007 " distance=2.05 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: 2.60 Conformation dependent library (CDL) restraints added in 1.4 seconds 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7104 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 12 sheets defined 68.3% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'B' and resid 14 through 20 removed outlier: 3.832A pdb=" N CYS B 20 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 110 removed outlier: 3.814A pdb=" N VAL B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 142 Processing helix chain 'B' and resid 143 through 151 Processing helix chain 'B' and resid 162 through 177 removed outlier: 3.859A pdb=" N HIS B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 247 through 259 Processing helix chain 'B' and resid 282 through 294 removed outlier: 3.694A pdb=" N LEU B 286 " --> pdb=" O ASP B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 317 Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 344 through 359 removed outlier: 3.786A pdb=" N LEU B 348 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 385 removed outlier: 4.030A pdb=" N THR B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 404 Processing helix chain 'B' and resid 406 through 414 removed outlier: 3.929A pdb=" N ALA B 410 " --> pdb=" O ARG B 406 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.708A pdb=" N LEU B 426 " --> pdb=" O ARG B 422 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER B 429 " --> pdb=" O HIS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 448 removed outlier: 3.509A pdb=" N HIS B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 456 Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'B' and resid 472 through 482 removed outlier: 3.823A pdb=" N ASN B 476 " --> pdb=" O SER B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 512 Processing helix chain 'B' and resid 558 through 569 Processing helix chain 'B' and resid 571 through 582 Processing helix chain 'B' and resid 584 through 602 removed outlier: 3.508A pdb=" N LEU B 602 " --> pdb=" O VAL B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 634 removed outlier: 3.548A pdb=" N SER B 634 " --> pdb=" O CYS B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 643 Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 663 through 668 removed outlier: 3.683A pdb=" N PHE B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 682 Processing helix chain 'B' and resid 689 through 699 removed outlier: 3.519A pdb=" N LEU B 693 " --> pdb=" O PRO B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 704 removed outlier: 3.703A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 700 through 704' Processing helix chain 'B' and resid 766 through 772 Processing helix chain 'B' and resid 774 through 799 Processing helix chain 'B' and resid 807 through 830 Processing helix chain 'B' and resid 849 through 857 Processing helix chain 'B' and resid 859 through 880 removed outlier: 3.998A pdb=" N LEU B 868 " --> pdb=" O ASP B 864 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR B 880 " --> pdb=" O GLY B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 901 removed outlier: 3.531A pdb=" N MET B 896 " --> pdb=" O CYS B 892 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE B 897 " --> pdb=" O LEU B 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 906 Processing helix chain 'B' and resid 907 through 909 No H-bonds generated for 'chain 'B' and resid 907 through 909' Processing helix chain 'B' and resid 912 through 920 removed outlier: 4.316A pdb=" N SER B 920 " --> pdb=" O ILE B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 948 Processing helix chain 'B' and resid 954 through 969 removed outlier: 4.615A pdb=" N ARG B 965 " --> pdb=" O ARG B 961 " (cutoff:3.500A) Proline residue: B 966 - end of helix Processing helix chain 'B' and resid 970 through 972 No H-bonds generated for 'chain 'B' and resid 970 through 972' Processing helix chain 'B' and resid 980 through 984 Processing helix chain 'B' and resid 1013 through 1029 Processing helix chain 'B' and resid 1029 through 1067 removed outlier: 5.313A pdb=" N GLY B1048 " --> pdb=" O SER B1044 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN B1049 " --> pdb=" O LYS B1045 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR B1059 " --> pdb=" O LYS B1055 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER B1060 " --> pdb=" O ALA B1056 " (cutoff:3.500A) Processing helix chain 'B' and resid 1072 through 1075 Processing helix chain 'B' and resid 1076 through 1090 removed outlier: 3.746A pdb=" N ARG B1090 " --> pdb=" O LYS B1086 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1141 Processing helix chain 'B' and resid 1142 through 1162 Processing helix chain 'A' and resid 14 through 20 removed outlier: 3.832A pdb=" N CYS A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 110 removed outlier: 3.814A pdb=" N VAL A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 143 through 151 Processing helix chain 'A' and resid 162 through 177 removed outlier: 3.859A pdb=" N HIS A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 247 through 259 Processing helix chain 'A' and resid 282 through 294 removed outlier: 3.694A pdb=" N LEU A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 317 Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 344 through 359 removed outlier: 3.785A pdb=" N LEU A 348 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 385 removed outlier: 4.029A pdb=" N THR A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 404 Processing helix chain 'A' and resid 406 through 414 removed outlier: 3.929A pdb=" N ALA A 410 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.709A pdb=" N LEU A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 448 removed outlier: 3.508A pdb=" N HIS A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 472 through 482 removed outlier: 3.823A pdb=" N ASN A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 512 Processing helix chain 'A' and resid 558 through 569 Processing helix chain 'A' and resid 571 through 582 Processing helix chain 'A' and resid 584 through 602 removed outlier: 3.508A pdb=" N LEU A 602 " --> pdb=" O VAL A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 634 removed outlier: 3.548A pdb=" N SER A 634 " --> pdb=" O CYS A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 643 Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 663 through 668 removed outlier: 3.683A pdb=" N PHE A 667 " --> pdb=" O ALA A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 682 Processing helix chain 'A' and resid 689 through 699 removed outlier: 3.519A pdb=" N LEU A 693 " --> pdb=" O PRO A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 704 removed outlier: 3.703A pdb=" N ILE A 703 " --> pdb=" O PRO A 700 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR A 704 " --> pdb=" O PRO A 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 700 through 704' Processing helix chain 'A' and resid 766 through 772 Processing helix chain 'A' and resid 774 through 799 Processing helix chain 'A' and resid 807 through 830 Processing helix chain 'A' and resid 849 through 857 Processing helix chain 'A' and resid 859 through 880 removed outlier: 3.998A pdb=" N LEU A 868 " --> pdb=" O ASP A 864 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 901 removed outlier: 3.531A pdb=" N MET A 896 " --> pdb=" O CYS A 892 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A 897 " --> pdb=" O LEU A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 906 Processing helix chain 'A' and resid 907 through 909 No H-bonds generated for 'chain 'A' and resid 907 through 909' Processing helix chain 'A' and resid 912 through 920 removed outlier: 4.316A pdb=" N SER A 920 " --> pdb=" O ILE A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 948 Processing helix chain 'A' and resid 954 through 969 removed outlier: 4.615A pdb=" N ARG A 965 " --> pdb=" O ARG A 961 " (cutoff:3.500A) Proline residue: A 966 - end of helix Processing helix chain 'A' and resid 970 through 972 No H-bonds generated for 'chain 'A' and resid 970 through 972' Processing helix chain 'A' and resid 980 through 984 Processing helix chain 'A' and resid 1013 through 1029 Processing helix chain 'A' and resid 1029 through 1067 removed outlier: 5.313A pdb=" N GLY A1048 " --> pdb=" O SER A1044 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN A1049 " --> pdb=" O LYS A1045 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR A1059 " --> pdb=" O LYS A1055 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER A1060 " --> pdb=" O ALA A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1075 Processing helix chain 'A' and resid 1076 through 1090 removed outlier: 3.745A pdb=" N ARG A1090 " --> pdb=" O LYS A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1141 Processing helix chain 'A' and resid 1142 through 1162 Processing helix chain 'C' and resid 14 through 20 removed outlier: 3.832A pdb=" N CYS C 20 " --> pdb=" O ARG C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 110 removed outlier: 3.814A pdb=" N VAL C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 142 Processing helix chain 'C' and resid 143 through 151 Processing helix chain 'C' and resid 162 through 177 removed outlier: 3.859A pdb=" N HIS C 166 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 247 through 259 Processing helix chain 'C' and resid 282 through 294 removed outlier: 3.695A pdb=" N LEU C 286 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 317 Processing helix chain 'C' and resid 332 through 338 Processing helix chain 'C' and resid 344 through 359 removed outlier: 3.786A pdb=" N LEU C 348 " --> pdb=" O ASP C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 385 removed outlier: 4.030A pdb=" N THR C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 404 Processing helix chain 'C' and resid 406 through 414 removed outlier: 3.929A pdb=" N ALA C 410 " --> pdb=" O ARG C 406 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.710A pdb=" N LEU C 426 " --> pdb=" O ARG C 422 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER C 429 " --> pdb=" O HIS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 448 removed outlier: 3.508A pdb=" N HIS C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 456 Processing helix chain 'C' and resid 457 through 465 Processing helix chain 'C' and resid 472 through 482 removed outlier: 3.823A pdb=" N ASN C 476 " --> pdb=" O SER C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 512 Processing helix chain 'C' and resid 558 through 569 Processing helix chain 'C' and resid 571 through 582 Processing helix chain 'C' and resid 584 through 602 removed outlier: 3.508A pdb=" N LEU C 602 " --> pdb=" O VAL C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 634 removed outlier: 3.548A pdb=" N SER C 634 " --> pdb=" O CYS C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 643 Processing helix chain 'C' and resid 653 through 661 Processing helix chain 'C' and resid 663 through 668 removed outlier: 3.683A pdb=" N PHE C 667 " --> pdb=" O ALA C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 682 Processing helix chain 'C' and resid 689 through 699 removed outlier: 3.519A pdb=" N LEU C 693 " --> pdb=" O PRO C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 700 through 704 removed outlier: 3.704A pdb=" N ILE C 703 " --> pdb=" O PRO C 700 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR C 704 " --> pdb=" O PRO C 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 700 through 704' Processing helix chain 'C' and resid 766 through 772 Processing helix chain 'C' and resid 774 through 799 Processing helix chain 'C' and resid 807 through 830 Processing helix chain 'C' and resid 849 through 857 Processing helix chain 'C' and resid 859 through 880 removed outlier: 3.997A pdb=" N LEU C 868 " --> pdb=" O ASP C 864 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR C 880 " --> pdb=" O GLY C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 901 removed outlier: 3.532A pdb=" N MET C 896 " --> pdb=" O CYS C 892 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE C 897 " --> pdb=" O LEU C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 906 Processing helix chain 'C' and resid 907 through 909 No H-bonds generated for 'chain 'C' and resid 907 through 909' Processing helix chain 'C' and resid 912 through 920 removed outlier: 4.316A pdb=" N SER C 920 " --> pdb=" O ILE C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 948 Processing helix chain 'C' and resid 954 through 969 removed outlier: 4.615A pdb=" N ARG C 965 " --> pdb=" O ARG C 961 " (cutoff:3.500A) Proline residue: C 966 - end of helix Processing helix chain 'C' and resid 970 through 972 No H-bonds generated for 'chain 'C' and resid 970 through 972' Processing helix chain 'C' and resid 980 through 984 Processing helix chain 'C' and resid 1013 through 1029 Processing helix chain 'C' and resid 1029 through 1067 removed outlier: 5.312A pdb=" N GLY C1048 " --> pdb=" O SER C1044 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN C1049 " --> pdb=" O LYS C1045 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR C1059 " --> pdb=" O LYS C1055 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER C1060 " --> pdb=" O ALA C1056 " (cutoff:3.500A) Processing helix chain 'C' and resid 1072 through 1075 Processing helix chain 'C' and resid 1076 through 1090 removed outlier: 3.746A pdb=" N ARG C1090 " --> pdb=" O LYS C1086 " (cutoff:3.500A) Processing helix chain 'C' and resid 1113 through 1141 Processing helix chain 'C' and resid 1142 through 1162 Processing helix chain 'D' and resid 14 through 20 removed outlier: 3.832A pdb=" N CYS D 20 " --> pdb=" O ARG D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 110 removed outlier: 3.814A pdb=" N VAL D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 142 Processing helix chain 'D' and resid 143 through 151 Processing helix chain 'D' and resid 162 through 177 removed outlier: 3.860A pdb=" N HIS D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 247 through 259 Processing helix chain 'D' and resid 282 through 294 removed outlier: 3.695A pdb=" N LEU D 286 " --> pdb=" O ASP D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 317 Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 344 through 359 removed outlier: 3.786A pdb=" N LEU D 348 " --> pdb=" O ASP D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 385 removed outlier: 4.030A pdb=" N THR D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 404 Processing helix chain 'D' and resid 406 through 414 removed outlier: 3.929A pdb=" N ALA D 410 " --> pdb=" O ARG D 406 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER D 412 " --> pdb=" O ASP D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.710A pdb=" N LEU D 426 " --> pdb=" O ARG D 422 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER D 429 " --> pdb=" O HIS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 448 removed outlier: 3.508A pdb=" N HIS D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 456 Processing helix chain 'D' and resid 457 through 465 Processing helix chain 'D' and resid 472 through 482 removed outlier: 3.823A pdb=" N ASN D 476 " --> pdb=" O SER D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 512 Processing helix chain 'D' and resid 558 through 569 Processing helix chain 'D' and resid 571 through 582 Processing helix chain 'D' and resid 584 through 602 removed outlier: 3.509A pdb=" N LEU D 602 " --> pdb=" O VAL D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 634 removed outlier: 3.548A pdb=" N SER D 634 " --> pdb=" O CYS D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 643 Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 663 through 668 removed outlier: 3.683A pdb=" N PHE D 667 " --> pdb=" O ALA D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 682 Processing helix chain 'D' and resid 689 through 699 removed outlier: 3.520A pdb=" N LEU D 693 " --> pdb=" O PRO D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 704 removed outlier: 3.704A pdb=" N ILE D 703 " --> pdb=" O PRO D 700 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR D 704 " --> pdb=" O PRO D 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 700 through 704' Processing helix chain 'D' and resid 766 through 772 Processing helix chain 'D' and resid 774 through 799 Processing helix chain 'D' and resid 807 through 830 Processing helix chain 'D' and resid 849 through 857 Processing helix chain 'D' and resid 859 through 880 removed outlier: 3.998A pdb=" N LEU D 868 " --> pdb=" O ASP D 864 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR D 880 " --> pdb=" O GLY D 876 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 901 removed outlier: 3.531A pdb=" N MET D 896 " --> pdb=" O CYS D 892 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE D 897 " --> pdb=" O LEU D 893 " (cutoff:3.500A) Processing helix chain 'D' and resid 901 through 906 Processing helix chain 'D' and resid 907 through 909 No H-bonds generated for 'chain 'D' and resid 907 through 909' Processing helix chain 'D' and resid 912 through 920 removed outlier: 4.316A pdb=" N SER D 920 " --> pdb=" O ILE D 916 " (cutoff:3.500A) Processing helix chain 'D' and resid 922 through 948 Processing helix chain 'D' and resid 954 through 969 removed outlier: 4.614A pdb=" N ARG D 965 " --> pdb=" O ARG D 961 " (cutoff:3.500A) Proline residue: D 966 - end of helix Processing helix chain 'D' and resid 970 through 972 No H-bonds generated for 'chain 'D' and resid 970 through 972' Processing helix chain 'D' and resid 980 through 984 Processing helix chain 'D' and resid 1013 through 1029 Processing helix chain 'D' and resid 1029 through 1067 removed outlier: 5.312A pdb=" N GLY D1048 " --> pdb=" O SER D1044 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN D1049 " --> pdb=" O LYS D1045 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR D1059 " --> pdb=" O LYS D1055 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER D1060 " --> pdb=" O ALA D1056 " (cutoff:3.500A) Processing helix chain 'D' and resid 1072 through 1075 Processing helix chain 'D' and resid 1076 through 1090 removed outlier: 3.745A pdb=" N ARG D1090 " --> pdb=" O LYS D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1113 through 1141 Processing helix chain 'D' and resid 1142 through 1162 Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain 'B' and resid 211 through 212 removed outlier: 8.103A pdb=" N TYR B 212 " --> pdb=" O ASP B 78 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASP B 80 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE B 233 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ALA B 186 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N PHE B 234 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY B 188 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL B 236 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ALA B 190 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ILE B 154 " --> pdb=" O MET B 187 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL B 189 " --> pdb=" O ILE B 154 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N THR B 156 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLY B 157 " --> pdb=" O VAL B 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 985 through 987 removed outlier: 3.973A pdb=" N ILE B 985 " --> pdb=" O HIS B 998 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TRP B 996 " --> pdb=" O GLY B 987 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 21 through 23 Processing sheet with id=AA5, first strand: chain 'A' and resid 211 through 212 removed outlier: 8.103A pdb=" N TYR A 212 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASP A 80 " --> pdb=" O TYR A 212 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 233 " --> pdb=" O ASN A 90 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ALA A 186 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N PHE A 234 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY A 188 " --> pdb=" O PHE A 234 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL A 236 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA A 190 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ILE A 154 " --> pdb=" O MET A 187 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL A 189 " --> pdb=" O ILE A 154 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N THR A 156 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N GLY A 157 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 985 through 987 removed outlier: 3.973A pdb=" N ILE A 985 " --> pdb=" O HIS A 998 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TRP A 996 " --> pdb=" O GLY A 987 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 21 through 23 Processing sheet with id=AA8, first strand: chain 'C' and resid 211 through 212 removed outlier: 8.102A pdb=" N TYR C 212 " --> pdb=" O ASP C 78 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASP C 80 " --> pdb=" O TYR C 212 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE C 233 " --> pdb=" O ASN C 90 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ALA C 186 " --> pdb=" O ALA C 232 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N PHE C 234 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY C 188 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL C 236 " --> pdb=" O GLY C 188 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA C 190 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ILE C 154 " --> pdb=" O MET C 187 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL C 189 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N THR C 156 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLY C 157 " --> pdb=" O VAL C 122 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 985 through 987 removed outlier: 3.972A pdb=" N ILE C 985 " --> pdb=" O HIS C 998 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TRP C 996 " --> pdb=" O GLY C 987 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 21 through 23 Processing sheet with id=AB2, first strand: chain 'D' and resid 211 through 212 removed outlier: 8.102A pdb=" N TYR D 212 " --> pdb=" O ASP D 78 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ASP D 80 " --> pdb=" O TYR D 212 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE D 233 " --> pdb=" O ASN D 90 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ALA D 186 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N PHE D 234 " --> pdb=" O ALA D 186 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY D 188 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL D 236 " --> pdb=" O GLY D 188 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ALA D 190 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ILE D 154 " --> pdb=" O MET D 187 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL D 189 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N THR D 156 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLY D 157 " --> pdb=" O VAL D 122 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 985 through 987 removed outlier: 3.973A pdb=" N ILE D 985 " --> pdb=" O HIS D 998 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TRP D 996 " --> pdb=" O GLY D 987 " (cutoff:3.500A) 1812 hydrogen bonds defined for protein. 5376 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: 6.91 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8968 1.34 - 1.46: 5868 1.46 - 1.58: 16064 1.58 - 1.70: 20 1.70 - 1.82: 208 Bond restraints: 31128 Sorted by residual: bond pdb=" C4 ATP C2000 " pdb=" C5 ATP C2000 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.46e+01 bond pdb=" C4 ATP D2000 " pdb=" C5 ATP D2000 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.46e+01 bond pdb=" C4 ATP A2000 " pdb=" C5 ATP A2000 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.37e+01 bond pdb=" C4 ATP B2000 " pdb=" C5 ATP B2000 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.30e+01 bond pdb=" C PHE D 81 " pdb=" N THR D 82 " ideal model delta sigma weight residual 1.331 1.224 0.106 1.41e-02 5.03e+03 5.65e+01 ... (remaining 31123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 41837 3.92 - 7.83: 356 7.83 - 11.75: 27 11.75 - 15.66: 0 15.66 - 19.58: 4 Bond angle restraints: 42224 Sorted by residual: angle pdb=" PB ATP D2000 " pdb=" O3B ATP D2000 " pdb=" PG ATP D2000 " ideal model delta sigma weight residual 139.87 120.29 19.58 1.00e+00 1.00e+00 3.83e+02 angle pdb=" PB ATP B2000 " pdb=" O3B ATP B2000 " pdb=" PG ATP B2000 " ideal model delta sigma weight residual 139.87 120.30 19.57 1.00e+00 1.00e+00 3.83e+02 angle pdb=" PB ATP A2000 " pdb=" O3B ATP A2000 " pdb=" PG ATP A2000 " ideal model delta sigma weight residual 139.87 120.31 19.56 1.00e+00 1.00e+00 3.83e+02 angle pdb=" PB ATP C2000 " pdb=" O3B ATP C2000 " pdb=" PG ATP C2000 " ideal model delta sigma weight residual 139.87 120.35 19.52 1.00e+00 1.00e+00 3.81e+02 angle pdb=" PA ATP C2000 " pdb=" O3A ATP C2000 " pdb=" PB ATP C2000 " ideal model delta sigma weight residual 136.83 127.20 9.63 1.00e+00 1.00e+00 9.27e+01 ... (remaining 42219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 17841 17.81 - 35.63: 546 35.63 - 53.44: 92 53.44 - 71.26: 13 71.26 - 89.07: 36 Dihedral angle restraints: 18528 sinusoidal: 7544 harmonic: 10984 Sorted by residual: dihedral pdb=" CA ILE C 279 " pdb=" C ILE C 279 " pdb=" N ASP C 280 " pdb=" CA ASP C 280 " ideal model delta harmonic sigma weight residual -180.00 -153.14 -26.86 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA ILE B 279 " pdb=" C ILE B 279 " pdb=" N ASP B 280 " pdb=" CA ASP B 280 " ideal model delta harmonic sigma weight residual -180.00 -153.15 -26.85 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA ILE A 279 " pdb=" C ILE A 279 " pdb=" N ASP A 280 " pdb=" CA ASP A 280 " ideal model delta harmonic sigma weight residual -180.00 -153.16 -26.84 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 18525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3903 0.065 - 0.131: 786 0.131 - 0.196: 51 0.196 - 0.261: 4 0.261 - 0.327: 12 Chirality restraints: 4756 Sorted by residual: chirality pdb=" CB VAL A1003 " pdb=" CA VAL A1003 " pdb=" CG1 VAL A1003 " pdb=" CG2 VAL A1003 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CB VAL B1003 " pdb=" CA VAL B1003 " pdb=" CG1 VAL B1003 " pdb=" CG2 VAL B1003 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CB VAL C1003 " pdb=" CA VAL C1003 " pdb=" CG1 VAL C1003 " pdb=" CG2 VAL C1003 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 4753 not shown) Planarity restraints: 5300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 816 " -0.026 2.00e-02 2.50e+03 2.37e-02 1.40e+01 pdb=" CG TRP B 816 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP B 816 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP B 816 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 816 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 816 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 816 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 816 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 816 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 816 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 816 " 0.026 2.00e-02 2.50e+03 2.36e-02 1.40e+01 pdb=" CG TRP C 816 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP C 816 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP C 816 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 816 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 816 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 816 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 816 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 816 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP C 816 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 816 " -0.026 2.00e-02 2.50e+03 2.36e-02 1.39e+01 pdb=" CG TRP A 816 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP A 816 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A 816 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 816 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 816 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 816 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 816 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 816 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 816 " -0.003 2.00e-02 2.50e+03 ... (remaining 5297 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 8360 2.81 - 3.33: 26718 3.33 - 3.85: 47227 3.85 - 4.38: 54996 4.38 - 4.90: 95636 Nonbonded interactions: 232937 Sorted by model distance: nonbonded pdb=" O ARG A 354 " pdb=" OG1 THR A 357 " model vdw 2.286 3.040 nonbonded pdb=" O ARG C 354 " pdb=" OG1 THR C 357 " model vdw 2.286 3.040 nonbonded pdb=" O ARG B 354 " pdb=" OG1 THR B 357 " model vdw 2.286 3.040 nonbonded pdb=" O ARG D 354 " pdb=" OG1 THR D 357 " model vdw 2.286 3.040 nonbonded pdb=" OG1 THR A 21 " pdb=" OE2 GLU A 70 " model vdw 2.294 3.040 ... (remaining 232932 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: 0.09 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' selection = chain 'D' } 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: 1.110 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: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 29.400 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 : 0.007 0.106 31132 Z= 0.342 Angle : 0.976 19.577 42232 Z= 0.573 Chirality : 0.052 0.327 4756 Planarity : 0.007 0.060 5300 Dihedral : 10.396 89.071 11412 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.37 % Allowed : 2.47 % Favored : 97.16 % 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: -4.72 (0.09), residues: 3744 helix: -3.11 (0.06), residues: 2360 sheet: -1.50 (0.34), residues: 232 loop : -3.05 (0.15), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B1146 TYR 0.017 0.002 TYR D 339 PHE 0.023 0.003 PHE B1039 TRP 0.063 0.003 TRP B 816 HIS 0.009 0.002 HIS A1080 Details of bonding type rmsd covalent geometry : bond 0.00724 (31128) covalent geometry : angle 0.97557 (42224) SS BOND : bond 0.01613 ( 4) SS BOND : angle 2.89660 ( 8) hydrogen bonds : bond 0.21753 ( 1812) hydrogen bonds : angle 8.29914 ( 5376) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 655 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.7443 (mt0) cc_final: 0.6845 (tp40) REVERT: B 214 TRP cc_start: 0.7026 (p-90) cc_final: 0.6819 (p-90) REVERT: B 864 ASP cc_start: 0.6749 (t0) cc_final: 0.6530 (t0) REVERT: B 952 ASP cc_start: 0.7296 (m-30) cc_final: 0.7087 (m-30) REVERT: A 79 LEU cc_start: 0.7271 (tm) cc_final: 0.6711 (mm) REVERT: A 175 GLN cc_start: 0.7351 (mt0) cc_final: 0.6908 (tp40) REVERT: A 214 TRP cc_start: 0.6919 (p-90) cc_final: 0.6698 (p-90) REVERT: A 864 ASP cc_start: 0.6685 (t0) cc_final: 0.6476 (t0) REVERT: A 952 ASP cc_start: 0.7323 (m-30) cc_final: 0.7116 (m-30) REVERT: C 156 THR cc_start: 0.8216 (m) cc_final: 0.7988 (p) REVERT: C 175 GLN cc_start: 0.7450 (mt0) cc_final: 0.6834 (tp40) REVERT: C 864 ASP cc_start: 0.6694 (t0) cc_final: 0.6478 (t0) REVERT: C 952 ASP cc_start: 0.7221 (m-30) cc_final: 0.6992 (m-30) REVERT: D 175 GLN cc_start: 0.7440 (mt0) cc_final: 0.6845 (tp40) REVERT: D 214 TRP cc_start: 0.7023 (p-90) cc_final: 0.6822 (p-90) REVERT: D 864 ASP cc_start: 0.6748 (t0) cc_final: 0.6514 (t0) REVERT: D 952 ASP cc_start: 0.7291 (m-30) cc_final: 0.7083 (m-30) outliers start: 12 outliers final: 4 residues processed: 663 average time/residue: 0.8486 time to fit residues: 644.1417 Evaluate side-chains 318 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 314 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain D residue 1008 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 20.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN B 197 ASN B 296 GLN B 349 GLN B 405 ASN B 420 GLN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 ASN ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 782 ASN B 904 HIS B1010 GLN B1013 ASN A 90 ASN A 197 ASN A 248 ASN A 296 GLN A 349 GLN A 405 ASN A 420 GLN ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 ASN A 904 HIS A1010 GLN A1013 ASN C 90 ASN C 197 ASN C 248 ASN C 296 GLN C 405 ASN C 420 GLN ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 ASN ** C 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 782 ASN C 802 GLN C 904 HIS ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 ASN D 90 ASN D 197 ASN D 296 GLN D 349 GLN D 405 ASN D 420 GLN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 ASN ** D 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 782 ASN D 904 HIS ** D1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1013 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.176222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.113932 restraints weight = 39820.517| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.02 r_work: 0.3058 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 31132 Z= 0.209 Angle : 0.694 10.360 42232 Z= 0.356 Chirality : 0.042 0.171 4756 Planarity : 0.006 0.060 5300 Dihedral : 7.978 89.475 4312 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.99 % Allowed : 9.22 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.12), residues: 3744 helix: -0.26 (0.10), residues: 2432 sheet: -0.81 (0.32), residues: 252 loop : -2.96 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1058 TYR 0.022 0.002 TYR A 228 PHE 0.040 0.002 PHE C 793 TRP 0.024 0.002 TRP B 816 HIS 0.004 0.001 HIS D 454 Details of bonding type rmsd covalent geometry : bond 0.00504 (31128) covalent geometry : angle 0.69330 (42224) SS BOND : bond 0.00826 ( 4) SS BOND : angle 2.54635 ( 8) hydrogen bonds : bond 0.06403 ( 1812) hydrogen bonds : angle 4.86120 ( 5376) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 383 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.5922 (mmt180) cc_final: 0.5560 (mpt180) REVERT: B 92 LEU cc_start: 0.7322 (tt) cc_final: 0.7086 (tt) REVERT: B 94 LEU cc_start: 0.7205 (tp) cc_final: 0.6747 (pt) REVERT: B 165 ARG cc_start: 0.7836 (tmt170) cc_final: 0.7343 (ttp-170) REVERT: B 175 GLN cc_start: 0.7604 (mt0) cc_final: 0.6824 (tp40) REVERT: B 187 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7638 (mtm) REVERT: B 198 ARG cc_start: 0.5977 (ptp90) cc_final: 0.5746 (ptp90) REVERT: B 214 TRP cc_start: 0.7026 (p-90) cc_final: 0.6824 (p-90) REVERT: B 235 LEU cc_start: 0.7870 (mt) cc_final: 0.7521 (mm) REVERT: B 359 LYS cc_start: 0.5310 (tppt) cc_final: 0.4750 (tptt) REVERT: B 599 MET cc_start: 0.8402 (mtp) cc_final: 0.8145 (mtp) REVERT: B 864 ASP cc_start: 0.6866 (t0) cc_final: 0.6309 (t0) REVERT: B 1155 ASP cc_start: 0.8296 (t0) cc_final: 0.8086 (t0) REVERT: A 86 ARG cc_start: 0.5917 (mmt180) cc_final: 0.5539 (mpt180) REVERT: A 92 LEU cc_start: 0.7170 (tt) cc_final: 0.6919 (tt) REVERT: A 94 LEU cc_start: 0.7012 (tp) cc_final: 0.6687 (pt) REVERT: A 165 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.6123 (ttm-80) REVERT: A 194 VAL cc_start: 0.7445 (t) cc_final: 0.6978 (m) REVERT: A 198 ARG cc_start: 0.5897 (ptp90) cc_final: 0.5662 (ptp90) REVERT: A 214 TRP cc_start: 0.7049 (p-90) cc_final: 0.6847 (p-90) REVERT: A 355 ILE cc_start: 0.6294 (mt) cc_final: 0.5993 (tt) REVERT: A 359 LYS cc_start: 0.6268 (tptm) cc_final: 0.5328 (tppt) REVERT: A 608 GLU cc_start: 0.7382 (mp0) cc_final: 0.7155 (mp0) REVERT: A 864 ASP cc_start: 0.6911 (t0) cc_final: 0.6328 (t0) REVERT: A 1155 ASP cc_start: 0.8320 (t0) cc_final: 0.8108 (t0) REVERT: C 86 ARG cc_start: 0.5917 (mmt180) cc_final: 0.5549 (mpt180) REVERT: C 92 LEU cc_start: 0.7270 (tt) cc_final: 0.7020 (tt) REVERT: C 94 LEU cc_start: 0.7161 (tp) cc_final: 0.6731 (pt) REVERT: C 175 GLN cc_start: 0.7601 (mt0) cc_final: 0.6838 (tp40) REVERT: C 187 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7582 (mtm) REVERT: C 198 ARG cc_start: 0.5976 (ptp90) cc_final: 0.5745 (ptp90) REVERT: C 214 TRP cc_start: 0.6983 (p-90) cc_final: 0.6766 (p-90) REVERT: C 235 LEU cc_start: 0.7836 (mt) cc_final: 0.7473 (mm) REVERT: C 353 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6485 (mm-30) REVERT: C 359 LYS cc_start: 0.5428 (tppt) cc_final: 0.4749 (tptt) REVERT: C 599 MET cc_start: 0.8416 (mtp) cc_final: 0.8163 (mtp) REVERT: C 864 ASP cc_start: 0.6910 (t0) cc_final: 0.6320 (t0) REVERT: C 1155 ASP cc_start: 0.8303 (t0) cc_final: 0.8034 (t0) REVERT: D 86 ARG cc_start: 0.5992 (mmt180) cc_final: 0.5651 (mpt180) REVERT: D 92 LEU cc_start: 0.7320 (tt) cc_final: 0.7079 (tt) REVERT: D 94 LEU cc_start: 0.7210 (tp) cc_final: 0.6799 (pt) REVERT: D 165 ARG cc_start: 0.7772 (tmt170) cc_final: 0.7345 (ttp-170) REVERT: D 175 GLN cc_start: 0.7548 (mt0) cc_final: 0.6804 (tp40) REVERT: D 187 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7620 (mtm) REVERT: D 198 ARG cc_start: 0.5967 (ptp90) cc_final: 0.5738 (ptp90) REVERT: D 235 LEU cc_start: 0.7871 (mt) cc_final: 0.7527 (mm) REVERT: D 359 LYS cc_start: 0.5371 (tppt) cc_final: 0.4811 (tptt) REVERT: D 599 MET cc_start: 0.8407 (mtp) cc_final: 0.8147 (mtp) REVERT: D 864 ASP cc_start: 0.6883 (t0) cc_final: 0.6334 (t0) REVERT: D 1155 ASP cc_start: 0.8290 (t0) cc_final: 0.8082 (t0) outliers start: 97 outliers final: 33 residues processed: 449 average time/residue: 0.7424 time to fit residues: 387.7889 Evaluate side-chains 339 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 302 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain A residue 1087 TRP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1051 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 87 optimal weight: 2.9990 chunk 297 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 300 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 365 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 176 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 GLN B 420 GLN ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 802 GLN B1013 ASN B1028 ASN A 248 ASN A 261 GLN A 420 GLN A 584 ASN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 GLN C 420 GLN C 584 ASN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1013 ASN D 261 GLN D 420 GLN ** D 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 802 GLN D1010 GLN D1013 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.173962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.108464 restraints weight = 40047.561| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.04 r_work: 0.3033 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 31132 Z= 0.241 Angle : 0.686 11.666 42232 Z= 0.350 Chirality : 0.043 0.150 4756 Planarity : 0.006 0.062 5300 Dihedral : 7.641 87.576 4312 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.30 % Allowed : 11.22 % Favored : 85.48 % 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 (0.13), residues: 3744 helix: 0.75 (0.10), residues: 2420 sheet: -0.71 (0.31), residues: 252 loop : -2.85 (0.16), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 243 TYR 0.023 0.002 TYR C 104 PHE 0.031 0.002 PHE A 793 TRP 0.017 0.002 TRP C1054 HIS 0.005 0.002 HIS A1127 Details of bonding type rmsd covalent geometry : bond 0.00594 (31128) covalent geometry : angle 0.68539 (42224) SS BOND : bond 0.00990 ( 4) SS BOND : angle 2.70929 ( 8) hydrogen bonds : bond 0.06735 ( 1812) hydrogen bonds : angle 4.63006 ( 5376) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 311 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.5937 (mmt180) cc_final: 0.5552 (mpt180) REVERT: B 92 LEU cc_start: 0.7067 (tt) cc_final: 0.6833 (tt) REVERT: B 94 LEU cc_start: 0.6952 (tp) cc_final: 0.6481 (pt) REVERT: B 165 ARG cc_start: 0.7914 (tmt170) cc_final: 0.7279 (ttp-170) REVERT: B 187 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7546 (mtm) REVERT: B 198 ARG cc_start: 0.5837 (ptp90) cc_final: 0.5561 (ptp90) REVERT: B 235 LEU cc_start: 0.7782 (mt) cc_final: 0.7442 (mm) REVERT: B 344 ASP cc_start: 0.4580 (m-30) cc_final: 0.3920 (t0) REVERT: B 359 LYS cc_start: 0.5148 (tppt) cc_final: 0.4714 (tptt) REVERT: B 599 MET cc_start: 0.8514 (mtp) cc_final: 0.8229 (mtp) REVERT: B 635 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7909 (mp0) REVERT: B 684 MET cc_start: 0.9229 (mtm) cc_final: 0.9016 (mtt) REVERT: B 864 ASP cc_start: 0.7135 (t0) cc_final: 0.6588 (t0) REVERT: B 952 ASP cc_start: 0.8307 (m-30) cc_final: 0.8097 (m-30) REVERT: B 1155 ASP cc_start: 0.8319 (t0) cc_final: 0.8105 (t0) REVERT: A 86 ARG cc_start: 0.5949 (mmt180) cc_final: 0.5522 (mpt180) REVERT: A 92 LEU cc_start: 0.7115 (tt) cc_final: 0.6888 (tt) REVERT: A 94 LEU cc_start: 0.7159 (tp) cc_final: 0.6629 (pt) REVERT: A 183 LYS cc_start: 0.8084 (mmtt) cc_final: 0.7704 (mmpt) REVERT: A 198 ARG cc_start: 0.5841 (ptp90) cc_final: 0.5572 (ptp90) REVERT: A 289 ILE cc_start: 0.7587 (mt) cc_final: 0.7367 (mt) REVERT: A 344 ASP cc_start: 0.4549 (m-30) cc_final: 0.3971 (t0) REVERT: A 355 ILE cc_start: 0.6061 (mt) cc_final: 0.5723 (tt) REVERT: A 599 MET cc_start: 0.8465 (mtp) cc_final: 0.8236 (mtp) REVERT: A 635 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8121 (mp0) REVERT: A 684 MET cc_start: 0.9236 (mtm) cc_final: 0.9020 (mtt) REVERT: A 826 ARG cc_start: 0.7361 (ttt-90) cc_final: 0.6940 (ttt-90) REVERT: A 864 ASP cc_start: 0.7144 (t0) cc_final: 0.6574 (t0) REVERT: A 952 ASP cc_start: 0.8301 (m-30) cc_final: 0.8093 (m-30) REVERT: A 1155 ASP cc_start: 0.8309 (t0) cc_final: 0.8103 (t0) REVERT: C 86 ARG cc_start: 0.5902 (mmt180) cc_final: 0.5538 (mpt180) REVERT: C 92 LEU cc_start: 0.7160 (tt) cc_final: 0.6958 (tt) REVERT: C 94 LEU cc_start: 0.6947 (tp) cc_final: 0.6475 (pt) REVERT: C 187 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7493 (mtm) REVERT: C 198 ARG cc_start: 0.5841 (ptp90) cc_final: 0.5549 (ptp90) REVERT: C 344 ASP cc_start: 0.4582 (m-30) cc_final: 0.3990 (t0) REVERT: C 353 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6535 (mm-30) REVERT: C 359 LYS cc_start: 0.5069 (tppt) cc_final: 0.4687 (tptt) REVERT: C 599 MET cc_start: 0.8488 (mtp) cc_final: 0.8220 (mtp) REVERT: C 635 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7911 (mp0) REVERT: C 826 ARG cc_start: 0.7325 (ttt-90) cc_final: 0.7071 (ttt90) REVERT: C 864 ASP cc_start: 0.7135 (t0) cc_final: 0.6511 (t0) REVERT: C 952 ASP cc_start: 0.8298 (m-30) cc_final: 0.8090 (m-30) REVERT: C 1155 ASP cc_start: 0.8276 (t0) cc_final: 0.8062 (t0) REVERT: D 86 ARG cc_start: 0.5933 (mmt180) cc_final: 0.5551 (mpt180) REVERT: D 92 LEU cc_start: 0.7064 (tt) cc_final: 0.6831 (tt) REVERT: D 94 LEU cc_start: 0.6950 (tp) cc_final: 0.6480 (pt) REVERT: D 165 ARG cc_start: 0.7915 (tmt170) cc_final: 0.7277 (ttp-170) REVERT: D 187 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7530 (mtm) REVERT: D 198 ARG cc_start: 0.5834 (ptp90) cc_final: 0.5549 (ptp90) REVERT: D 235 LEU cc_start: 0.7782 (mt) cc_final: 0.7449 (mm) REVERT: D 344 ASP cc_start: 0.4609 (m-30) cc_final: 0.3977 (t0) REVERT: D 359 LYS cc_start: 0.5155 (tppt) cc_final: 0.4721 (tptt) REVERT: D 599 MET cc_start: 0.8525 (mtp) cc_final: 0.8240 (mtp) REVERT: D 635 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7901 (mp0) REVERT: D 684 MET cc_start: 0.9241 (mtm) cc_final: 0.9031 (mtt) REVERT: D 864 ASP cc_start: 0.7140 (t0) cc_final: 0.6572 (t0) REVERT: D 952 ASP cc_start: 0.8297 (m-30) cc_final: 0.8087 (m-30) REVERT: D 1155 ASP cc_start: 0.8310 (t0) cc_final: 0.8097 (t0) outliers start: 107 outliers final: 50 residues processed: 385 average time/residue: 0.6902 time to fit residues: 311.4355 Evaluate side-chains 346 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 289 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 635 GLU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain A residue 1087 TRP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 561 ASP Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1051 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 222 optimal weight: 20.0000 chunk 168 optimal weight: 0.5980 chunk 150 optimal weight: 2.9990 chunk 352 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 297 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1013 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN A1028 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 GLN C1013 ASN C1028 ASN D 420 GLN D1013 ASN D1028 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.177605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.112395 restraints weight = 40023.662| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.03 r_work: 0.3112 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 31132 Z= 0.121 Angle : 0.545 8.676 42232 Z= 0.278 Chirality : 0.038 0.142 4756 Planarity : 0.004 0.052 5300 Dihedral : 7.143 88.260 4312 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.16 % Allowed : 13.44 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.14), residues: 3744 helix: 1.51 (0.11), residues: 2436 sheet: -0.82 (0.30), residues: 252 loop : -2.69 (0.16), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 337 TYR 0.014 0.001 TYR D 339 PHE 0.012 0.001 PHE C 793 TRP 0.013 0.001 TRP C1054 HIS 0.004 0.001 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00270 (31128) covalent geometry : angle 0.54476 (42224) SS BOND : bond 0.00516 ( 4) SS BOND : angle 1.54461 ( 8) hydrogen bonds : bond 0.04435 ( 1812) hydrogen bonds : angle 4.18413 ( 5376) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 353 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 LEU cc_start: 0.6970 (tt) cc_final: 0.6727 (tt) REVERT: B 94 LEU cc_start: 0.6771 (tp) cc_final: 0.6455 (pt) REVERT: B 165 ARG cc_start: 0.7793 (tmt170) cc_final: 0.7216 (ttp-170) REVERT: B 183 LYS cc_start: 0.7882 (mmtt) cc_final: 0.7573 (mmpt) REVERT: B 187 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7438 (mtm) REVERT: B 198 ARG cc_start: 0.6024 (ptp90) cc_final: 0.5686 (ptp90) REVERT: B 337 ARG cc_start: 0.5275 (ttm110) cc_final: 0.4764 (ttm110) REVERT: B 397 GLU cc_start: 0.7597 (pt0) cc_final: 0.7396 (pp20) REVERT: B 599 MET cc_start: 0.8407 (mtp) cc_final: 0.8139 (mtp) REVERT: B 640 ARG cc_start: 0.8529 (mtm110) cc_final: 0.8303 (ttm110) REVERT: B 1155 ASP cc_start: 0.8243 (t0) cc_final: 0.7976 (t0) REVERT: A 92 LEU cc_start: 0.7120 (tt) cc_final: 0.6828 (tt) REVERT: A 94 LEU cc_start: 0.6746 (tp) cc_final: 0.6397 (pt) REVERT: A 183 LYS cc_start: 0.8113 (mmtt) cc_final: 0.7759 (mmpt) REVERT: A 198 ARG cc_start: 0.5929 (ptp90) cc_final: 0.5605 (ptp90) REVERT: A 235 LEU cc_start: 0.7774 (mt) cc_final: 0.7568 (mm) REVERT: A 289 ILE cc_start: 0.7646 (mt) cc_final: 0.7398 (mt) REVERT: A 355 ILE cc_start: 0.5978 (mt) cc_final: 0.5661 (tt) REVERT: A 359 LYS cc_start: 0.6038 (tptt) cc_final: 0.5267 (tptt) REVERT: A 397 GLU cc_start: 0.7663 (pt0) cc_final: 0.7446 (pp20) REVERT: A 599 MET cc_start: 0.8356 (mtp) cc_final: 0.8147 (mtp) REVERT: A 826 ARG cc_start: 0.7292 (ttt-90) cc_final: 0.7026 (ttt90) REVERT: C 92 LEU cc_start: 0.6806 (tt) cc_final: 0.6501 (tt) REVERT: C 94 LEU cc_start: 0.6728 (tp) cc_final: 0.6383 (pt) REVERT: C 183 LYS cc_start: 0.7870 (mmtt) cc_final: 0.7559 (mmpt) REVERT: C 187 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7506 (mtm) REVERT: C 198 ARG cc_start: 0.6027 (ptp90) cc_final: 0.5714 (ptp90) REVERT: C 235 LEU cc_start: 0.7592 (mt) cc_final: 0.7363 (mm) REVERT: C 300 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7090 (tt) REVERT: C 599 MET cc_start: 0.8281 (mtp) cc_final: 0.8032 (mtp) REVERT: C 640 ARG cc_start: 0.8545 (mtm110) cc_final: 0.8317 (ttm110) REVERT: C 826 ARG cc_start: 0.7207 (ttt-90) cc_final: 0.6945 (ttt90) REVERT: C 1087 TRP cc_start: 0.6571 (t60) cc_final: 0.6262 (t-100) REVERT: C 1155 ASP cc_start: 0.8247 (t0) cc_final: 0.7975 (t0) REVERT: D 92 LEU cc_start: 0.6968 (tt) cc_final: 0.6729 (tt) REVERT: D 94 LEU cc_start: 0.6772 (tp) cc_final: 0.6459 (pt) REVERT: D 165 ARG cc_start: 0.7804 (tmt170) cc_final: 0.7226 (ttp-170) REVERT: D 183 LYS cc_start: 0.7893 (mmtt) cc_final: 0.7579 (mmpt) REVERT: D 187 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.7459 (mtm) REVERT: D 198 ARG cc_start: 0.6028 (ptp90) cc_final: 0.5689 (ptp90) REVERT: D 337 ARG cc_start: 0.5193 (ttm110) cc_final: 0.4907 (ttm110) REVERT: D 397 GLU cc_start: 0.7666 (pt0) cc_final: 0.7452 (pp20) REVERT: D 599 MET cc_start: 0.8422 (mtp) cc_final: 0.8152 (mtp) REVERT: D 640 ARG cc_start: 0.8547 (mtm110) cc_final: 0.8316 (ttm110) REVERT: D 1155 ASP cc_start: 0.8268 (t0) cc_final: 0.8059 (t0) outliers start: 70 outliers final: 23 residues processed: 399 average time/residue: 0.7561 time to fit residues: 350.8451 Evaluate side-chains 315 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 288 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1051 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 8 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 211 optimal weight: 0.0770 chunk 299 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 138 optimal weight: 6.9990 chunk 218 optimal weight: 30.0000 chunk 318 optimal weight: 9.9990 chunk 104 optimal weight: 20.0000 overall best weight: 6.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 420 GLN B 669 GLN B 706 ASN B1013 ASN ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN A 669 GLN A 706 ASN A1013 ASN C 261 GLN C 420 GLN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 706 ASN C1013 ASN D 420 GLN ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 706 ASN D1013 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.172296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.108376 restraints weight = 40055.054| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.16 r_work: 0.2999 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 31132 Z= 0.299 Angle : 0.723 14.431 42232 Z= 0.369 Chirality : 0.046 0.179 4756 Planarity : 0.006 0.067 5300 Dihedral : 7.471 86.990 4312 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.05 % Allowed : 13.53 % Favored : 83.42 % 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: 0.00 (0.14), residues: 3744 helix: 1.24 (0.11), residues: 2436 sheet: -1.14 (0.29), residues: 260 loop : -2.74 (0.16), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 960 TYR 0.021 0.003 TYR A 228 PHE 0.025 0.003 PHE A 793 TRP 0.016 0.002 TRP C1054 HIS 0.006 0.002 HIS C 454 Details of bonding type rmsd covalent geometry : bond 0.00744 (31128) covalent geometry : angle 0.72239 (42224) SS BOND : bond 0.00995 ( 4) SS BOND : angle 2.70226 ( 8) hydrogen bonds : bond 0.07075 ( 1812) hydrogen bonds : angle 4.50352 ( 5376) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 308 time to evaluate : 1.179 Fit side-chains REVERT: B 92 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7120 (tt) REVERT: B 94 LEU cc_start: 0.6913 (tp) cc_final: 0.6646 (pt) REVERT: B 165 ARG cc_start: 0.7911 (tmt170) cc_final: 0.7522 (ttp80) REVERT: B 183 LYS cc_start: 0.8100 (mmtt) cc_final: 0.7705 (mmpt) REVERT: B 187 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7526 (mtm) REVERT: B 198 ARG cc_start: 0.5693 (ptp90) cc_final: 0.5409 (ptp90) REVERT: B 337 ARG cc_start: 0.5168 (ttm110) cc_final: 0.4803 (ttm110) REVERT: B 344 ASP cc_start: 0.4610 (m-30) cc_final: 0.3936 (t0) REVERT: B 599 MET cc_start: 0.8517 (mtp) cc_final: 0.8235 (mtp) REVERT: B 614 ASP cc_start: 0.8802 (t0) cc_final: 0.8566 (t0) REVERT: B 640 ARG cc_start: 0.8567 (mtm110) cc_final: 0.8364 (ttm110) REVERT: B 864 ASP cc_start: 0.7178 (t0) cc_final: 0.6683 (t0) REVERT: A 92 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.7065 (tt) REVERT: A 94 LEU cc_start: 0.6879 (tp) cc_final: 0.6574 (pt) REVERT: A 183 LYS cc_start: 0.8128 (mmtt) cc_final: 0.7716 (mmpt) REVERT: A 198 ARG cc_start: 0.5835 (ptp90) cc_final: 0.5546 (ptp90) REVERT: A 289 ILE cc_start: 0.7590 (mt) cc_final: 0.7374 (mt) REVERT: A 344 ASP cc_start: 0.4528 (m-30) cc_final: 0.3859 (t0) REVERT: A 599 MET cc_start: 0.8450 (mtp) cc_final: 0.8231 (mtp) REVERT: A 614 ASP cc_start: 0.8794 (t0) cc_final: 0.8555 (t0) REVERT: A 826 ARG cc_start: 0.7374 (ttt-90) cc_final: 0.7015 (ttt90) REVERT: A 864 ASP cc_start: 0.7177 (t0) cc_final: 0.6650 (t0) REVERT: C 92 LEU cc_start: 0.7184 (tt) cc_final: 0.6952 (tt) REVERT: C 94 LEU cc_start: 0.6857 (tp) cc_final: 0.6566 (pt) REVERT: C 183 LYS cc_start: 0.8091 (mmtt) cc_final: 0.7713 (mmpt) REVERT: C 198 ARG cc_start: 0.5699 (ptp90) cc_final: 0.5405 (ptp90) REVERT: C 300 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7400 (tt) REVERT: C 344 ASP cc_start: 0.4728 (m-30) cc_final: 0.4170 (t0) REVERT: C 397 GLU cc_start: 0.8638 (pp20) cc_final: 0.8239 (pp20) REVERT: C 599 MET cc_start: 0.8523 (mtp) cc_final: 0.8265 (mtp) REVERT: C 614 ASP cc_start: 0.8797 (t0) cc_final: 0.8561 (t0) REVERT: C 640 ARG cc_start: 0.8575 (mtm110) cc_final: 0.8369 (ttm110) REVERT: C 864 ASP cc_start: 0.7167 (t0) cc_final: 0.6635 (t0) REVERT: D 92 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.7138 (tt) REVERT: D 94 LEU cc_start: 0.6905 (tp) cc_final: 0.6641 (pt) REVERT: D 165 ARG cc_start: 0.7896 (tmt170) cc_final: 0.7505 (ttp80) REVERT: D 183 LYS cc_start: 0.8108 (mmtt) cc_final: 0.7702 (mmpt) REVERT: D 187 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7523 (mtm) REVERT: D 198 ARG cc_start: 0.5692 (ptp90) cc_final: 0.5402 (ptp90) REVERT: D 337 ARG cc_start: 0.5144 (ttm110) cc_final: 0.4773 (ttm110) REVERT: D 344 ASP cc_start: 0.4592 (m-30) cc_final: 0.3932 (t0) REVERT: D 599 MET cc_start: 0.8525 (mtp) cc_final: 0.8243 (mtp) REVERT: D 614 ASP cc_start: 0.8791 (t0) cc_final: 0.8554 (t0) REVERT: D 640 ARG cc_start: 0.8576 (mtm110) cc_final: 0.8372 (ttm110) REVERT: D 864 ASP cc_start: 0.7164 (t0) cc_final: 0.6665 (t0) outliers start: 99 outliers final: 48 residues processed: 375 average time/residue: 0.6674 time to fit residues: 295.2722 Evaluate side-chains 332 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 278 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 561 ASP Chi-restraints excluded: chain C residue 1003 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 1003 VAL Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1051 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 358 optimal weight: 2.9990 chunk 376 optimal weight: 1.9990 chunk 379 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 259 optimal weight: 6.9990 chunk 332 optimal weight: 4.9990 chunk 294 optimal weight: 4.9990 chunk 304 optimal weight: 10.0000 chunk 321 optimal weight: 4.9990 chunk 362 optimal weight: 0.7980 chunk 237 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 GLN B 175 GLN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 ASN B 706 ASN B1013 ASN A 148 GLN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN A1013 ASN C 148 GLN C 175 GLN C 248 ASN C 420 GLN ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 ASN D 148 GLN D 175 GLN D 420 GLN D 584 ASN D 706 ASN D1013 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.176847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.111976 restraints weight = 40274.182| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.09 r_work: 0.3074 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31132 Z= 0.123 Angle : 0.548 12.199 42232 Z= 0.281 Chirality : 0.038 0.150 4756 Planarity : 0.004 0.054 5300 Dihedral : 7.069 89.160 4312 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.07 % Allowed : 14.70 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.14), residues: 3744 helix: 1.80 (0.11), residues: 2432 sheet: -0.91 (0.30), residues: 252 loop : -2.62 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 826 TYR 0.014 0.001 TYR D 339 PHE 0.011 0.001 PHE C 793 TRP 0.013 0.001 TRP A1054 HIS 0.007 0.001 HIS D 454 Details of bonding type rmsd covalent geometry : bond 0.00279 (31128) covalent geometry : angle 0.54804 (42224) SS BOND : bond 0.00577 ( 4) SS BOND : angle 1.65833 ( 8) hydrogen bonds : bond 0.04452 ( 1812) hydrogen bonds : angle 4.09116 ( 5376) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 323 time to evaluate : 1.253 Fit side-chains REVERT: B 92 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6702 (tt) REVERT: B 94 LEU cc_start: 0.6741 (tp) cc_final: 0.6533 (pt) REVERT: B 141 ARG cc_start: 0.7017 (ppt90) cc_final: 0.6803 (ptm-80) REVERT: B 165 ARG cc_start: 0.7852 (tmt170) cc_final: 0.7211 (ttp-170) REVERT: B 183 LYS cc_start: 0.7996 (mmtt) cc_final: 0.7616 (mmpt) REVERT: B 187 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7460 (mtm) REVERT: B 198 ARG cc_start: 0.5873 (ptp90) cc_final: 0.5556 (ptp90) REVERT: B 300 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7545 (mm) REVERT: B 337 ARG cc_start: 0.5241 (ttm110) cc_final: 0.4826 (ttm110) REVERT: B 344 ASP cc_start: 0.4731 (m-30) cc_final: 0.4102 (t0) REVERT: B 599 MET cc_start: 0.8429 (mtp) cc_final: 0.8160 (mtp) REVERT: B 864 ASP cc_start: 0.6832 (t0) cc_final: 0.5532 (m-30) REVERT: A 92 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6754 (tt) REVERT: A 94 LEU cc_start: 0.6715 (tp) cc_final: 0.6469 (pt) REVERT: A 141 ARG cc_start: 0.7056 (ppt90) cc_final: 0.6849 (ptm-80) REVERT: A 183 LYS cc_start: 0.8013 (mmtt) cc_final: 0.7657 (mmpt) REVERT: A 198 ARG cc_start: 0.5865 (ptp90) cc_final: 0.5515 (ptp90) REVERT: A 289 ILE cc_start: 0.7681 (mt) cc_final: 0.7472 (mt) REVERT: A 344 ASP cc_start: 0.4666 (m-30) cc_final: 0.4107 (t0) REVERT: A 359 LYS cc_start: 0.6005 (tptt) cc_final: 0.5337 (tptt) REVERT: A 614 ASP cc_start: 0.8484 (t0) cc_final: 0.8266 (t0) REVERT: A 864 ASP cc_start: 0.6850 (t0) cc_final: 0.5559 (m-30) REVERT: C 92 LEU cc_start: 0.7172 (tt) cc_final: 0.6951 (tt) REVERT: C 94 LEU cc_start: 0.6735 (tp) cc_final: 0.6464 (pt) REVERT: C 141 ARG cc_start: 0.7041 (ppt90) cc_final: 0.6811 (ptm-80) REVERT: C 198 ARG cc_start: 0.5885 (ptp90) cc_final: 0.5570 (ptp90) REVERT: C 224 PHE cc_start: 0.7627 (m-80) cc_final: 0.7369 (m-80) REVERT: C 300 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7360 (tt) REVERT: C 344 ASP cc_start: 0.4656 (m-30) cc_final: 0.4049 (t0) REVERT: C 359 LYS cc_start: 0.5775 (tptt) cc_final: 0.5149 (tptt) REVERT: C 394 TYR cc_start: 0.7505 (m-80) cc_final: 0.7258 (m-80) REVERT: C 397 GLU cc_start: 0.8480 (pp20) cc_final: 0.8192 (pp20) REVERT: C 599 MET cc_start: 0.8321 (mtp) cc_final: 0.8064 (mtp) REVERT: C 826 ARG cc_start: 0.7221 (ttt-90) cc_final: 0.7000 (ttt90) REVERT: C 864 ASP cc_start: 0.6845 (t0) cc_final: 0.6325 (t0) REVERT: D 92 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6702 (tt) REVERT: D 94 LEU cc_start: 0.6736 (tp) cc_final: 0.6510 (pt) REVERT: D 141 ARG cc_start: 0.7027 (ppt90) cc_final: 0.6810 (ptm-80) REVERT: D 165 ARG cc_start: 0.7793 (tmt170) cc_final: 0.7152 (ttp-170) REVERT: D 183 LYS cc_start: 0.7993 (mmtt) cc_final: 0.7614 (mmpt) REVERT: D 187 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7487 (mtm) REVERT: D 198 ARG cc_start: 0.5972 (ptp90) cc_final: 0.5645 (ptp90) REVERT: D 300 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7550 (mm) REVERT: D 337 ARG cc_start: 0.5312 (ttm110) cc_final: 0.4951 (ttm110) REVERT: D 344 ASP cc_start: 0.4754 (m-30) cc_final: 0.4137 (t0) REVERT: D 359 LYS cc_start: 0.5735 (tptt) cc_final: 0.5061 (tptt) REVERT: D 599 MET cc_start: 0.8438 (mtp) cc_final: 0.8169 (mtp) REVERT: D 864 ASP cc_start: 0.6841 (t0) cc_final: 0.5540 (m-30) outliers start: 67 outliers final: 27 residues processed: 368 average time/residue: 0.7442 time to fit residues: 319.3268 Evaluate side-chains 321 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 286 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 1003 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 780 LEU Chi-restraints excluded: chain D residue 1003 VAL Chi-restraints excluded: chain D residue 1008 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 310 optimal weight: 20.0000 chunk 144 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 369 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 chunk 233 optimal weight: 9.9990 chunk 271 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 373 optimal weight: 6.9990 chunk 245 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 420 GLN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 706 ASN B1013 ASN ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN A1013 ASN C 248 ASN C 420 GLN ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 669 GLN C 706 ASN C1013 ASN D 248 ASN D 420 GLN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 GLN D 706 ASN D1013 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.173344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.109265 restraints weight = 40130.498| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.07 r_work: 0.2999 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 31132 Z= 0.230 Angle : 0.649 12.030 42232 Z= 0.331 Chirality : 0.043 0.152 4756 Planarity : 0.005 0.061 5300 Dihedral : 7.220 86.571 4312 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.25 % Allowed : 15.14 % Favored : 82.61 % 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: 0.39 (0.14), residues: 3744 helix: 1.59 (0.11), residues: 2440 sheet: -1.13 (0.29), residues: 260 loop : -2.68 (0.16), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 826 TYR 0.018 0.002 TYR B 228 PHE 0.017 0.002 PHE A 793 TRP 0.015 0.002 TRP C1054 HIS 0.008 0.002 HIS C 454 Details of bonding type rmsd covalent geometry : bond 0.00569 (31128) covalent geometry : angle 0.64787 (42224) SS BOND : bond 0.00853 ( 4) SS BOND : angle 2.36596 ( 8) hydrogen bonds : bond 0.06198 ( 1812) hydrogen bonds : angle 4.29195 ( 5376) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 298 time to evaluate : 1.217 Fit side-chains REVERT: B 92 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.7135 (tt) REVERT: B 94 LEU cc_start: 0.6824 (tp) cc_final: 0.6620 (pt) REVERT: B 141 ARG cc_start: 0.7160 (ppt90) cc_final: 0.6764 (ptm-80) REVERT: B 165 ARG cc_start: 0.7910 (tmt170) cc_final: 0.7522 (ttp80) REVERT: B 183 LYS cc_start: 0.8128 (mmtt) cc_final: 0.7710 (mmpt) REVERT: B 187 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7577 (mmt) REVERT: B 198 ARG cc_start: 0.5759 (ptp90) cc_final: 0.5452 (ptp90) REVERT: B 337 ARG cc_start: 0.5093 (ttm110) cc_final: 0.4818 (ttm110) REVERT: B 344 ASP cc_start: 0.4789 (m-30) cc_final: 0.4071 (t0) REVERT: B 518 ARG cc_start: 0.5772 (OUTLIER) cc_final: 0.5096 (mtm-85) REVERT: B 599 MET cc_start: 0.8526 (mtp) cc_final: 0.8258 (mtp) REVERT: B 605 GLU cc_start: 0.7421 (tp30) cc_final: 0.7188 (tp30) REVERT: B 614 ASP cc_start: 0.8731 (t0) cc_final: 0.8515 (t0) REVERT: B 635 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7934 (mp0) REVERT: B 864 ASP cc_start: 0.7078 (t0) cc_final: 0.6548 (t0) REVERT: A 92 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.7018 (tt) REVERT: A 94 LEU cc_start: 0.6819 (tp) cc_final: 0.6575 (pt) REVERT: A 183 LYS cc_start: 0.8160 (mmtt) cc_final: 0.7753 (mmpt) REVERT: A 198 ARG cc_start: 0.5798 (ptp90) cc_final: 0.5483 (ptp90) REVERT: A 235 LEU cc_start: 0.7695 (mt) cc_final: 0.7369 (mm) REVERT: A 289 ILE cc_start: 0.7719 (mt) cc_final: 0.7500 (mt) REVERT: A 300 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7588 (mm) REVERT: A 344 ASP cc_start: 0.4779 (m-30) cc_final: 0.4121 (t0) REVERT: A 518 ARG cc_start: 0.5769 (OUTLIER) cc_final: 0.5096 (mtm-85) REVERT: A 614 ASP cc_start: 0.8763 (t0) cc_final: 0.8528 (t0) REVERT: A 635 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: A 864 ASP cc_start: 0.7089 (t0) cc_final: 0.6567 (t0) REVERT: C 78 ASP cc_start: 0.7004 (t0) cc_final: 0.6740 (t0) REVERT: C 94 LEU cc_start: 0.6792 (tp) cc_final: 0.6566 (pt) REVERT: C 198 ARG cc_start: 0.5781 (ptp90) cc_final: 0.5469 (ptp90) REVERT: C 300 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7424 (tt) REVERT: C 344 ASP cc_start: 0.4783 (m-30) cc_final: 0.4231 (t0) REVERT: C 359 LYS cc_start: 0.5949 (tptt) cc_final: 0.5185 (tptt) REVERT: C 518 ARG cc_start: 0.5777 (OUTLIER) cc_final: 0.5089 (mtm-85) REVERT: C 599 MET cc_start: 0.8510 (mtp) cc_final: 0.8265 (mtp) REVERT: C 605 GLU cc_start: 0.7429 (tp30) cc_final: 0.7195 (tp30) REVERT: C 614 ASP cc_start: 0.8734 (t0) cc_final: 0.8514 (t0) REVERT: C 635 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: C 864 ASP cc_start: 0.7080 (t0) cc_final: 0.6533 (t0) REVERT: C 952 ASP cc_start: 0.8342 (m-30) cc_final: 0.8117 (m-30) REVERT: D 92 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7134 (tt) REVERT: D 94 LEU cc_start: 0.6779 (tp) cc_final: 0.6567 (pt) REVERT: D 141 ARG cc_start: 0.7134 (ppt90) cc_final: 0.6721 (ptm-80) REVERT: D 165 ARG cc_start: 0.7917 (tmt170) cc_final: 0.7526 (ttp80) REVERT: D 183 LYS cc_start: 0.8126 (mmtt) cc_final: 0.7708 (mmpt) REVERT: D 187 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7577 (mmt) REVERT: D 198 ARG cc_start: 0.5763 (ptp90) cc_final: 0.5454 (ptp90) REVERT: D 344 ASP cc_start: 0.4794 (m-30) cc_final: 0.4082 (t0) REVERT: D 359 LYS cc_start: 0.5887 (tptt) cc_final: 0.5109 (tptt) REVERT: D 397 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8404 (pp20) REVERT: D 599 MET cc_start: 0.8537 (mtp) cc_final: 0.8268 (mtp) REVERT: D 605 GLU cc_start: 0.7429 (tp30) cc_final: 0.7204 (tp30) REVERT: D 614 ASP cc_start: 0.8733 (t0) cc_final: 0.8516 (t0) REVERT: D 635 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7936 (mp0) REVERT: D 864 ASP cc_start: 0.7072 (t0) cc_final: 0.6554 (t0) outliers start: 73 outliers final: 34 residues processed: 350 average time/residue: 0.7349 time to fit residues: 300.0105 Evaluate side-chains 329 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 280 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 420 GLN Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 635 GLU Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 420 GLN Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 420 GLN Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 1003 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 420 GLN Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain D residue 1003 VAL Chi-restraints excluded: chain D residue 1008 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 209 optimal weight: 6.9990 chunk 282 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 180 optimal weight: 0.6980 chunk 342 optimal weight: 2.9990 chunk 254 optimal weight: 9.9990 chunk 339 optimal weight: 6.9990 chunk 374 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 248 ASN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 ASN ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN A1013 ASN C 248 ASN C 420 GLN ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 706 ASN C1013 ASN D 248 ASN D 420 GLN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 706 ASN D1013 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.174698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.109630 restraints weight = 40252.017| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.09 r_work: 0.3043 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 31132 Z= 0.163 Angle : 0.593 11.614 42232 Z= 0.304 Chirality : 0.040 0.144 4756 Planarity : 0.005 0.057 5300 Dihedral : 7.084 86.401 4312 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.07 % Allowed : 15.63 % Favored : 82.31 % 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: 0.59 (0.14), residues: 3744 helix: 1.74 (0.11), residues: 2444 sheet: -1.07 (0.30), residues: 260 loop : -2.62 (0.16), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 253 TYR 0.017 0.002 TYR C 104 PHE 0.013 0.002 PHE A 793 TRP 0.014 0.002 TRP C1054 HIS 0.008 0.001 HIS D 454 Details of bonding type rmsd covalent geometry : bond 0.00391 (31128) covalent geometry : angle 0.59223 (42224) SS BOND : bond 0.00739 ( 4) SS BOND : angle 2.07005 ( 8) hydrogen bonds : bond 0.05276 ( 1812) hydrogen bonds : angle 4.16425 ( 5376) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 315 time to evaluate : 1.256 Fit side-chains REVERT: B 92 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.7050 (tt) REVERT: B 141 ARG cc_start: 0.7159 (ppt90) cc_final: 0.6763 (ptm-80) REVERT: B 165 ARG cc_start: 0.7896 (tmt170) cc_final: 0.7513 (ttp80) REVERT: B 183 LYS cc_start: 0.8143 (mmtt) cc_final: 0.7761 (mmpt) REVERT: B 187 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7567 (mmt) REVERT: B 198 ARG cc_start: 0.5771 (ptp90) cc_final: 0.5449 (ptp90) REVERT: B 344 ASP cc_start: 0.4861 (m-30) cc_final: 0.4172 (t0) REVERT: B 518 ARG cc_start: 0.5849 (OUTLIER) cc_final: 0.5140 (mtm-85) REVERT: B 599 MET cc_start: 0.8422 (mtp) cc_final: 0.8140 (mtp) REVERT: B 864 ASP cc_start: 0.6823 (t0) cc_final: 0.6321 (t0) REVERT: A 78 ASP cc_start: 0.6947 (t0) cc_final: 0.6683 (t0) REVERT: A 92 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6927 (tt) REVERT: A 94 LEU cc_start: 0.6718 (tp) cc_final: 0.6478 (pt) REVERT: A 141 ARG cc_start: 0.7070 (ppt90) cc_final: 0.6843 (ptm-80) REVERT: A 183 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7730 (mmpt) REVERT: A 198 ARG cc_start: 0.5851 (ptp90) cc_final: 0.5504 (ptp90) REVERT: A 235 LEU cc_start: 0.7638 (mt) cc_final: 0.7350 (mm) REVERT: A 289 ILE cc_start: 0.7701 (mt) cc_final: 0.7482 (mt) REVERT: A 300 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7612 (mm) REVERT: A 344 ASP cc_start: 0.4818 (m-30) cc_final: 0.4308 (t0) REVERT: A 518 ARG cc_start: 0.5852 (OUTLIER) cc_final: 0.5153 (mtm-85) REVERT: A 864 ASP cc_start: 0.6848 (t0) cc_final: 0.6341 (t0) REVERT: C 78 ASP cc_start: 0.6954 (t0) cc_final: 0.6689 (t0) REVERT: C 141 ARG cc_start: 0.7092 (ppt90) cc_final: 0.6843 (ptm-80) REVERT: C 183 LYS cc_start: 0.7844 (mmtt) cc_final: 0.7597 (mmtt) REVERT: C 198 ARG cc_start: 0.5805 (ptp90) cc_final: 0.5483 (ptp90) REVERT: C 300 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7354 (tt) REVERT: C 344 ASP cc_start: 0.4829 (m-30) cc_final: 0.4221 (t0) REVERT: C 508 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7535 (ttp80) REVERT: C 518 ARG cc_start: 0.5834 (OUTLIER) cc_final: 0.5136 (mtm-85) REVERT: C 599 MET cc_start: 0.8440 (mtp) cc_final: 0.8214 (mtp) REVERT: C 864 ASP cc_start: 0.6943 (t0) cc_final: 0.6469 (t0) REVERT: C 952 ASP cc_start: 0.8259 (m-30) cc_final: 0.8035 (m-30) REVERT: D 92 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6913 (tt) REVERT: D 141 ARG cc_start: 0.7162 (ppt90) cc_final: 0.6765 (ptm-80) REVERT: D 165 ARG cc_start: 0.7910 (tmt170) cc_final: 0.7523 (ttp80) REVERT: D 183 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7783 (mmpt) REVERT: D 198 ARG cc_start: 0.5809 (ptp90) cc_final: 0.5465 (ptp90) REVERT: D 255 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8107 (mt-10) REVERT: D 344 ASP cc_start: 0.4914 (m-30) cc_final: 0.4203 (t0) REVERT: D 359 LYS cc_start: 0.5700 (tptt) cc_final: 0.5015 (tptt) REVERT: D 397 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8313 (pp20) REVERT: D 599 MET cc_start: 0.8437 (mtp) cc_final: 0.8157 (mtp) REVERT: D 864 ASP cc_start: 0.6832 (t0) cc_final: 0.6320 (t0) outliers start: 67 outliers final: 36 residues processed: 357 average time/residue: 0.7088 time to fit residues: 296.4831 Evaluate side-chains 340 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 292 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1006 SER Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 420 GLN Chi-restraints excluded: chain C residue 508 ARG Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 1003 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 420 GLN Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 780 LEU Chi-restraints excluded: chain D residue 1003 VAL Chi-restraints excluded: chain D residue 1008 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 158 optimal weight: 6.9990 chunk 216 optimal weight: 10.0000 chunk 14 optimal weight: 0.0770 chunk 35 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 371 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 311 optimal weight: 10.0000 chunk 7 optimal weight: 0.4980 chunk 67 optimal weight: 0.9990 overall best weight: 1.9144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 GLN B 248 ASN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS B 706 ASN B1013 ASN ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS A 706 ASN A1013 ASN C 148 GLN C 248 ASN ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 HIS C 706 ASN C1013 ASN D 148 GLN D 248 ASN D 454 HIS D 706 ASN D1013 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.175825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.111703 restraints weight = 40336.291| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.14 r_work: 0.3052 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31132 Z= 0.135 Angle : 0.565 11.234 42232 Z= 0.290 Chirality : 0.038 0.168 4756 Planarity : 0.005 0.052 5300 Dihedral : 6.973 87.231 4312 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.88 % Allowed : 16.25 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.14), residues: 3744 helix: 1.89 (0.11), residues: 2448 sheet: -1.02 (0.30), residues: 260 loop : -2.55 (0.16), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 253 TYR 0.014 0.001 TYR D 339 PHE 0.010 0.001 PHE A 793 TRP 0.014 0.001 TRP A1054 HIS 0.008 0.001 HIS D 454 Details of bonding type rmsd covalent geometry : bond 0.00314 (31128) covalent geometry : angle 0.56421 (42224) SS BOND : bond 0.00618 ( 4) SS BOND : angle 1.68864 ( 8) hydrogen bonds : bond 0.04725 ( 1812) hydrogen bonds : angle 4.06487 ( 5376) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 304 time to evaluate : 1.113 Fit side-chains REVERT: B 141 ARG cc_start: 0.7081 (ppt90) cc_final: 0.6846 (ptm-80) REVERT: B 165 ARG cc_start: 0.7869 (tmt170) cc_final: 0.7169 (ttp-170) REVERT: B 183 LYS cc_start: 0.8152 (mmtt) cc_final: 0.7729 (mmpt) REVERT: B 187 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7602 (mtm) REVERT: B 198 ARG cc_start: 0.5778 (ptp90) cc_final: 0.5422 (ptp90) REVERT: B 300 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7591 (mm) REVERT: B 344 ASP cc_start: 0.4808 (m-30) cc_final: 0.4013 (t0) REVERT: B 359 LYS cc_start: 0.5707 (tptt) cc_final: 0.4865 (tptt) REVERT: B 518 ARG cc_start: 0.5811 (OUTLIER) cc_final: 0.5105 (mtm-85) REVERT: B 599 MET cc_start: 0.8387 (mtp) cc_final: 0.8109 (mtp) REVERT: B 864 ASP cc_start: 0.6730 (t0) cc_final: 0.5495 (m-30) REVERT: A 78 ASP cc_start: 0.6922 (t0) cc_final: 0.6677 (t0) REVERT: A 92 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6783 (tt) REVERT: A 94 LEU cc_start: 0.6661 (tp) cc_final: 0.6428 (pt) REVERT: A 183 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7734 (mmpt) REVERT: A 198 ARG cc_start: 0.5839 (ptp90) cc_final: 0.5475 (ptp90) REVERT: A 235 LEU cc_start: 0.7596 (mt) cc_final: 0.7336 (mm) REVERT: A 289 ILE cc_start: 0.7694 (mt) cc_final: 0.7485 (mt) REVERT: A 300 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7656 (mm) REVERT: A 344 ASP cc_start: 0.4839 (m-30) cc_final: 0.4275 (t0) REVERT: A 359 LYS cc_start: 0.5894 (tptt) cc_final: 0.5353 (tptt) REVERT: A 518 ARG cc_start: 0.5801 (OUTLIER) cc_final: 0.5113 (mtm-85) REVERT: A 864 ASP cc_start: 0.6746 (t0) cc_final: 0.5502 (m-30) REVERT: C 141 ARG cc_start: 0.7101 (ppt90) cc_final: 0.6844 (ptm-80) REVERT: C 198 ARG cc_start: 0.5805 (ptp90) cc_final: 0.5447 (ptp90) REVERT: C 300 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7366 (tt) REVERT: C 344 ASP cc_start: 0.4831 (m-30) cc_final: 0.4157 (t0) REVERT: C 359 LYS cc_start: 0.5741 (tptt) cc_final: 0.4969 (tptt) REVERT: C 518 ARG cc_start: 0.5813 (OUTLIER) cc_final: 0.5116 (mtm-85) REVERT: C 599 MET cc_start: 0.8378 (mtp) cc_final: 0.8137 (mtp) REVERT: C 605 GLU cc_start: 0.7574 (tp30) cc_final: 0.7361 (tp30) REVERT: C 864 ASP cc_start: 0.6790 (t0) cc_final: 0.6277 (t0) REVERT: C 952 ASP cc_start: 0.8252 (m-30) cc_final: 0.8051 (m-30) REVERT: C 1087 TRP cc_start: 0.6363 (t60) cc_final: 0.5966 (t-100) REVERT: D 141 ARG cc_start: 0.7079 (ppt90) cc_final: 0.6846 (ptm-80) REVERT: D 165 ARG cc_start: 0.7878 (tmt170) cc_final: 0.7171 (ttp-170) REVERT: D 183 LYS cc_start: 0.8149 (mmtt) cc_final: 0.7722 (mmpt) REVERT: D 198 ARG cc_start: 0.5782 (ptp90) cc_final: 0.5424 (ptp90) REVERT: D 255 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7995 (mt-10) REVERT: D 300 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7580 (mm) REVERT: D 344 ASP cc_start: 0.4834 (m-30) cc_final: 0.4069 (t0) REVERT: D 359 LYS cc_start: 0.5747 (tptt) cc_final: 0.5045 (tptt) REVERT: D 599 MET cc_start: 0.8406 (mtp) cc_final: 0.8130 (mtp) REVERT: D 864 ASP cc_start: 0.6741 (t0) cc_final: 0.5505 (m-30) REVERT: D 1000 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7514 (mp0) outliers start: 61 outliers final: 25 residues processed: 339 average time/residue: 0.7066 time to fit residues: 280.3512 Evaluate side-chains 318 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 283 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 1003 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 1003 VAL Chi-restraints excluded: chain D residue 1008 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 36 optimal weight: 3.9990 chunk 353 optimal weight: 10.0000 chunk 238 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 chunk 236 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 363 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 306 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 197 optimal weight: 20.0000 overall best weight: 5.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 248 ASN B 420 GLN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 706 ASN B1013 ASN A 148 GLN ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS A 706 ASN A1013 ASN C 148 GLN C 248 ASN C 420 GLN ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 HIS C 706 ASN C1013 ASN D 248 ASN D 420 GLN D 706 ASN D1013 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.171927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.107751 restraints weight = 40020.285| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.01 r_work: 0.3007 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 31132 Z= 0.288 Angle : 0.711 11.842 42232 Z= 0.366 Chirality : 0.046 0.184 4756 Planarity : 0.006 0.066 5300 Dihedral : 7.297 85.540 4312 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.66 % Allowed : 16.49 % Favored : 81.84 % 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: 0.19 (0.14), residues: 3744 helix: 1.38 (0.10), residues: 2448 sheet: -1.05 (0.30), residues: 260 loop : -2.69 (0.16), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 253 TYR 0.021 0.003 TYR B 228 PHE 0.027 0.003 PHE A 250 TRP 0.015 0.002 TRP A1054 HIS 0.009 0.002 HIS C 454 Details of bonding type rmsd covalent geometry : bond 0.00716 (31128) covalent geometry : angle 0.71019 (42224) SS BOND : bond 0.01034 ( 4) SS BOND : angle 2.83834 ( 8) hydrogen bonds : bond 0.06842 ( 1812) hydrogen bonds : angle 4.39886 ( 5376) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7488 Ramachandran restraints generated. 3744 Oldfield, 0 Emsley, 3744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 294 time to evaluate : 1.161 Fit side-chains REVERT: B 78 ASP cc_start: 0.6752 (t0) cc_final: 0.6538 (t70) REVERT: B 165 ARG cc_start: 0.7821 (tmt170) cc_final: 0.7440 (ttp80) REVERT: B 183 LYS cc_start: 0.8129 (mmtt) cc_final: 0.7701 (mmpt) REVERT: B 194 VAL cc_start: 0.7165 (OUTLIER) cc_final: 0.6825 (p) REVERT: B 344 ASP cc_start: 0.4748 (m-30) cc_final: 0.4134 (t0) REVERT: B 518 ARG cc_start: 0.5930 (OUTLIER) cc_final: 0.5135 (mtm-85) REVERT: B 599 MET cc_start: 0.8489 (mtp) cc_final: 0.8212 (mtp) REVERT: B 614 ASP cc_start: 0.8746 (t0) cc_final: 0.8520 (t0) REVERT: B 864 ASP cc_start: 0.7074 (t0) cc_final: 0.6537 (t0) REVERT: A 78 ASP cc_start: 0.6915 (t0) cc_final: 0.6709 (t70) REVERT: A 183 LYS cc_start: 0.8124 (mmtt) cc_final: 0.7721 (mmpt) REVERT: A 194 VAL cc_start: 0.7220 (OUTLIER) cc_final: 0.6775 (p) REVERT: A 198 ARG cc_start: 0.5806 (ptp90) cc_final: 0.5562 (ptp90) REVERT: A 289 ILE cc_start: 0.7610 (mt) cc_final: 0.7402 (mt) REVERT: A 344 ASP cc_start: 0.4723 (m-30) cc_final: 0.4140 (t0) REVERT: A 518 ARG cc_start: 0.5969 (OUTLIER) cc_final: 0.5165 (mtm-85) REVERT: A 605 GLU cc_start: 0.7618 (tp30) cc_final: 0.7389 (tp30) REVERT: A 614 ASP cc_start: 0.8733 (t0) cc_final: 0.8514 (t0) REVERT: A 864 ASP cc_start: 0.7102 (t0) cc_final: 0.6543 (t0) REVERT: C 141 ARG cc_start: 0.7100 (ppt90) cc_final: 0.6681 (ptm-80) REVERT: C 194 VAL cc_start: 0.7170 (OUTLIER) cc_final: 0.6743 (p) REVERT: C 198 ARG cc_start: 0.5783 (ptp90) cc_final: 0.5550 (ptp90) REVERT: C 300 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7459 (tt) REVERT: C 344 ASP cc_start: 0.4817 (m-30) cc_final: 0.4259 (t0) REVERT: C 508 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7579 (ttp80) REVERT: C 518 ARG cc_start: 0.5928 (OUTLIER) cc_final: 0.5142 (mtm-85) REVERT: C 599 MET cc_start: 0.8492 (mtp) cc_final: 0.8243 (mtp) REVERT: C 614 ASP cc_start: 0.8743 (t0) cc_final: 0.8521 (t0) REVERT: C 864 ASP cc_start: 0.7113 (t0) cc_final: 0.6551 (t0) REVERT: D 78 ASP cc_start: 0.6764 (t0) cc_final: 0.6551 (t70) REVERT: D 165 ARG cc_start: 0.7833 (tmt170) cc_final: 0.7444 (ttp80) REVERT: D 183 LYS cc_start: 0.8131 (mmtt) cc_final: 0.7700 (mmpt) REVERT: D 194 VAL cc_start: 0.7178 (OUTLIER) cc_final: 0.6835 (p) REVERT: D 255 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: D 344 ASP cc_start: 0.4755 (m-30) cc_final: 0.4146 (t0) REVERT: D 508 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7559 (ttp80) REVERT: D 599 MET cc_start: 0.8499 (mtp) cc_final: 0.8221 (mtp) REVERT: D 614 ASP cc_start: 0.8735 (t0) cc_final: 0.8508 (t0) REVERT: D 864 ASP cc_start: 0.7082 (t0) cc_final: 0.6534 (t0) outliers start: 54 outliers final: 29 residues processed: 330 average time/residue: 0.7238 time to fit residues: 278.4326 Evaluate side-chains 320 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 280 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 420 GLN Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 420 GLN Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 508 ARG Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 1003 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 508 ARG Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 1003 VAL Chi-restraints excluded: chain D residue 1008 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 354 optimal weight: 3.9990 chunk 256 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 238 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 224 optimal weight: 6.9990 chunk 298 optimal weight: 6.9990 chunk 309 optimal weight: 7.9990 chunk 347 optimal weight: 0.9980 chunk 258 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 248 ASN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 ASN A 148 GLN A 248 ASN ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS A1013 ASN C 148 GLN C 248 ASN C 420 GLN ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 HIS C1013 ASN D 248 ASN D 420 GLN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1013 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.174526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.109999 restraints weight = 40261.052| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.30 r_work: 0.3042 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 31132 Z= 0.158 Angle : 0.597 11.277 42232 Z= 0.309 Chirality : 0.040 0.171 4756 Planarity : 0.005 0.062 5300 Dihedral : 7.078 86.261 4312 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.70 % Allowed : 16.68 % Favored : 81.63 % 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 (0.14), residues: 3744 helix: 1.67 (0.11), residues: 2444 sheet: -0.97 (0.31), residues: 260 loop : -2.63 (0.16), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 141 TYR 0.020 0.002 TYR B 104 PHE 0.029 0.002 PHE B 250 TRP 0.013 0.001 TRP C1054 HIS 0.009 0.001 HIS C 454 Details of bonding type rmsd covalent geometry : bond 0.00379 (31128) covalent geometry : angle 0.59595 (42224) SS BOND : bond 0.00731 ( 4) SS BOND : angle 2.06433 ( 8) hydrogen bonds : bond 0.05208 ( 1812) hydrogen bonds : angle 4.20226 ( 5376) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14333.57 seconds wall clock time: 243 minutes 17.44 seconds (14597.44 seconds total)