Starting phenix.real_space_refine on Mon Sep 14 12:03:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6bco_7083/09_2026/6bco_7083.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bco_7083/09_2026/6bco_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 { model { file = "/net/cci-nas-00/data/ceres_data/6bco_7083/09_2026/6bco_7083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bco_7083/09_2026/6bco_7083.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6bco_7083/09_2026/6bco_7083.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6bco_7083/09_2026/6bco_7083.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6bco_7083/09_2026/6bco_7083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bco_7083/09_2026/6bco_7083.map" } 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-2.2.1-6174/lib/python3.11/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: 6.57, per 1000 atoms: 0.22 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: 2.51 Conformation dependent library (CDL) restraints added in 1.7 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: 1.28 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: 6.86 Time building geometry restraints manager: 3.41 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: 17817 17.81 - 35.63: 471 35.63 - 53.44: 79 53.44 - 71.26: 13 71.26 - 89.07: 24 Dihedral angle restraints: 18404 sinusoidal: 7420 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 18401 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: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 29.280 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 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 : 9.771 89.071 11288 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/Z covalent geometry : bond 0.00724 / 0.34 (31128) covalent geometry : angle 0.97557 / 0.57 (42224) SS BOND : bond 0.01613 / 0.97 ( 4) SS BOND : angle 2.89660 / 1.76 ( 8) hydrogen bonds : bond 0.21753 / 14.40 ( 1812) hydrogen bonds : angle 8.29914 / 5.79 ( 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 : 1.231 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: 0.7324 (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: 0.7610 time to fit residues: 581.7815 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 : 1.124 ------------------------------------------------------------------------------- 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... 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 ASN A 90 ASN A 197 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.176390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.110572 restraints weight = 39912.221| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.01 r_work: 0.3082 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2647 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= 0.212 Angle : 0.694 10.542 42232 Z= 0.355 Chirality : 0.043 0.172 4756 Planarity : 0.006 0.060 5300 Dihedral : 6.210 83.922 4188 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % 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: -1.65 (0.12), residues: 3744 helix: -0.27 (0.10), residues: 2432 sheet: -0.82 (0.32), residues: 252 loop : -2.95 (0.15), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1058 TYR 0.023 0.002 TYR A 228 PHE 0.041 0.002 PHE A 793 TRP 0.024 0.002 TRP A 816 HIS 0.005 0.002 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.21 (31128) covalent geometry : angle 0.69289 / 0.35 (42224) SS BOND : bond 0.00855 / 0.51 ( 4) SS BOND : angle 2.49525 / 1.49 ( 8) hydrogen bonds : bond 0.06351 / 4.27 ( 1812) hydrogen bonds : angle 4.84372 / 3.40 ( 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 485 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 388 time to evaluate : 1.307 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: 0.5906 (mmt180) cc_final: 0.5545 (mpt180) REVERT: B 92 LEU cc_start: 0.7252 (tt) cc_final: 0.7019 (tt) REVERT: B 94 LEU cc_start: 0.7181 (tp) cc_final: 0.6675 (pt) REVERT: B 165 ARG cc_start: 0.7816 (tmt170) cc_final: 0.7306 (ttp-170) REVERT: B 187 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7549 (mtm) REVERT: B 198 ARG cc_start: 0.5940 (ptp90) cc_final: 0.5693 (ptp90) REVERT: B 235 LEU cc_start: 0.7813 (mt) cc_final: 0.7474 (mm) REVERT: B 358 ARG cc_start: 0.6035 (mmt180) cc_final: 0.5802 (mmt-90) REVERT: B 599 MET cc_start: 0.8339 (mtp) cc_final: 0.8070 (mtp) REVERT: B 608 GLU cc_start: 0.7307 (mp0) cc_final: 0.7080 (mp0) REVERT: B 864 ASP cc_start: 0.6791 (t0) cc_final: 0.6293 (t0) REVERT: B 1155 ASP cc_start: 0.8261 (t0) cc_final: 0.8048 (t0) REVERT: A 86 ARG cc_start: 0.5888 (mmt180) cc_final: 0.5515 (mpt180) REVERT: A 92 LEU cc_start: 0.7104 (tt) cc_final: 0.6853 (tt) REVERT: A 94 LEU cc_start: 0.6961 (tp) cc_final: 0.6587 (pt) REVERT: A 165 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6118 (ttm-80) REVERT: A 194 VAL cc_start: 0.7433 (t) cc_final: 0.6970 (m) REVERT: A 198 ARG cc_start: 0.5856 (ptp90) cc_final: 0.5561 (ptp90) REVERT: A 214 TRP cc_start: 0.7042 (p-90) cc_final: 0.6830 (p-90) REVERT: A 252 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6662 (mt) REVERT: A 288 ARG cc_start: 0.6688 (tpm-80) cc_final: 0.6444 (mmp80) REVERT: A 355 ILE cc_start: 0.6226 (mt) cc_final: 0.5916 (tt) REVERT: A 358 ARG cc_start: 0.6014 (mmt180) cc_final: 0.5787 (mmt-90) REVERT: A 608 GLU cc_start: 0.7289 (mp0) cc_final: 0.7081 (mp0) REVERT: A 864 ASP cc_start: 0.6791 (t0) cc_final: 0.6263 (t0) REVERT: A 1155 ASP cc_start: 0.8287 (t0) cc_final: 0.8082 (t0) REVERT: C 86 ARG cc_start: 0.5900 (mmt180) cc_final: 0.5526 (mpt180) REVERT: C 92 LEU cc_start: 0.7201 (tt) cc_final: 0.6956 (tt) REVERT: C 94 LEU cc_start: 0.7042 (tp) cc_final: 0.6667 (pt) REVERT: C 175 GLN cc_start: 0.7580 (mt0) cc_final: 0.6832 (tp40) REVERT: C 187 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7492 (mtm) REVERT: C 198 ARG cc_start: 0.5938 (ptp90) cc_final: 0.5698 (ptp90) REVERT: C 235 LEU cc_start: 0.7774 (mt) cc_final: 0.7423 (mm) REVERT: C 353 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6505 (mm-30) REVERT: C 358 ARG cc_start: 0.6054 (mmt180) cc_final: 0.5827 (mmt-90) REVERT: C 359 LYS cc_start: 0.5328 (tppt) cc_final: 0.4674 (tptt) REVERT: C 599 MET cc_start: 0.8344 (mtp) cc_final: 0.8085 (mtp) REVERT: C 608 GLU cc_start: 0.7303 (mp0) cc_final: 0.7076 (mp0) REVERT: C 864 ASP cc_start: 0.6787 (t0) cc_final: 0.6230 (t0) REVERT: C 1155 ASP cc_start: 0.8274 (t0) cc_final: 0.7999 (t0) REVERT: D 86 ARG cc_start: 0.5971 (mmt180) cc_final: 0.5631 (mpt180) REVERT: D 92 LEU cc_start: 0.7247 (tt) cc_final: 0.7004 (tt) REVERT: D 94 LEU cc_start: 0.7212 (tp) cc_final: 0.6770 (pt) REVERT: D 165 ARG cc_start: 0.7767 (tmt170) cc_final: 0.7271 (ttp-170) REVERT: D 187 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7543 (mtm) REVERT: D 198 ARG cc_start: 0.5937 (ptp90) cc_final: 0.5681 (ptp90) REVERT: D 235 LEU cc_start: 0.7824 (mt) cc_final: 0.7487 (mm) REVERT: D 358 ARG cc_start: 0.6031 (mmt180) cc_final: 0.5793 (mmt-90) REVERT: D 599 MET cc_start: 0.8350 (mtp) cc_final: 0.8079 (mtp) REVERT: D 608 GLU cc_start: 0.7320 (mp0) cc_final: 0.7096 (mp0) REVERT: D 864 ASP cc_start: 0.6803 (t0) cc_final: 0.6316 (t0) REVERT: D 1155 ASP cc_start: 0.8264 (t0) cc_final: 0.8050 (t0) outliers start: 97 outliers final: 32 residues processed: 454 average time/residue: 0.6899 time to fit residues: 367.1994 Evaluate side-chains 336 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 299 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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 408 ASP 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 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 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 408 ASP 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: 1.9990 chunk 297 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 300 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 365 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 176 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 B1010 GLN B1013 ASN B1028 ASN A 261 GLN A 420 GLN ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 GLN A1010 GLN A1013 ASN C 420 GLN ** C 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 802 GLN C1010 GLN D 261 GLN D 420 GLN ** 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 = 0.4089 r_free = 0.4089 target = 0.174457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.109661 restraints weight = 39976.235| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.02 r_work: 0.3027 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 31132 Z= 0.225 Angle : 0.668 11.216 42232 Z= 0.340 Chirality : 0.043 0.144 4756 Planarity : 0.006 0.060 5300 Dihedral : 5.977 81.005 4188 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.39 % Allowed : 11.07 % Favored : 85.54 % 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: -0.46 (0.13), residues: 3744 helix: 0.80 (0.10), residues: 2424 sheet: -0.69 (0.31), residues: 252 loop : -2.81 (0.16), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 243 TYR 0.023 0.002 TYR C 104 PHE 0.029 0.002 PHE A 793 TRP 0.017 0.002 TRP D1054 HIS 0.004 0.002 HIS D1127 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.22 (31128) covalent geometry : angle 0.66665 / 0.34 (42224) SS BOND : bond 0.00911 / 0.55 ( 4) SS BOND : angle 2.56229 / 1.52 ( 8) hydrogen bonds : bond 0.06538 / 4.38 ( 1812) hydrogen bonds : angle 4.59374 / 3.23 ( 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 420 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 310 time to evaluate : 1.230 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: 0.5925 (mmt180) cc_final: 0.5556 (mpt180) REVERT: B 92 LEU cc_start: 0.7221 (tt) cc_final: 0.6933 (tt) REVERT: B 94 LEU cc_start: 0.7011 (tp) cc_final: 0.6566 (pt) REVERT: B 165 ARG cc_start: 0.7938 (tmt170) cc_final: 0.7330 (ttp-170) REVERT: B 183 LYS cc_start: 0.8147 (mmtt) cc_final: 0.7768 (mmpt) REVERT: B 187 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7583 (mtm) REVERT: B 198 ARG cc_start: 0.5972 (ptp90) cc_final: 0.5712 (ptp90) REVERT: B 235 LEU cc_start: 0.7811 (mt) cc_final: 0.7550 (mm) REVERT: B 344 ASP cc_start: 0.4549 (m-30) cc_final: 0.3897 (t0) REVERT: B 355 ILE cc_start: 0.6131 (mt) cc_final: 0.5712 (tt) REVERT: B 359 LYS cc_start: 0.5264 (tppt) cc_final: 0.4826 (tptm) REVERT: B 599 MET cc_start: 0.8514 (mtp) cc_final: 0.8213 (mtp) REVERT: B 635 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7920 (mp0) REVERT: B 684 MET cc_start: 0.9230 (mtm) cc_final: 0.9026 (mtt) REVERT: B 826 ARG cc_start: 0.7415 (ttt-90) cc_final: 0.7004 (ttt-90) REVERT: B 864 ASP cc_start: 0.7122 (t0) cc_final: 0.6558 (t0) REVERT: B 1155 ASP cc_start: 0.8338 (t0) cc_final: 0.8125 (t0) REVERT: A 86 ARG cc_start: 0.5928 (mmt180) cc_final: 0.5489 (mpt180) REVERT: A 92 LEU cc_start: 0.7248 (tt) cc_final: 0.6998 (tt) REVERT: A 94 LEU cc_start: 0.7124 (tp) cc_final: 0.6617 (pt) REVERT: A 183 LYS cc_start: 0.8090 (mmtt) cc_final: 0.7704 (mmpt) REVERT: A 187 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7433 (mtm) REVERT: A 198 ARG cc_start: 0.5864 (ptp90) cc_final: 0.5580 (ptp90) REVERT: A 358 ARG cc_start: 0.6154 (mmt180) cc_final: 0.5945 (mmt-90) REVERT: A 599 MET cc_start: 0.8474 (mtp) cc_final: 0.8239 (mtp) REVERT: A 635 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8122 (mp0) REVERT: A 684 MET cc_start: 0.9231 (mtm) cc_final: 0.9024 (mtt) REVERT: A 864 ASP cc_start: 0.7123 (t0) cc_final: 0.6508 (t0) REVERT: A 1155 ASP cc_start: 0.8330 (t0) cc_final: 0.8122 (t0) REVERT: C 86 ARG cc_start: 0.5884 (mmt180) cc_final: 0.5499 (mpt180) REVERT: C 94 LEU cc_start: 0.6973 (tp) cc_final: 0.6512 (pt) REVERT: C 187 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7549 (mtm) REVERT: C 198 ARG cc_start: 0.5951 (ptp90) cc_final: 0.5685 (ptp90) REVERT: C 235 LEU cc_start: 0.7783 (mt) cc_final: 0.7461 (mm) REVERT: C 344 ASP cc_start: 0.4578 (m-30) cc_final: 0.3985 (t0) REVERT: C 353 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6528 (mm-30) REVERT: C 599 MET cc_start: 0.8495 (mtp) cc_final: 0.8228 (mtp) REVERT: C 635 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: C 826 ARG cc_start: 0.7363 (ttt-90) cc_final: 0.7160 (ttt-90) REVERT: C 864 ASP cc_start: 0.7127 (t0) cc_final: 0.6496 (t0) REVERT: C 1155 ASP cc_start: 0.8297 (t0) cc_final: 0.8084 (t0) REVERT: D 86 ARG cc_start: 0.5928 (mmt180) cc_final: 0.5564 (mpt180) REVERT: D 92 LEU cc_start: 0.7217 (tt) cc_final: 0.6933 (tt) REVERT: D 94 LEU cc_start: 0.7007 (tp) cc_final: 0.6561 (pt) REVERT: D 165 ARG cc_start: 0.7965 (tmt170) cc_final: 0.7353 (ttp-170) REVERT: D 183 LYS cc_start: 0.8147 (mmtt) cc_final: 0.7774 (mmpt) REVERT: D 187 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7564 (mtm) REVERT: D 198 ARG cc_start: 0.5855 (ptp90) cc_final: 0.5568 (ptp90) REVERT: D 235 LEU cc_start: 0.7807 (mt) cc_final: 0.7552 (mm) REVERT: D 344 ASP cc_start: 0.4547 (m-30) cc_final: 0.3905 (t0) REVERT: D 355 ILE cc_start: 0.6165 (mt) cc_final: 0.5767 (tt) REVERT: D 358 ARG cc_start: 0.6160 (mmt180) cc_final: 0.5947 (mmt-90) REVERT: D 359 LYS cc_start: 0.5270 (tppt) cc_final: 0.4826 (tptm) REVERT: D 599 MET cc_start: 0.8534 (mtp) cc_final: 0.8231 (mtp) REVERT: D 635 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8112 (mp0) REVERT: D 684 MET cc_start: 0.9239 (mtm) cc_final: 0.9039 (mtt) REVERT: D 826 ARG cc_start: 0.7408 (ttt-90) cc_final: 0.6994 (ttt-90) REVERT: D 864 ASP cc_start: 0.7121 (t0) cc_final: 0.6545 (t0) REVERT: D 952 ASP cc_start: 0.8326 (m-30) cc_final: 0.8125 (m-30) REVERT: D 1155 ASP cc_start: 0.8330 (t0) cc_final: 0.8118 (t0) outliers start: 110 outliers final: 49 residues processed: 390 average time/residue: 0.6565 time to fit residues: 302.4649 Evaluate side-chains 351 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 294 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 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 187 MET 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 301 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 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: 0.2980 chunk 150 optimal weight: 2.9990 chunk 352 optimal weight: 4.9990 chunk 175 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 297 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1013 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN A1028 ASN C 420 GLN C 584 ASN C1013 ASN C1028 ASN D 420 GLN D1013 ASN D1028 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.177563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.113485 restraints weight = 39863.504| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.17 r_work: 0.3066 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 31132 Z= 0.124 Angle : 0.549 8.595 42232 Z= 0.279 Chirality : 0.038 0.162 4756 Planarity : 0.004 0.052 5300 Dihedral : 5.596 83.439 4188 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.40 % Allowed : 13.13 % Favored : 84.46 % 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: 0.37 (0.14), residues: 3744 helix: 1.55 (0.11), residues: 2436 sheet: -0.78 (0.30), residues: 252 loop : -2.70 (0.16), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 826 TYR 0.013 0.001 TYR D 339 PHE 0.013 0.001 PHE C 793 TRP 0.014 0.001 TRP A1054 HIS 0.004 0.001 HIS B1127 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (31128) covalent geometry : angle 0.54837 / 0.28 (42224) SS BOND : bond 0.00531 / 0.32 ( 4) SS BOND : angle 1.52016 / 0.90 ( 8) hydrogen bonds : bond 0.04536 / 3.05 ( 1812) hydrogen bonds : angle 4.19687 / 2.96 ( 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 429 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 351 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 LEU cc_start: 0.7061 (tt) cc_final: 0.6823 (tt) REVERT: B 94 LEU cc_start: 0.6805 (tp) cc_final: 0.6490 (pt) REVERT: B 165 ARG cc_start: 0.7896 (tmt170) cc_final: 0.7311 (ttp-170) REVERT: B 183 LYS cc_start: 0.8099 (mmtt) cc_final: 0.7738 (mmpt) REVERT: B 187 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7515 (mtm) REVERT: B 198 ARG cc_start: 0.6035 (ptp90) cc_final: 0.5713 (ptp90) REVERT: B 359 LYS cc_start: 0.5425 (tppt) cc_final: 0.4924 (tptt) REVERT: B 397 GLU cc_start: 0.7708 (pt0) cc_final: 0.7496 (pp20) REVERT: B 599 MET cc_start: 0.8462 (mtp) cc_final: 0.8213 (mtp) REVERT: B 640 ARG cc_start: 0.8589 (mtm110) cc_final: 0.8363 (ttm110) REVERT: B 1155 ASP cc_start: 0.8323 (t0) cc_final: 0.8104 (t0) REVERT: A 92 LEU cc_start: 0.7043 (tt) cc_final: 0.6795 (tt) REVERT: A 94 LEU cc_start: 0.6766 (tp) cc_final: 0.6417 (pt) REVERT: A 183 LYS cc_start: 0.8089 (mmtt) cc_final: 0.7744 (mmpt) REVERT: A 187 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7611 (mtm) REVERT: A 198 ARG cc_start: 0.5971 (ptp90) cc_final: 0.5657 (ptp90) REVERT: A 235 LEU cc_start: 0.7789 (mt) cc_final: 0.7479 (mm) REVERT: A 355 ILE cc_start: 0.6232 (mt) cc_final: 0.5789 (tt) REVERT: A 397 GLU cc_start: 0.7721 (pt0) cc_final: 0.7489 (pp20) REVERT: A 640 ARG cc_start: 0.8592 (mtm110) cc_final: 0.8366 (ttm110) REVERT: C 94 LEU cc_start: 0.6965 (tp) cc_final: 0.6747 (pt) REVERT: C 183 LYS cc_start: 0.7880 (mmtt) cc_final: 0.7570 (mmpt) REVERT: C 187 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7582 (mtm) REVERT: C 198 ARG cc_start: 0.6046 (ptp90) cc_final: 0.5723 (ptp90) REVERT: C 300 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7172 (tt) REVERT: C 397 GLU cc_start: 0.7701 (pt0) cc_final: 0.7490 (pp20) REVERT: C 599 MET cc_start: 0.8351 (mtp) cc_final: 0.8118 (mtp) REVERT: C 640 ARG cc_start: 0.8605 (mtm110) cc_final: 0.8377 (ttm110) REVERT: C 864 ASP cc_start: 0.6912 (t0) cc_final: 0.6336 (t0) REVERT: C 1087 TRP cc_start: 0.6578 (t60) cc_final: 0.6265 (t-100) REVERT: C 1155 ASP cc_start: 0.8301 (t0) cc_final: 0.8033 (t0) REVERT: D 92 LEU cc_start: 0.7052 (tt) cc_final: 0.6817 (tt) REVERT: D 94 LEU cc_start: 0.6825 (tp) cc_final: 0.6524 (pt) REVERT: D 165 ARG cc_start: 0.7905 (tmt170) cc_final: 0.7320 (ttp-170) REVERT: D 183 LYS cc_start: 0.8097 (mmtt) cc_final: 0.7735 (mmpt) REVERT: D 187 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7510 (mtm) REVERT: D 198 ARG cc_start: 0.6037 (ptp90) cc_final: 0.5713 (ptp90) REVERT: D 359 LYS cc_start: 0.5341 (tppt) cc_final: 0.4844 (tptt) REVERT: D 397 GLU cc_start: 0.7717 (pt0) cc_final: 0.7494 (pp20) REVERT: D 599 MET cc_start: 0.8469 (mtp) cc_final: 0.8215 (mtp) REVERT: D 864 ASP cc_start: 0.6911 (t0) cc_final: 0.6631 (t0) outliers start: 78 outliers final: 25 residues processed: 404 average time/residue: 0.6673 time to fit residues: 317.0136 Evaluate side-chains 327 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 297 time to evaluate : 1.186 ------------------------------------------------------------------------------- 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 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 187 MET Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 274 VAL 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: 4.9990 chunk 211 optimal weight: 0.9980 chunk 299 optimal weight: 8.9990 chunk 97 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 chunk 218 optimal weight: 30.0000 chunk 318 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 420 GLN B 584 ASN B 669 GLN B 706 ASN B1013 ASN A 420 GLN A 584 ASN 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 584 ASN ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4065 r_free = 0.4065 target = 0.172526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.108448 restraints weight = 40062.698| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.16 r_work: 0.2990 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 31132 Z= 0.298 Angle : 0.721 14.586 42232 Z= 0.366 Chirality : 0.046 0.179 4756 Planarity : 0.006 0.067 5300 Dihedral : 5.846 77.096 4188 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.36 % Allowed : 13.26 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.14), residues: 3744 helix: 1.28 (0.11), residues: 2432 sheet: -1.07 (0.29), residues: 260 loop : -2.71 (0.16), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 826 TYR 0.020 0.003 TYR A 228 PHE 0.023 0.003 PHE C 793 TRP 0.016 0.002 TRP C1054 HIS 0.007 0.002 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00743 / 0.30 (31128) covalent geometry : angle 0.71972 / 0.37 (42224) SS BOND : bond 0.00974 / 0.58 ( 4) SS BOND : angle 2.65096 / 1.55 ( 8) hydrogen bonds : bond 0.07000 / 4.68 ( 1812) hydrogen bonds : angle 4.48599 / 3.15 ( 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 415 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 306 time to evaluate : 1.235 Fit side-chains REVERT: B 92 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7155 (tt) REVERT: B 94 LEU cc_start: 0.6914 (tp) cc_final: 0.6649 (pt) REVERT: B 165 ARG cc_start: 0.7890 (tmt170) cc_final: 0.7501 (ttp80) REVERT: B 183 LYS cc_start: 0.8113 (mmtt) cc_final: 0.7694 (mmpt) REVERT: B 187 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7557 (mtm) REVERT: B 198 ARG cc_start: 0.5879 (ptp90) cc_final: 0.5529 (ptp90) REVERT: B 344 ASP cc_start: 0.4550 (m-30) cc_final: 0.3858 (t0) REVERT: B 359 LYS cc_start: 0.5075 (tppt) cc_final: 0.4664 (tptt) REVERT: B 599 MET cc_start: 0.8526 (mtp) cc_final: 0.8248 (mtp) REVERT: B 614 ASP cc_start: 0.8776 (t0) cc_final: 0.8561 (t0) REVERT: B 640 ARG cc_start: 0.8582 (mtm110) cc_final: 0.8378 (ttm110) REVERT: B 864 ASP cc_start: 0.7151 (t0) cc_final: 0.6641 (t0) REVERT: A 91 PHE cc_start: 0.7136 (OUTLIER) cc_final: 0.6806 (t80) REVERT: A 92 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.7085 (tt) REVERT: A 94 LEU cc_start: 0.6896 (tp) cc_final: 0.6602 (pt) REVERT: A 183 LYS cc_start: 0.8125 (mmtt) cc_final: 0.7714 (mmpt) REVERT: A 198 ARG cc_start: 0.5794 (ptp90) cc_final: 0.5498 (ptp90) REVERT: A 344 ASP cc_start: 0.4512 (m-30) cc_final: 0.3848 (t0) REVERT: A 614 ASP cc_start: 0.8804 (t0) cc_final: 0.8565 (t0) REVERT: A 640 ARG cc_start: 0.8577 (mtm110) cc_final: 0.8373 (ttm110) REVERT: A 864 ASP cc_start: 0.7177 (t0) cc_final: 0.6623 (t0) REVERT: C 94 LEU cc_start: 0.7006 (tp) cc_final: 0.6764 (pt) REVERT: C 183 LYS cc_start: 0.8089 (mmtt) cc_final: 0.7708 (mmpt) REVERT: C 198 ARG cc_start: 0.5707 (ptp90) cc_final: 0.5394 (ptp90) REVERT: C 300 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7351 (tt) REVERT: C 344 ASP cc_start: 0.4733 (m-30) cc_final: 0.4173 (t0) REVERT: C 358 ARG cc_start: 0.6095 (OUTLIER) cc_final: 0.5807 (mmt-90) REVERT: C 599 MET cc_start: 0.8538 (mtp) cc_final: 0.8281 (mtp) REVERT: C 614 ASP cc_start: 0.8787 (t0) cc_final: 0.8571 (t0) REVERT: C 640 ARG cc_start: 0.8592 (mtm110) cc_final: 0.8386 (ttm110) REVERT: C 864 ASP cc_start: 0.7172 (t0) cc_final: 0.6630 (t0) REVERT: D 92 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.7007 (tt) REVERT: D 94 LEU cc_start: 0.6858 (tp) cc_final: 0.6602 (pt) REVERT: D 165 ARG cc_start: 0.7891 (tmt170) cc_final: 0.7499 (ttp80) REVERT: D 183 LYS cc_start: 0.8118 (mmtt) cc_final: 0.7698 (mmpt) REVERT: D 187 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7539 (mtm) REVERT: D 198 ARG cc_start: 0.5876 (ptp90) cc_final: 0.5525 (ptp90) REVERT: D 344 ASP cc_start: 0.4640 (m-30) cc_final: 0.3978 (t0) REVERT: D 359 LYS cc_start: 0.5120 (tppt) cc_final: 0.4696 (tptt) REVERT: D 599 MET cc_start: 0.8536 (mtp) cc_final: 0.8254 (mtp) REVERT: D 614 ASP cc_start: 0.8768 (t0) cc_final: 0.8554 (t0) REVERT: D 640 ARG cc_start: 0.8593 (mtm110) cc_final: 0.8389 (ttm110) REVERT: D 864 ASP cc_start: 0.7129 (t0) cc_final: 0.6631 (t0) outliers start: 109 outliers final: 54 residues processed: 375 average time/residue: 0.6089 time to fit residues: 272.2338 Evaluate side-chains 341 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 279 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 408 ASP 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 B residue 1051 ASP Chi-restraints excluded: chain A residue 91 PHE 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 301 LEU Chi-restraints excluded: chain A residue 408 ASP 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 358 ARG 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 1006 SER 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 408 ASP 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 1006 SER 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: 1.9990 chunk 376 optimal weight: 2.9990 chunk 379 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 259 optimal weight: 0.8980 chunk 332 optimal weight: 4.9990 chunk 294 optimal weight: 3.9990 chunk 304 optimal weight: 8.9990 chunk 321 optimal weight: 2.9990 chunk 362 optimal weight: 0.9980 chunk 237 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 148 GLN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 706 ASN B1013 ASN A 148 GLN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN C 148 GLN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 ASN D 148 GLN D 706 ASN D1013 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.177219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.111541 restraints weight = 40296.902| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.96 r_work: 0.3111 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3586 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= 0.118 Angle : 0.549 12.157 42232 Z= 0.279 Chirality : 0.038 0.149 4756 Planarity : 0.004 0.054 5300 Dihedral : 5.432 80.563 4188 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.03 % Allowed : 14.83 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.14), residues: 3744 helix: 1.86 (0.11), residues: 2432 sheet: -0.84 (0.30), residues: 252 loop : -2.66 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 249 TYR 0.013 0.001 TYR D 339 PHE 0.010 0.001 PHE C 793 TRP 0.012 0.001 TRP C1054 HIS 0.006 0.001 HIS C 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (31128) covalent geometry : angle 0.54825 / 0.28 (42224) SS BOND : bond 0.00501 / 0.30 ( 4) SS BOND : angle 1.61757 / 0.96 ( 8) hydrogen bonds : bond 0.04366 / 2.94 ( 1812) hydrogen bonds : angle 4.07266 / 2.87 ( 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 391 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 325 time to evaluate : 0.828 Fit side-chains REVERT: B 92 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6640 (tt) REVERT: B 94 LEU cc_start: 0.6694 (tp) cc_final: 0.6475 (pt) REVERT: B 141 ARG cc_start: 0.6908 (ppt90) cc_final: 0.6701 (ptm-80) REVERT: B 165 ARG cc_start: 0.7809 (tmt170) cc_final: 0.7162 (ttp-170) REVERT: B 183 LYS cc_start: 0.8116 (mmtt) cc_final: 0.7718 (mmpt) REVERT: B 187 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.7341 (mtm) REVERT: B 198 ARG cc_start: 0.5926 (ptp90) cc_final: 0.5569 (ptp90) REVERT: B 300 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7378 (mm) REVERT: B 344 ASP cc_start: 0.4694 (m-30) cc_final: 0.4051 (t0) REVERT: B 358 ARG cc_start: 0.5931 (OUTLIER) cc_final: 0.5589 (mmt-90) REVERT: B 359 LYS cc_start: 0.5198 (tppt) cc_final: 0.4857 (tptt) REVERT: B 599 MET cc_start: 0.8346 (mtp) cc_final: 0.8086 (mtp) REVERT: B 864 ASP cc_start: 0.6725 (t0) cc_final: 0.5435 (m-30) REVERT: B 1139 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8374 (tppt) REVERT: A 91 PHE cc_start: 0.6965 (OUTLIER) cc_final: 0.6704 (t80) REVERT: A 92 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6783 (tt) REVERT: A 94 LEU cc_start: 0.6675 (tp) cc_final: 0.6435 (pt) REVERT: A 141 ARG cc_start: 0.6950 (ppt90) cc_final: 0.6732 (ptm-80) REVERT: A 183 LYS cc_start: 0.8003 (mmtt) cc_final: 0.7647 (mmpt) REVERT: A 198 ARG cc_start: 0.5842 (ptp90) cc_final: 0.5474 (ptp90) REVERT: A 300 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7393 (mm) REVERT: A 337 ARG cc_start: 0.5147 (ttm110) cc_final: 0.4897 (ttm110) REVERT: A 344 ASP cc_start: 0.4615 (m-30) cc_final: 0.4059 (t0) REVERT: A 864 ASP cc_start: 0.6727 (t0) cc_final: 0.5432 (m-30) REVERT: C 94 LEU cc_start: 0.6911 (tp) cc_final: 0.6647 (pt) REVERT: C 141 ARG cc_start: 0.6937 (ppt90) cc_final: 0.6710 (ptm-80) REVERT: C 183 LYS cc_start: 0.7983 (mmtt) cc_final: 0.7610 (mmpt) REVERT: C 198 ARG cc_start: 0.5935 (ptp90) cc_final: 0.5571 (ptp90) REVERT: C 300 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7229 (tt) REVERT: C 344 ASP cc_start: 0.4626 (m-30) cc_final: 0.4022 (t0) REVERT: C 358 ARG cc_start: 0.5920 (OUTLIER) cc_final: 0.5529 (mmt-90) REVERT: C 599 MET cc_start: 0.8249 (mtp) cc_final: 0.7965 (mtp) REVERT: C 864 ASP cc_start: 0.6755 (t0) cc_final: 0.5456 (m-30) REVERT: D 92 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6636 (tt) REVERT: D 94 LEU cc_start: 0.6682 (tp) cc_final: 0.6448 (pt) REVERT: D 141 ARG cc_start: 0.6920 (ppt90) cc_final: 0.6703 (ptm-80) REVERT: D 165 ARG cc_start: 0.7811 (tmt170) cc_final: 0.7163 (ttp-170) REVERT: D 183 LYS cc_start: 0.8118 (mmtt) cc_final: 0.7718 (mmpt) REVERT: D 187 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7344 (mtm) REVERT: D 198 ARG cc_start: 0.5888 (ptp90) cc_final: 0.5553 (ptp90) REVERT: D 344 ASP cc_start: 0.4638 (m-30) cc_final: 0.4045 (t0) REVERT: D 359 LYS cc_start: 0.5251 (tppt) cc_final: 0.4923 (tptt) REVERT: D 599 MET cc_start: 0.8351 (mtp) cc_final: 0.8091 (mtp) REVERT: D 864 ASP cc_start: 0.6779 (t0) cc_final: 0.5515 (m-30) outliers start: 66 outliers final: 29 residues processed: 369 average time/residue: 0.6854 time to fit residues: 297.7128 Evaluate side-chains 328 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 287 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 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 358 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 1008 VAL Chi-restraints excluded: chain B residue 1139 LYS Chi-restraints excluded: chain A residue 91 PHE 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 300 LEU Chi-restraints excluded: chain A residue 301 LEU 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 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 358 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 187 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 780 LEU 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: 6.9990 chunk 144 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 369 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 233 optimal weight: 9.9990 chunk 271 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 373 optimal weight: 8.9990 chunk 245 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 248 ASN B 420 GLN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 706 ASN B1013 ASN A 248 ASN 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 669 GLN D 706 ASN D1013 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.175379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.111045 restraints weight = 40188.840| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.09 r_work: 0.3047 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 31132 Z= 0.157 Angle : 0.581 11.818 42232 Z= 0.295 Chirality : 0.039 0.169 4756 Planarity : 0.005 0.054 5300 Dihedral : 5.455 81.431 4188 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.97 % Allowed : 15.51 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.14), residues: 3744 helix: 1.87 (0.11), residues: 2440 sheet: -0.98 (0.30), residues: 260 loop : -2.65 (0.16), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 249 TYR 0.014 0.002 TYR D 339 PHE 0.013 0.002 PHE A 793 TRP 0.013 0.001 TRP C1054 HIS 0.008 0.001 HIS C 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (31128) covalent geometry : angle 0.58005 / 0.29 (42224) SS BOND : bond 0.00663 / 0.40 ( 4) SS BOND : angle 1.92285 / 1.12 ( 8) hydrogen bonds : bond 0.05169 / 3.47 ( 1812) hydrogen bonds : angle 4.11664 / 2.90 ( 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: 64 poor density : 307 time to evaluate : 1.172 Fit side-chains REVERT: B 92 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6861 (tt) REVERT: B 94 LEU cc_start: 0.6745 (tp) cc_final: 0.6527 (pt) REVERT: B 165 ARG cc_start: 0.7870 (tmt170) cc_final: 0.7195 (ttp-170) REVERT: B 183 LYS cc_start: 0.8123 (mmtt) cc_final: 0.7766 (mmpt) REVERT: B 187 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7598 (mtm) REVERT: B 198 ARG cc_start: 0.5855 (ptp90) cc_final: 0.5505 (ptp90) REVERT: B 344 ASP cc_start: 0.4699 (m-30) cc_final: 0.3950 (t0) REVERT: B 358 ARG cc_start: 0.6072 (OUTLIER) cc_final: 0.5742 (mmt-90) REVERT: B 359 LYS cc_start: 0.4933 (tppt) cc_final: 0.4731 (tptt) REVERT: B 397 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8326 (pp20) REVERT: B 518 ARG cc_start: 0.5839 (OUTLIER) cc_final: 0.5172 (mtm-85) REVERT: B 599 MET cc_start: 0.8441 (mtp) cc_final: 0.8170 (mtp) REVERT: B 635 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: B 864 ASP cc_start: 0.6933 (t0) cc_final: 0.6431 (t0) REVERT: A 91 PHE cc_start: 0.7097 (OUTLIER) cc_final: 0.6796 (t80) REVERT: A 92 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6987 (tt) REVERT: A 94 LEU cc_start: 0.6716 (tp) cc_final: 0.6479 (pt) REVERT: A 141 ARG cc_start: 0.7166 (ppt90) cc_final: 0.6891 (ptm-80) REVERT: A 183 LYS cc_start: 0.8109 (mmtt) cc_final: 0.7721 (mmpt) REVERT: A 198 ARG cc_start: 0.5884 (ptp90) cc_final: 0.5512 (ptp90) REVERT: A 344 ASP cc_start: 0.4701 (m-30) cc_final: 0.4049 (t0) REVERT: A 518 ARG cc_start: 0.5834 (OUTLIER) cc_final: 0.5152 (mtm-85) REVERT: A 635 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.7934 (mp0) REVERT: A 864 ASP cc_start: 0.6928 (t0) cc_final: 0.6392 (t0) REVERT: C 183 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7757 (mmpt) REVERT: C 198 ARG cc_start: 0.5909 (ptp90) cc_final: 0.5558 (ptp90) REVERT: C 300 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7415 (tt) REVERT: C 344 ASP cc_start: 0.4860 (m-30) cc_final: 0.4145 (t0) REVERT: C 358 ARG cc_start: 0.6035 (OUTLIER) cc_final: 0.5637 (mmt-90) REVERT: C 397 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8325 (pp20) REVERT: C 518 ARG cc_start: 0.5820 (OUTLIER) cc_final: 0.5143 (mtm-85) REVERT: C 599 MET cc_start: 0.8471 (mtp) cc_final: 0.8229 (mtp) REVERT: C 635 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: C 864 ASP cc_start: 0.6894 (t0) cc_final: 0.6413 (t0) REVERT: C 952 ASP cc_start: 0.8303 (m-30) cc_final: 0.8085 (m-30) REVERT: D 92 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6857 (tt) REVERT: D 94 LEU cc_start: 0.6711 (tp) cc_final: 0.6500 (pt) REVERT: D 141 ARG cc_start: 0.7108 (ppt90) cc_final: 0.6871 (ptm-80) REVERT: D 165 ARG cc_start: 0.7883 (tmt170) cc_final: 0.7199 (ttp-170) REVERT: D 183 LYS cc_start: 0.8125 (mmtt) cc_final: 0.7752 (mmpt) REVERT: D 187 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7577 (mtm) REVERT: D 198 ARG cc_start: 0.5862 (ptp90) cc_final: 0.5493 (ptp90) REVERT: D 344 ASP cc_start: 0.4898 (m-30) cc_final: 0.4156 (t0) REVERT: D 397 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8323 (pp20) REVERT: D 599 MET cc_start: 0.8442 (mtp) cc_final: 0.8169 (mtp) REVERT: D 635 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.7936 (mp0) REVERT: D 864 ASP cc_start: 0.6894 (t0) cc_final: 0.6358 (t0) REVERT: D 952 ASP cc_start: 0.8315 (m-30) cc_final: 0.8098 (m-30) outliers start: 64 outliers final: 34 residues processed: 349 average time/residue: 0.6506 time to fit residues: 267.7638 Evaluate side-chains 336 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 283 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 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 358 ARG Chi-restraints excluded: chain B residue 397 GLU 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 780 LEU Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1139 LYS Chi-restraints excluded: chain A residue 91 PHE 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 301 LEU 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 780 LEU 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 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 358 ARG Chi-restraints excluded: chain C residue 397 GLU 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 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 187 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 635 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 209 optimal weight: 10.0000 chunk 282 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 180 optimal weight: 0.7980 chunk 342 optimal weight: 2.9990 chunk 254 optimal weight: 9.9990 chunk 339 optimal weight: 8.9990 chunk 374 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 148 GLN B 248 ASN B 706 ASN B1013 ASN A 248 ASN ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN A1013 ASN C 148 GLN C 248 ASN C 706 ASN C1013 ASN D 248 ASN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 706 ASN D1013 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.175058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.109414 restraints weight = 40275.710| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.16 r_work: 0.3053 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31132 Z= 0.171 Angle : 0.599 11.676 42232 Z= 0.304 Chirality : 0.040 0.164 4756 Planarity : 0.005 0.055 5300 Dihedral : 5.451 80.921 4188 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.28 % Allowed : 15.63 % Favored : 82.09 % 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: 0.69 (0.14), residues: 3744 helix: 1.82 (0.11), residues: 2448 sheet: -0.95 (0.30), residues: 260 loop : -2.61 (0.16), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 249 TYR 0.016 0.002 TYR C 104 PHE 0.029 0.002 PHE B 250 TRP 0.013 0.001 TRP C1054 HIS 0.007 0.001 HIS C 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 (31128) covalent geometry : angle 0.59850 / 0.30 (42224) SS BOND : bond 0.00708 / 0.43 ( 4) SS BOND : angle 2.05914 / 1.20 ( 8) hydrogen bonds : bond 0.05305 / 3.56 ( 1812) hydrogen bonds : angle 4.12129 / 2.90 ( 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 373 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 299 time to evaluate : 1.147 Fit side-chains REVERT: B 165 ARG cc_start: 0.7874 (tmt170) cc_final: 0.7520 (ttp80) REVERT: B 183 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7730 (mmpt) REVERT: B 187 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7525 (mtm) REVERT: B 198 ARG cc_start: 0.5826 (ptp90) cc_final: 0.5461 (ptp90) REVERT: B 344 ASP cc_start: 0.4877 (m-30) cc_final: 0.4117 (t0) REVERT: B 359 LYS cc_start: 0.4936 (tppt) cc_final: 0.4649 (tptt) REVERT: B 397 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8314 (pp20) REVERT: B 518 ARG cc_start: 0.5756 (OUTLIER) cc_final: 0.5071 (mtm-85) REVERT: B 599 MET cc_start: 0.8384 (mtp) cc_final: 0.8081 (mtp) REVERT: B 635 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: B 864 ASP cc_start: 0.6872 (t0) cc_final: 0.6310 (t0) REVERT: A 141 ARG cc_start: 0.7076 (ppt90) cc_final: 0.6822 (ptm-80) REVERT: A 183 LYS cc_start: 0.8111 (mmtt) cc_final: 0.7709 (mmpt) REVERT: A 198 ARG cc_start: 0.5858 (ptp90) cc_final: 0.5483 (ptp90) REVERT: A 300 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7522 (mm) REVERT: A 344 ASP cc_start: 0.4939 (m-30) cc_final: 0.4247 (t0) REVERT: A 518 ARG cc_start: 0.5779 (OUTLIER) cc_final: 0.5092 (mtm-85) REVERT: A 635 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: A 864 ASP cc_start: 0.6855 (t0) cc_final: 0.6293 (t0) REVERT: C 91 PHE cc_start: 0.7284 (OUTLIER) cc_final: 0.7013 (t80) REVERT: C 183 LYS cc_start: 0.8141 (mmtt) cc_final: 0.7687 (mmpt) REVERT: C 198 ARG cc_start: 0.5840 (ptp90) cc_final: 0.5467 (ptp90) REVERT: C 300 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7225 (tt) REVERT: C 344 ASP cc_start: 0.4883 (m-30) cc_final: 0.4213 (t0) REVERT: C 358 ARG cc_start: 0.5983 (OUTLIER) cc_final: 0.5608 (mmt-90) REVERT: C 397 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8316 (pp20) REVERT: C 518 ARG cc_start: 0.5774 (OUTLIER) cc_final: 0.5092 (mtm-85) REVERT: C 599 MET cc_start: 0.8417 (mtp) cc_final: 0.8132 (mtp) REVERT: C 635 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7846 (mp0) REVERT: C 864 ASP cc_start: 0.6837 (t0) cc_final: 0.6340 (t0) REVERT: C 952 ASP cc_start: 0.8205 (m-30) cc_final: 0.7967 (m-30) REVERT: D 92 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6857 (tt) REVERT: D 141 ARG cc_start: 0.7053 (ppt90) cc_final: 0.6765 (ptm-80) REVERT: D 165 ARG cc_start: 0.7840 (tmt170) cc_final: 0.7498 (ttp80) REVERT: D 183 LYS cc_start: 0.8127 (mmtt) cc_final: 0.7756 (mmpt) REVERT: D 187 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7507 (mtm) REVERT: D 198 ARG cc_start: 0.5826 (ptp90) cc_final: 0.5450 (ptp90) REVERT: D 300 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7412 (mm) REVERT: D 344 ASP cc_start: 0.4920 (m-30) cc_final: 0.4207 (t0) REVERT: D 397 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8346 (pp20) REVERT: D 599 MET cc_start: 0.8386 (mtp) cc_final: 0.8081 (mtp) REVERT: D 635 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7835 (mp0) REVERT: D 864 ASP cc_start: 0.6830 (t0) cc_final: 0.6379 (t0) REVERT: D 952 ASP cc_start: 0.8221 (m-30) cc_final: 0.7980 (m-30) REVERT: D 1000 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7437 (mp0) outliers start: 74 outliers final: 37 residues processed: 346 average time/residue: 0.6996 time to fit residues: 285.6940 Evaluate side-chains 341 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 286 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 236 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 397 GLU 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 780 LEU Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1139 LYS 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 252 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 301 LEU 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 780 LEU 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 91 PHE 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 301 LEU Chi-restraints excluded: chain C residue 358 ARG Chi-restraints excluded: chain C residue 397 GLU 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 780 LEU 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 187 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 236 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 560 SER Chi-restraints excluded: chain D residue 635 GLU 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: 0.4980 chunk 216 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 371 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 311 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 248 ASN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS B 706 ASN B1013 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS A 706 ASN A1013 ASN C 175 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 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 ASN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 706 ASN D1013 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.178747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.115400 restraints weight = 40528.313| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.01 r_work: 0.3110 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 31132 Z= 0.104 Angle : 0.520 10.532 42232 Z= 0.264 Chirality : 0.037 0.152 4756 Planarity : 0.004 0.050 5300 Dihedral : 5.244 86.064 4188 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.60 % Allowed : 16.31 % Favored : 82.09 % 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: 1.14 (0.14), residues: 3744 helix: 2.17 (0.11), residues: 2444 sheet: -0.74 (0.30), residues: 252 loop : -2.45 (0.16), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 826 TYR 0.013 0.001 TYR C 339 PHE 0.025 0.001 PHE B 250 TRP 0.012 0.001 TRP C 691 HIS 0.008 0.001 HIS C 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (31128) covalent geometry : angle 0.51945 / 0.26 (42224) SS BOND : bond 0.00343 / 0.21 ( 4) SS BOND : angle 1.05068 / 0.62 ( 8) hydrogen bonds : bond 0.03706 / 2.50 ( 1812) hydrogen bonds : angle 3.87949 / 2.74 ( 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 382 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 330 time to evaluate : 1.209 Fit side-chains REVERT: B 141 ARG cc_start: 0.6967 (ppt90) cc_final: 0.6756 (ptm-80) REVERT: B 165 ARG cc_start: 0.7830 (tmt170) cc_final: 0.7213 (ttp-170) REVERT: B 183 LYS cc_start: 0.8054 (mmtt) cc_final: 0.7686 (mmpt) REVERT: B 198 ARG cc_start: 0.6035 (ptp90) cc_final: 0.5729 (ptp90) REVERT: B 300 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7676 (mm) REVERT: B 301 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6865 (mt) REVERT: B 344 ASP cc_start: 0.4866 (m-30) cc_final: 0.4098 (t0) REVERT: B 599 MET cc_start: 0.8397 (mtp) cc_final: 0.8166 (mtp) REVERT: B 1000 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7515 (mp0) REVERT: A 91 PHE cc_start: 0.6988 (OUTLIER) cc_final: 0.6778 (t80) REVERT: A 141 ARG cc_start: 0.7037 (ppt90) cc_final: 0.6623 (ptm-80) REVERT: A 183 LYS cc_start: 0.8082 (mmtt) cc_final: 0.7725 (mmpt) REVERT: A 198 ARG cc_start: 0.6103 (ptp90) cc_final: 0.5751 (ptp90) REVERT: A 344 ASP cc_start: 0.4945 (m-30) cc_final: 0.4169 (t0) REVERT: A 359 LYS cc_start: 0.5591 (tptt) cc_final: 0.4714 (tptt) REVERT: C 91 PHE cc_start: 0.7220 (OUTLIER) cc_final: 0.6973 (t80) REVERT: C 141 ARG cc_start: 0.6984 (ppt90) cc_final: 0.6763 (ptm-80) REVERT: C 183 LYS cc_start: 0.8091 (mmtt) cc_final: 0.7747 (mmpt) REVERT: C 198 ARG cc_start: 0.6071 (ptp90) cc_final: 0.5716 (ptp90) REVERT: C 300 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7368 (tt) REVERT: C 344 ASP cc_start: 0.4989 (m-30) cc_final: 0.4208 (t0) REVERT: C 358 ARG cc_start: 0.5825 (OUTLIER) cc_final: 0.5578 (mmt-90) REVERT: C 359 LYS cc_start: 0.4632 (tptt) cc_final: 0.4289 (tptt) REVERT: C 599 MET cc_start: 0.8320 (mtp) cc_final: 0.8098 (mtp) REVERT: C 1087 TRP cc_start: 0.6381 (t60) cc_final: 0.6012 (t-100) REVERT: D 141 ARG cc_start: 0.7066 (ppt90) cc_final: 0.6678 (ptm-80) REVERT: D 165 ARG cc_start: 0.7825 (tmt170) cc_final: 0.7191 (ttp-170) REVERT: D 198 ARG cc_start: 0.5989 (ptp90) cc_final: 0.5684 (ptp90) REVERT: D 300 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7682 (mm) REVERT: D 344 ASP cc_start: 0.4950 (m-30) cc_final: 0.4171 (t0) REVERT: D 359 LYS cc_start: 0.4821 (tptt) cc_final: 0.4344 (tptt) REVERT: D 599 MET cc_start: 0.8406 (mtp) cc_final: 0.8177 (mtp) REVERT: D 1000 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7478 (mp0) outliers start: 52 outliers final: 22 residues processed: 364 average time/residue: 0.6675 time to fit residues: 287.3561 Evaluate side-chains 302 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 273 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 560 SER Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain A residue 91 PHE 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 301 LEU 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 91 PHE 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 358 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 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: 9.9990 chunk 238 optimal weight: 0.5980 chunk 110 optimal weight: 0.5980 chunk 236 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 363 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 306 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 197 optimal weight: 0.0870 overall best weight: 2.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 148 GLN B 248 ASN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 706 ASN B1013 ASN A 148 GLN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS A 706 ASN A1013 ASN C 148 GLN C 175 GLN C 248 ASN ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 HIS C 706 ASN C1013 ASN D 248 ASN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4109 r_free = 0.4109 target = 0.176469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.112741 restraints weight = 40155.970| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.04 r_work: 0.3066 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31132 Z= 0.138 Angle : 0.566 10.766 42232 Z= 0.287 Chirality : 0.039 0.169 4756 Planarity : 0.004 0.051 5300 Dihedral : 5.295 85.820 4188 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.33 % Allowed : 17.08 % Favored : 81.60 % 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: 1.09 (0.14), residues: 3744 helix: 2.08 (0.11), residues: 2452 sheet: -0.63 (0.31), residues: 248 loop : -2.40 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 253 TYR 0.018 0.001 TYR C 104 PHE 0.025 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/Z covalent geometry : bond 0.00327 / 0.14 (31128) covalent geometry : angle 0.56544 / 0.29 (42224) SS BOND : bond 0.00567 / 0.34 ( 4) SS BOND : angle 1.51200 / 0.91 ( 8) hydrogen bonds : bond 0.04659 / 3.13 ( 1812) hydrogen bonds : angle 3.96801 / 2.80 ( 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 334 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 291 time to evaluate : 1.302 Fit side-chains REVERT: B 165 ARG cc_start: 0.7849 (tmt170) cc_final: 0.7194 (ttp-170) REVERT: B 183 LYS cc_start: 0.8071 (mmtt) cc_final: 0.7713 (mmpt) REVERT: B 198 ARG cc_start: 0.6026 (ptp90) cc_final: 0.5711 (ptp90) REVERT: B 300 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7624 (mm) REVERT: B 344 ASP cc_start: 0.4955 (m-30) cc_final: 0.4185 (t0) REVERT: B 359 LYS cc_start: 0.4844 (tptt) cc_final: 0.4449 (tptt) REVERT: B 599 MET cc_start: 0.8441 (mtp) cc_final: 0.8179 (mtp) REVERT: B 864 ASP cc_start: 0.6763 (t0) cc_final: 0.6184 (t0) REVERT: A 141 ARG cc_start: 0.7086 (ppt90) cc_final: 0.6812 (ptm-80) REVERT: A 183 LYS cc_start: 0.8025 (mmtt) cc_final: 0.7654 (mmpt) REVERT: A 198 ARG cc_start: 0.5916 (ptp90) cc_final: 0.5558 (ptp90) REVERT: A 344 ASP cc_start: 0.4917 (m-30) cc_final: 0.4200 (t0) REVERT: A 359 LYS cc_start: 0.5686 (tptt) cc_final: 0.4788 (tptt) REVERT: C 91 PHE cc_start: 0.7295 (OUTLIER) cc_final: 0.6947 (t80) REVERT: C 183 LYS cc_start: 0.8035 (mmtt) cc_final: 0.7707 (mmpt) REVERT: C 198 ARG cc_start: 0.6046 (ptp90) cc_final: 0.5691 (ptp90) REVERT: C 344 ASP cc_start: 0.4985 (m-30) cc_final: 0.4244 (t0) REVERT: C 359 LYS cc_start: 0.4687 (tptt) cc_final: 0.4276 (tptt) REVERT: C 599 MET cc_start: 0.8424 (mtp) cc_final: 0.8180 (mtp) REVERT: C 1087 TRP cc_start: 0.6374 (t60) cc_final: 0.6072 (t-100) REVERT: D 141 ARG cc_start: 0.7132 (ppt90) cc_final: 0.6878 (ptm-80) REVERT: D 165 ARG cc_start: 0.7866 (tmt170) cc_final: 0.7189 (ttp-170) REVERT: D 198 ARG cc_start: 0.5972 (ptp90) cc_final: 0.5611 (ptp90) REVERT: D 300 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7648 (mm) REVERT: D 344 ASP cc_start: 0.4908 (m-30) cc_final: 0.4134 (t0) REVERT: D 599 MET cc_start: 0.8447 (mtp) cc_final: 0.8187 (mtp) REVERT: D 864 ASP cc_start: 0.6775 (t0) cc_final: 0.6213 (t0) outliers start: 43 outliers final: 20 residues processed: 324 average time/residue: 0.6818 time to fit residues: 260.6052 Evaluate side-chains 305 residues out of total 3244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 282 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 560 SER 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 560 SER Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain C residue 91 PHE Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 194 VAL 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 300 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 354 optimal weight: 4.9990 chunk 256 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 238 optimal weight: 0.0000 chunk 171 optimal weight: 0.9980 chunk 224 optimal weight: 7.9990 chunk 298 optimal weight: 20.0000 chunk 309 optimal weight: 3.9990 chunk 347 optimal weight: 4.9990 chunk 258 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 148 GLN B 248 ASN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 706 ASN B1013 ASN A 148 GLN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS A 706 ASN A1013 ASN C 148 GLN C 175 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 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4107 r_free = 0.4107 target = 0.176149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.111480 restraints weight = 40308.255| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.06 r_work: 0.3073 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31132 Z= 0.141 Angle : 0.572 10.431 42232 Z= 0.292 Chirality : 0.039 0.166 4756 Planarity : 0.005 0.063 5300 Dihedral : 5.317 86.103 4188 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.20 % Allowed : 17.39 % Favored : 81.41 % 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: 1.04 (0.14), residues: 3744 helix: 2.02 (0.11), residues: 2456 sheet: -0.59 (0.31), residues: 248 loop : -2.38 (0.17), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 253 TYR 0.016 0.001 TYR B 104 PHE 0.025 0.002 PHE D 250 TRP 0.013 0.001 TRP C1054 HIS 0.009 0.001 HIS C 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (31128) covalent geometry : angle 0.57177 / 0.29 (42224) SS BOND : bond 0.00594 / 0.35 ( 4) SS BOND : angle 1.61881 / 0.96 ( 8) hydrogen bonds : bond 0.04765 / 3.20 ( 1812) hydrogen bonds : angle 4.03169 / 2.85 ( 5376) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13407.61 seconds wall clock time: 227 minutes 56.50 seconds (13676.50 seconds total)