Starting phenix.real_space_refine on Thu Nov 20 03:46:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wra_32720/11_2025/7wra_32720.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wra_32720/11_2025/7wra_32720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wra_32720/11_2025/7wra_32720.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wra_32720/11_2025/7wra_32720.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wra_32720/11_2025/7wra_32720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wra_32720/11_2025/7wra_32720.map" } resolution = 2.98 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= 0.003 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 S 140 5.16 5 Na 1 4.78 5 C 19756 2.51 5 N 5040 2.21 5 O 5436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30373 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 9.46, per 1000 atoms: 0.31 Number of scatterers: 30373 At special positions: 0 Unit cell: (153.114, 153.114, 156.156, 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 Na 1 11.00 O 5436 8.00 N 5040 7.00 C 19756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 929 " - pdb=" SG CYS A 940 " distance=2.01 Simple disulfide: pdb=" SG CYS B 929 " - pdb=" SG CYS B 940 " distance=2.01 Simple disulfide: pdb=" SG CYS C 929 " - pdb=" SG CYS C 940 " distance=2.01 Simple disulfide: pdb=" SG CYS D 929 " - pdb=" SG CYS D 940 " distance=2.01 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: 2.47 Conformation dependent library (CDL) restraints added in 1.2 seconds 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7080 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 8 sheets defined 70.9% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 126 through 136 Processing helix chain 'A' and resid 158 through 176 Processing helix chain 'A' and resid 186 through 204 removed outlier: 3.685A pdb=" N LYS A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 288 Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.877A pdb=" N LEU A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER A 322 " --> pdb=" O THR A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 343 removed outlier: 3.805A pdb=" N VAL A 338 " --> pdb=" O GLN A 334 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 362 removed outlier: 3.811A pdb=" N ARG A 360 " --> pdb=" O GLU A 356 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 370 through 386 removed outlier: 4.446A pdb=" N SER A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 418 removed outlier: 3.843A pdb=" N TYR A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 418 " --> pdb=" O LYS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 458 through 468 Processing helix chain 'A' and resid 470 through 481 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 489 through 499 removed outlier: 3.697A pdb=" N LEU A 493 " --> pdb=" O THR A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 516 Processing helix chain 'A' and resid 518 through 533 removed outlier: 3.921A pdb=" N ARG A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 571 Processing helix chain 'A' and resid 575 through 582 removed outlier: 3.586A pdb=" N VAL A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 603 Processing helix chain 'A' and resid 607 through 636 removed outlier: 3.797A pdb=" N GLU A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP A 636 " --> pdb=" O CYS A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 644 removed outlier: 3.633A pdb=" N ALA A 640 " --> pdb=" O ASP A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 663 removed outlier: 3.989A pdb=" N ALA A 660 " --> pdb=" O CYS A 656 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.783A pdb=" N ILE A 669 " --> pdb=" O ASP A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 684 removed outlier: 3.628A pdb=" N GLY A 684 " --> pdb=" O LYS A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 701 removed outlier: 3.867A pdb=" N ILE A 695 " --> pdb=" O LYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 705 Processing helix chain 'A' and resid 723 through 732 Processing helix chain 'A' and resid 733 through 758 removed outlier: 3.888A pdb=" N VAL A 743 " --> pdb=" O SER A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 790 Processing helix chain 'A' and resid 791 through 795 Processing helix chain 'A' and resid 796 through 817 Processing helix chain 'A' and resid 821 through 847 removed outlier: 3.737A pdb=" N ARG A 829 " --> pdb=" O LEU A 825 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE A 838 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU A 843 " --> pdb=" O PHE A 839 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE A 844 " --> pdb=" O THR A 840 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N HIS A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 850 No H-bonds generated for 'chain 'A' and resid 848 through 850' Processing helix chain 'A' and resid 852 through 861 removed outlier: 4.592A pdb=" N LYS A 856 " --> pdb=" O ASN A 852 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN A 861 " --> pdb=" O ILE A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 890 removed outlier: 3.879A pdb=" N ALA A 884 " --> pdb=" O ALA A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 904 removed outlier: 3.859A pdb=" N SER A 902 " --> pdb=" O TRP A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 910 Processing helix chain 'A' and resid 925 through 929 removed outlier: 3.991A pdb=" N HIS A 928 " --> pdb=" O ASP A 925 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS A 929 " --> pdb=" O PHE A 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 925 through 929' Processing helix chain 'A' and resid 952 through 969 Proline residue: A 958 - end of helix Processing helix chain 'A' and resid 969 through 1007 removed outlier: 3.651A pdb=" N LEU A 975 " --> pdb=" O LEU A 971 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 977 " --> pdb=" O ASN A 973 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN A 987 " --> pdb=" O VAL A 983 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLU A 988 " --> pdb=" O GLY A 984 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ASN A 989 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR A 999 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU A1001 " --> pdb=" O GLN A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1014 No H-bonds generated for 'chain 'A' and resid 1012 through 1014' Processing helix chain 'A' and resid 1015 through 1030 Processing helix chain 'A' and resid 1046 through 1069 removed outlier: 3.831A pdb=" N VAL A1058 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N MET A1059 " --> pdb=" O TRP A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1104 removed outlier: 3.923A pdb=" N LYS A1104 " --> pdb=" O ALA A1100 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 136 Processing helix chain 'B' and resid 158 through 176 Processing helix chain 'B' and resid 186 through 204 removed outlier: 3.685A pdb=" N LYS B 190 " --> pdb=" O TYR B 186 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG B 203 " --> pdb=" O ASN B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 309 through 322 removed outlier: 3.876A pdb=" N LEU B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER B 322 " --> pdb=" O THR B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 343 removed outlier: 3.806A pdb=" N VAL B 338 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL B 343 " --> pdb=" O ILE B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 362 removed outlier: 3.810A pdb=" N ARG B 360 " --> pdb=" O GLU B 356 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 362 " --> pdb=" O LEU B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 369 Processing helix chain 'B' and resid 370 through 386 removed outlier: 4.446A pdb=" N SER B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 418 removed outlier: 3.844A pdb=" N TYR B 410 " --> pdb=" O ASN B 406 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B 418 " --> pdb=" O LYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 436 Processing helix chain 'B' and resid 439 through 446 Processing helix chain 'B' and resid 458 through 468 Processing helix chain 'B' and resid 470 through 481 Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 489 through 499 removed outlier: 3.697A pdb=" N LEU B 493 " --> pdb=" O THR B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 516 Processing helix chain 'B' and resid 518 through 533 removed outlier: 3.922A pdb=" N ARG B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 571 Processing helix chain 'B' and resid 575 through 582 removed outlier: 3.586A pdb=" N VAL B 579 " --> pdb=" O GLU B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 603 Processing helix chain 'B' and resid 607 through 636 removed outlier: 3.797A pdb=" N GLU B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP B 636 " --> pdb=" O CYS B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 644 removed outlier: 3.633A pdb=" N ALA B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 663 removed outlier: 3.989A pdb=" N ALA B 660 " --> pdb=" O CYS B 656 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 670 removed outlier: 3.784A pdb=" N ILE B 669 " --> pdb=" O ASP B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 684 removed outlier: 3.628A pdb=" N GLY B 684 " --> pdb=" O LYS B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 701 removed outlier: 3.867A pdb=" N ILE B 695 " --> pdb=" O LYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 705 Processing helix chain 'B' and resid 723 through 732 Processing helix chain 'B' and resid 733 through 758 removed outlier: 3.889A pdb=" N VAL B 743 " --> pdb=" O SER B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 790 Processing helix chain 'B' and resid 791 through 795 Processing helix chain 'B' and resid 796 through 817 Processing helix chain 'B' and resid 821 through 847 removed outlier: 3.737A pdb=" N ARG B 829 " --> pdb=" O LEU B 825 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE B 838 " --> pdb=" O LEU B 834 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU B 843 " --> pdb=" O PHE B 839 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE B 844 " --> pdb=" O THR B 840 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N HIS B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 850 No H-bonds generated for 'chain 'B' and resid 848 through 850' Processing helix chain 'B' and resid 852 through 861 removed outlier: 4.592A pdb=" N LYS B 856 " --> pdb=" O ASN B 852 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN B 861 " --> pdb=" O ILE B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 890 removed outlier: 3.880A pdb=" N ALA B 884 " --> pdb=" O ALA B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 904 removed outlier: 3.859A pdb=" N SER B 902 " --> pdb=" O TRP B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 910 Processing helix chain 'B' and resid 925 through 929 removed outlier: 3.991A pdb=" N HIS B 928 " --> pdb=" O ASP B 925 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS B 929 " --> pdb=" O PHE B 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 925 through 929' Processing helix chain 'B' and resid 952 through 969 Proline residue: B 958 - end of helix Processing helix chain 'B' and resid 969 through 1007 removed outlier: 3.651A pdb=" N LEU B 975 " --> pdb=" O LEU B 971 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 977 " --> pdb=" O ASN B 973 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN B 987 " --> pdb=" O VAL B 983 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLU B 988 " --> pdb=" O GLY B 984 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ASN B 989 " --> pdb=" O ILE B 985 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR B 999 " --> pdb=" O LYS B 995 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU B1001 " --> pdb=" O GLN B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1014 No H-bonds generated for 'chain 'B' and resid 1012 through 1014' Processing helix chain 'B' and resid 1015 through 1030 Processing helix chain 'B' and resid 1046 through 1069 removed outlier: 3.831A pdb=" N VAL B1058 " --> pdb=" O ALA B1054 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N MET B1059 " --> pdb=" O TRP B1055 " (cutoff:3.500A) Processing helix chain 'B' and resid 1074 through 1104 removed outlier: 3.923A pdb=" N LYS B1104 " --> pdb=" O ALA B1100 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 136 Processing helix chain 'C' and resid 158 through 176 Processing helix chain 'C' and resid 186 through 204 removed outlier: 3.685A pdb=" N LYS C 190 " --> pdb=" O TYR C 186 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 309 through 322 removed outlier: 3.877A pdb=" N LEU C 313 " --> pdb=" O GLY C 309 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C 322 " --> pdb=" O THR C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 343 removed outlier: 3.805A pdb=" N VAL C 338 " --> pdb=" O GLN C 334 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL C 343 " --> pdb=" O ILE C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 362 removed outlier: 3.811A pdb=" N ARG C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 362 " --> pdb=" O LEU C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 370 through 386 removed outlier: 4.446A pdb=" N SER C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 418 removed outlier: 3.843A pdb=" N TYR C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 436 Processing helix chain 'C' and resid 439 through 446 Processing helix chain 'C' and resid 458 through 468 Processing helix chain 'C' and resid 470 through 481 Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 489 through 499 removed outlier: 3.697A pdb=" N LEU C 493 " --> pdb=" O THR C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 516 Processing helix chain 'C' and resid 518 through 533 removed outlier: 3.921A pdb=" N ARG C 533 " --> pdb=" O ALA C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 571 Processing helix chain 'C' and resid 575 through 582 removed outlier: 3.586A pdb=" N VAL C 579 " --> pdb=" O GLU C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 603 Processing helix chain 'C' and resid 607 through 636 removed outlier: 3.797A pdb=" N GLU C 631 " --> pdb=" O GLU C 627 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP C 636 " --> pdb=" O CYS C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 644 removed outlier: 3.633A pdb=" N ALA C 640 " --> pdb=" O ASP C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 663 removed outlier: 3.989A pdb=" N ALA C 660 " --> pdb=" O CYS C 656 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 670 removed outlier: 3.783A pdb=" N ILE C 669 " --> pdb=" O ASP C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 684 removed outlier: 3.628A pdb=" N GLY C 684 " --> pdb=" O LYS C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 701 removed outlier: 3.867A pdb=" N ILE C 695 " --> pdb=" O LYS C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 705 Processing helix chain 'C' and resid 723 through 732 Processing helix chain 'C' and resid 733 through 758 removed outlier: 3.889A pdb=" N VAL C 743 " --> pdb=" O SER C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 765 through 790 Processing helix chain 'C' and resid 791 through 795 Processing helix chain 'C' and resid 796 through 817 Processing helix chain 'C' and resid 821 through 847 removed outlier: 3.737A pdb=" N ARG C 829 " --> pdb=" O LEU C 825 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE C 838 " --> pdb=" O LEU C 834 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU C 843 " --> pdb=" O PHE C 839 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE C 844 " --> pdb=" O THR C 840 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N HIS C 845 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 850 No H-bonds generated for 'chain 'C' and resid 848 through 850' Processing helix chain 'C' and resid 852 through 861 removed outlier: 4.592A pdb=" N LYS C 856 " --> pdb=" O ASN C 852 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN C 861 " --> pdb=" O ILE C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 890 removed outlier: 3.880A pdb=" N ALA C 884 " --> pdb=" O ALA C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 904 removed outlier: 3.859A pdb=" N SER C 902 " --> pdb=" O TRP C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 910 Processing helix chain 'C' and resid 925 through 929 removed outlier: 3.992A pdb=" N HIS C 928 " --> pdb=" O ASP C 925 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS C 929 " --> pdb=" O PHE C 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 925 through 929' Processing helix chain 'C' and resid 952 through 969 Proline residue: C 958 - end of helix Processing helix chain 'C' and resid 969 through 1007 removed outlier: 3.651A pdb=" N LEU C 975 " --> pdb=" O LEU C 971 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA C 977 " --> pdb=" O ASN C 973 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN C 987 " --> pdb=" O VAL C 983 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLU C 988 " --> pdb=" O GLY C 984 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ASN C 989 " --> pdb=" O ILE C 985 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR C 999 " --> pdb=" O LYS C 995 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE C1000 " --> pdb=" O PHE C 996 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU C1001 " --> pdb=" O GLN C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1014 No H-bonds generated for 'chain 'C' and resid 1012 through 1014' Processing helix chain 'C' and resid 1015 through 1030 Processing helix chain 'C' and resid 1046 through 1069 removed outlier: 3.831A pdb=" N VAL C1058 " --> pdb=" O ALA C1054 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N MET C1059 " --> pdb=" O TRP C1055 " (cutoff:3.500A) Processing helix chain 'C' and resid 1074 through 1104 removed outlier: 3.923A pdb=" N LYS C1104 " --> pdb=" O ALA C1100 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 136 Processing helix chain 'D' and resid 158 through 176 Processing helix chain 'D' and resid 186 through 204 removed outlier: 3.684A pdb=" N LYS D 190 " --> pdb=" O TYR D 186 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG D 203 " --> pdb=" O ASN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 288 Processing helix chain 'D' and resid 309 through 322 removed outlier: 3.876A pdb=" N LEU D 313 " --> pdb=" O GLY D 309 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER D 322 " --> pdb=" O THR D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 343 removed outlier: 3.805A pdb=" N VAL D 338 " --> pdb=" O GLN D 334 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL D 343 " --> pdb=" O ILE D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 362 removed outlier: 3.810A pdb=" N ARG D 360 " --> pdb=" O GLU D 356 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D 362 " --> pdb=" O LEU D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 369 Processing helix chain 'D' and resid 370 through 386 removed outlier: 4.446A pdb=" N SER D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 418 removed outlier: 3.843A pdb=" N TYR D 410 " --> pdb=" O ASN D 406 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR D 418 " --> pdb=" O LYS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 436 Processing helix chain 'D' and resid 439 through 446 Processing helix chain 'D' and resid 458 through 468 Processing helix chain 'D' and resid 470 through 481 Processing helix chain 'D' and resid 483 through 488 Processing helix chain 'D' and resid 489 through 499 removed outlier: 3.697A pdb=" N LEU D 493 " --> pdb=" O THR D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 516 Processing helix chain 'D' and resid 518 through 533 removed outlier: 3.922A pdb=" N ARG D 533 " --> pdb=" O ALA D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 571 Processing helix chain 'D' and resid 575 through 582 removed outlier: 3.586A pdb=" N VAL D 579 " --> pdb=" O GLU D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 603 Processing helix chain 'D' and resid 607 through 636 removed outlier: 3.797A pdb=" N GLU D 631 " --> pdb=" O GLU D 627 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP D 636 " --> pdb=" O CYS D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 644 removed outlier: 3.633A pdb=" N ALA D 640 " --> pdb=" O ASP D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 663 removed outlier: 3.989A pdb=" N ALA D 660 " --> pdb=" O CYS D 656 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL D 661 " --> pdb=" O LEU D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 670 removed outlier: 3.784A pdb=" N ILE D 669 " --> pdb=" O ASP D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 684 removed outlier: 3.628A pdb=" N GLY D 684 " --> pdb=" O LYS D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 701 removed outlier: 3.867A pdb=" N ILE D 695 " --> pdb=" O LYS D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 705 Processing helix chain 'D' and resid 723 through 732 Processing helix chain 'D' and resid 733 through 758 removed outlier: 3.889A pdb=" N VAL D 743 " --> pdb=" O SER D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 790 Processing helix chain 'D' and resid 791 through 795 Processing helix chain 'D' and resid 796 through 817 Processing helix chain 'D' and resid 821 through 847 removed outlier: 3.737A pdb=" N ARG D 829 " --> pdb=" O LEU D 825 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE D 838 " --> pdb=" O LEU D 834 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU D 843 " --> pdb=" O PHE D 839 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE D 844 " --> pdb=" O THR D 840 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N HIS D 845 " --> pdb=" O LEU D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 848 through 850 No H-bonds generated for 'chain 'D' and resid 848 through 850' Processing helix chain 'D' and resid 852 through 861 removed outlier: 4.592A pdb=" N LYS D 856 " --> pdb=" O ASN D 852 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN D 861 " --> pdb=" O ILE D 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 863 through 890 removed outlier: 3.880A pdb=" N ALA D 884 " --> pdb=" O ALA D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 904 removed outlier: 3.859A pdb=" N SER D 902 " --> pdb=" O TRP D 898 " (cutoff:3.500A) Processing helix chain 'D' and resid 904 through 910 Processing helix chain 'D' and resid 925 through 929 removed outlier: 3.991A pdb=" N HIS D 928 " --> pdb=" O ASP D 925 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS D 929 " --> pdb=" O PHE D 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 925 through 929' Processing helix chain 'D' and resid 952 through 969 Proline residue: D 958 - end of helix Processing helix chain 'D' and resid 969 through 1007 removed outlier: 3.651A pdb=" N LEU D 975 " --> pdb=" O LEU D 971 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA D 977 " --> pdb=" O ASN D 973 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN D 987 " --> pdb=" O VAL D 983 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLU D 988 " --> pdb=" O GLY D 984 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ASN D 989 " --> pdb=" O ILE D 985 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP D 991 " --> pdb=" O GLN D 987 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR D 999 " --> pdb=" O LYS D 995 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE D1000 " --> pdb=" O PHE D 996 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU D1001 " --> pdb=" O GLN D 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1012 through 1014 No H-bonds generated for 'chain 'D' and resid 1012 through 1014' Processing helix chain 'D' and resid 1015 through 1030 Processing helix chain 'D' and resid 1046 through 1069 removed outlier: 3.831A pdb=" N VAL D1058 " --> pdb=" O ALA D1054 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N MET D1059 " --> pdb=" O TRP D1055 " (cutoff:3.500A) Processing helix chain 'D' and resid 1074 through 1104 removed outlier: 3.923A pdb=" N LYS D1104 " --> pdb=" O ALA D1100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 117 removed outlier: 3.981A pdb=" N GLY A 104 " --> pdb=" O TYR A 117 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY A 234 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 121 removed outlier: 5.874A pdb=" N ALA A 211 " --> pdb=" O HIS A 259 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU A 261 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLY A 213 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL A 263 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ALA A 215 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU A 144 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N PHE A 304 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE A 146 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL A 328 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS A 303 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N GLU A 330 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ALA A 305 " --> pdb=" O GLU A 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 116 through 117 removed outlier: 3.981A pdb=" N GLY B 104 " --> pdb=" O TYR B 117 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY B 234 " --> pdb=" O ASP B 105 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 119 through 121 removed outlier: 5.873A pdb=" N ALA B 211 " --> pdb=" O HIS B 259 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU B 261 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLY B 213 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL B 263 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ALA B 215 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL B 145 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU B 144 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N PHE B 304 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE B 146 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N VAL B 328 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N CYS B 303 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N GLU B 330 " --> pdb=" O CYS B 303 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ALA B 305 " --> pdb=" O GLU B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 116 through 117 removed outlier: 3.981A pdb=" N GLY C 104 " --> pdb=" O TYR C 117 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY C 234 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 119 through 121 removed outlier: 5.874A pdb=" N ALA C 211 " --> pdb=" O HIS C 259 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU C 261 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLY C 213 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL C 263 " --> pdb=" O GLY C 213 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ALA C 215 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU C 144 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N PHE C 304 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE C 146 " --> pdb=" O PHE C 304 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N VAL C 328 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS C 303 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N GLU C 330 " --> pdb=" O CYS C 303 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ALA C 305 " --> pdb=" O GLU C 330 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 116 through 117 removed outlier: 3.981A pdb=" N GLY D 104 " --> pdb=" O TYR D 117 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY D 234 " --> pdb=" O ASP D 105 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 119 through 121 removed outlier: 5.873A pdb=" N ALA D 211 " --> pdb=" O HIS D 259 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU D 261 " --> pdb=" O ALA D 211 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLY D 213 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL D 263 " --> pdb=" O GLY D 213 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ALA D 215 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL D 145 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU D 144 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N PHE D 304 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE D 146 " --> pdb=" O PHE D 304 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N VAL D 328 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N CYS D 303 " --> pdb=" O VAL D 328 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N GLU D 330 " --> pdb=" O CYS D 303 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ALA D 305 " --> pdb=" O GLU D 330 " (cutoff:3.500A) 1774 hydrogen bonds defined for protein. 5262 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: 5.97 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8676 1.34 - 1.46: 6675 1.46 - 1.58: 15519 1.58 - 1.70: 6 1.70 - 1.82: 212 Bond restraints: 31088 Sorted by residual: bond pdb=" CA ILE D1011 " pdb=" C ILE D1011 " ideal model delta sigma weight residual 1.524 1.591 -0.067 1.05e-02 9.07e+03 4.07e+01 bond pdb=" CA ILE A1011 " pdb=" C ILE A1011 " ideal model delta sigma weight residual 1.524 1.588 -0.064 1.05e-02 9.07e+03 3.71e+01 bond pdb=" C PRO D1012 " pdb=" O PRO D1012 " ideal model delta sigma weight residual 1.233 1.290 -0.057 1.21e-02 6.83e+03 2.24e+01 bond pdb=" C PRO A1012 " pdb=" O PRO A1012 " ideal model delta sigma weight residual 1.233 1.288 -0.055 1.21e-02 6.83e+03 2.06e+01 bond pdb=" CA PHE B1013 " pdb=" C PHE B1013 " ideal model delta sigma weight residual 1.522 1.579 -0.058 1.29e-02 6.01e+03 1.99e+01 ... (remaining 31083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 40251 2.17 - 4.34: 1574 4.34 - 6.51: 215 6.51 - 8.68: 52 8.68 - 10.85: 20 Bond angle restraints: 42112 Sorted by residual: angle pdb=" N PHE B1013 " pdb=" CA PHE B1013 " pdb=" C PHE B1013 " ideal model delta sigma weight residual 113.45 124.02 -10.57 1.39e+00 5.18e-01 5.78e+01 angle pdb=" N PHE D1013 " pdb=" CA PHE D1013 " pdb=" C PHE D1013 " ideal model delta sigma weight residual 113.45 123.93 -10.48 1.39e+00 5.18e-01 5.68e+01 angle pdb=" N PHE A1013 " pdb=" CA PHE A1013 " pdb=" C PHE A1013 " ideal model delta sigma weight residual 113.45 123.65 -10.20 1.39e+00 5.18e-01 5.38e+01 angle pdb=" N PHE C1013 " pdb=" CA PHE C1013 " pdb=" C PHE C1013 " ideal model delta sigma weight residual 113.45 123.10 -9.65 1.39e+00 5.18e-01 4.82e+01 angle pdb=" N ARG D 452 " pdb=" CA ARG D 452 " pdb=" C ARG D 452 " ideal model delta sigma weight residual 108.26 119.11 -10.85 1.66e+00 3.63e-01 4.27e+01 ... (remaining 42107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.95: 17020 14.95 - 29.91: 976 29.91 - 44.86: 243 44.86 - 59.82: 13 59.82 - 74.77: 28 Dihedral angle restraints: 18280 sinusoidal: 7368 harmonic: 10912 Sorted by residual: dihedral pdb=" CA ILE D 985 " pdb=" C ILE D 985 " pdb=" N VAL D 986 " pdb=" CA VAL D 986 " ideal model delta harmonic sigma weight residual -180.00 -152.48 -27.52 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA ILE A 985 " pdb=" C ILE A 985 " pdb=" N VAL A 986 " pdb=" CA VAL A 986 " ideal model delta harmonic sigma weight residual 180.00 -152.48 -27.52 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA ILE C 985 " pdb=" C ILE C 985 " pdb=" N VAL C 986 " pdb=" CA VAL C 986 " ideal model delta harmonic sigma weight residual 180.00 -152.49 -27.51 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 18277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 4287 0.089 - 0.178: 405 0.178 - 0.268: 12 0.268 - 0.357: 1 0.357 - 0.446: 3 Chirality restraints: 4708 Sorted by residual: chirality pdb=" CA ILE D1011 " pdb=" N ILE D1011 " pdb=" C ILE D1011 " pdb=" CB ILE D1011 " both_signs ideal model delta sigma weight residual False 2.43 2.88 -0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" CA ILE A1011 " pdb=" N ILE A1011 " pdb=" C ILE A1011 " pdb=" CB ILE A1011 " both_signs ideal model delta sigma weight residual False 2.43 2.86 -0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CA ILE B1011 " pdb=" N ILE B1011 " pdb=" C ILE B1011 " pdb=" CB ILE B1011 " both_signs ideal model delta sigma weight residual False 2.43 2.83 -0.40 2.00e-01 2.50e+01 3.90e+00 ... (remaining 4705 not shown) Planarity restraints: 5264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D1011 " -0.076 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO D1012 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO D1012 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO D1012 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A1011 " -0.075 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO A1012 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO A1012 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO A1012 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B1011 " -0.074 5.00e-02 4.00e+02 1.12e-01 1.99e+01 pdb=" N PRO B1012 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO B1012 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO B1012 " -0.060 5.00e-02 4.00e+02 ... (remaining 5261 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 5307 2.76 - 3.30: 28769 3.30 - 3.83: 48828 3.83 - 4.37: 57261 4.37 - 4.90: 97374 Nonbonded interactions: 237539 Sorted by model distance: nonbonded pdb=" O VAL C1065 " pdb=" OG1 THR C1069 " model vdw 2.231 3.040 nonbonded pdb=" O VAL A1065 " pdb=" OG1 THR A1069 " model vdw 2.231 3.040 nonbonded pdb=" O VAL B1065 " pdb=" OG1 THR B1069 " model vdw 2.232 3.040 nonbonded pdb=" O VAL D1065 " pdb=" OG1 THR D1069 " model vdw 2.232 3.040 nonbonded pdb=" O VAL A 196 " pdb=" OG1 THR A 200 " model vdw 2.292 3.040 ... (remaining 237534 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 102 through 1104) selection = chain 'B' 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 29.890 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 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 : 0.006 0.078 31092 Z= 0.290 Angle : 0.995 10.847 42120 Z= 0.568 Chirality : 0.055 0.446 4708 Planarity : 0.007 0.117 5264 Dihedral : 10.557 74.772 11188 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.60 % Allowed : 2.28 % Favored : 97.12 % 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: -3.96 (0.10), residues: 3656 helix: -2.20 (0.08), residues: 2472 sheet: -1.38 (0.36), residues: 184 loop : -3.51 (0.15), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 816 TYR 0.030 0.003 TYR B 808 PHE 0.030 0.003 PHE C 832 TRP 0.024 0.003 TRP A 651 HIS 0.006 0.002 HIS D 257 Details of bonding type rmsd covalent geometry : bond 0.00608 (31088) covalent geometry : angle 0.99283 (42112) SS BOND : bond 0.02419 ( 4) SS BOND : angle 4.31654 ( 8) hydrogen bonds : bond 0.14987 ( 1774) hydrogen bonds : angle 6.70817 ( 5262) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 776 time to evaluate : 1.266 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 VAL cc_start: 0.8855 (t) cc_final: 0.8636 (p) REVERT: A 518 ASP cc_start: 0.7655 (m-30) cc_final: 0.7272 (m-30) REVERT: A 615 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7515 (tp30) REVERT: A 619 ASN cc_start: 0.7769 (m110) cc_final: 0.7569 (m-40) REVERT: A 779 PHE cc_start: 0.8445 (t80) cc_final: 0.8206 (t80) REVERT: B 302 VAL cc_start: 0.8856 (t) cc_final: 0.8638 (p) REVERT: B 518 ASP cc_start: 0.7666 (m-30) cc_final: 0.7279 (m-30) REVERT: B 615 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7519 (tp30) REVERT: B 779 PHE cc_start: 0.8447 (t80) cc_final: 0.8208 (t80) REVERT: C 302 VAL cc_start: 0.8859 (t) cc_final: 0.8638 (p) REVERT: C 426 TRP cc_start: 0.6606 (p-90) cc_final: 0.6016 (p-90) REVERT: C 518 ASP cc_start: 0.7669 (m-30) cc_final: 0.7280 (m-30) REVERT: C 615 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7513 (tp30) REVERT: C 619 ASN cc_start: 0.7775 (m110) cc_final: 0.7575 (m-40) REVERT: C 779 PHE cc_start: 0.8452 (t80) cc_final: 0.8211 (t80) REVERT: D 302 VAL cc_start: 0.8856 (t) cc_final: 0.8636 (p) REVERT: D 518 ASP cc_start: 0.7675 (m-30) cc_final: 0.7286 (m-30) REVERT: D 615 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7517 (tp30) REVERT: D 779 PHE cc_start: 0.8446 (t80) cc_final: 0.8209 (t80) outliers start: 20 outliers final: 8 residues processed: 788 average time/residue: 0.7788 time to fit residues: 708.2903 Evaluate side-chains 384 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 376 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 1012 PRO Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 1012 PRO Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 1012 PRO Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 1012 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 8.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 HIS A 279 ASN A 438 GLN A 510 GLN A 671 GLN A 675 GLN A 681 GLN A 987 GLN A 997 GLN A1047 ASN B 136 HIS ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 HIS B 279 ASN B 510 GLN B 619 ASN B 671 GLN B 675 GLN B 681 GLN B 987 GLN B 997 GLN B1047 ASN C 136 HIS ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 HIS C 279 ASN C 510 GLN C 671 GLN C 675 GLN C 681 GLN C 987 GLN C 997 GLN C1047 ASN D 136 HIS ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 HIS D 279 ASN D 438 GLN D 510 GLN D 619 ASN D 671 GLN D 675 GLN D 681 GLN D 987 GLN D 997 GLN D1047 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.146478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.105185 restraints weight = 62498.846| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.71 r_work: 0.3398 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 31092 Z= 0.209 Angle : 0.733 10.076 42120 Z= 0.386 Chirality : 0.044 0.179 4708 Planarity : 0.006 0.067 5264 Dihedral : 5.772 35.063 4020 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.94 % Allowed : 12.86 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.12), residues: 3656 helix: -0.55 (0.10), residues: 2460 sheet: -1.62 (0.34), residues: 188 loop : -3.21 (0.15), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 452 TYR 0.018 0.002 TYR C1005 PHE 0.020 0.002 PHE D1082 TRP 0.038 0.002 TRP D 453 HIS 0.005 0.001 HIS C 559 Details of bonding type rmsd covalent geometry : bond 0.00485 (31088) covalent geometry : angle 0.73290 (42112) SS BOND : bond 0.00867 ( 4) SS BOND : angle 2.12711 ( 8) hydrogen bonds : bond 0.05657 ( 1774) hydrogen bonds : angle 4.94124 ( 5262) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 456 time to evaluate : 1.244 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 HIS cc_start: 0.7799 (OUTLIER) cc_final: 0.7386 (t-90) REVERT: A 189 MET cc_start: 0.7743 (mpp) cc_final: 0.6880 (mtt) REVERT: A 353 MET cc_start: 0.6842 (mpt) cc_final: 0.6534 (mpp) REVERT: A 396 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7615 (mpm) REVERT: A 518 ASP cc_start: 0.7621 (m-30) cc_final: 0.7249 (m-30) REVERT: A 615 GLU cc_start: 0.8389 (tm-30) cc_final: 0.7983 (tm-30) REVERT: A 622 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8081 (pt0) REVERT: A 731 PHE cc_start: 0.7154 (OUTLIER) cc_final: 0.6657 (t80) REVERT: A 779 PHE cc_start: 0.8847 (t80) cc_final: 0.8559 (t80) REVERT: A 920 ASP cc_start: 0.8555 (t0) cc_final: 0.8075 (t0) REVERT: B 185 HIS cc_start: 0.7815 (OUTLIER) cc_final: 0.7404 (t-90) REVERT: B 189 MET cc_start: 0.7759 (mpp) cc_final: 0.6886 (mtt) REVERT: B 353 MET cc_start: 0.6769 (mpt) cc_final: 0.6459 (mpp) REVERT: B 396 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7601 (mpm) REVERT: B 518 ASP cc_start: 0.7625 (m-30) cc_final: 0.7253 (m-30) REVERT: B 615 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7794 (tp30) REVERT: B 622 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8088 (pt0) REVERT: B 731 PHE cc_start: 0.7156 (OUTLIER) cc_final: 0.6660 (t80) REVERT: B 779 PHE cc_start: 0.8848 (t80) cc_final: 0.8564 (t80) REVERT: B 920 ASP cc_start: 0.8563 (t0) cc_final: 0.8082 (t0) REVERT: C 185 HIS cc_start: 0.7816 (OUTLIER) cc_final: 0.7401 (t-90) REVERT: C 189 MET cc_start: 0.7732 (mpp) cc_final: 0.6879 (mtt) REVERT: C 353 MET cc_start: 0.6846 (mpt) cc_final: 0.6536 (mpp) REVERT: C 396 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7610 (mpm) REVERT: C 518 ASP cc_start: 0.7632 (m-30) cc_final: 0.7257 (m-30) REVERT: C 615 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7973 (tm-30) REVERT: C 622 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8085 (pt0) REVERT: C 731 PHE cc_start: 0.7159 (OUTLIER) cc_final: 0.6662 (t80) REVERT: C 779 PHE cc_start: 0.8855 (t80) cc_final: 0.8568 (t80) REVERT: C 920 ASP cc_start: 0.8559 (t0) cc_final: 0.8072 (t0) REVERT: D 185 HIS cc_start: 0.7830 (OUTLIER) cc_final: 0.7423 (t-90) REVERT: D 189 MET cc_start: 0.7801 (mpp) cc_final: 0.6936 (mtt) REVERT: D 353 MET cc_start: 0.6757 (mpt) cc_final: 0.6448 (mpp) REVERT: D 396 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7610 (mpm) REVERT: D 518 ASP cc_start: 0.7633 (m-30) cc_final: 0.7265 (m-30) REVERT: D 615 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7792 (tp30) REVERT: D 622 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8083 (pt0) REVERT: D 731 PHE cc_start: 0.7153 (OUTLIER) cc_final: 0.6653 (t80) REVERT: D 779 PHE cc_start: 0.8854 (t80) cc_final: 0.8568 (t80) REVERT: D 920 ASP cc_start: 0.8564 (t0) cc_final: 0.8086 (t0) outliers start: 98 outliers final: 12 residues processed: 537 average time/residue: 0.6953 time to fit residues: 437.9576 Evaluate side-chains 381 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 353 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 731 PHE Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 622 GLU Chi-restraints excluded: chain D residue 731 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 175 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 270 optimal weight: 0.0170 chunk 172 optimal weight: 0.6980 chunk 102 optimal weight: 20.0000 chunk 73 optimal weight: 2.9990 chunk 258 optimal weight: 3.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 GLN A 635 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN B 459 GLN B 619 ASN ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 438 GLN C 459 GLN C 635 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 459 GLN D 619 ASN D 635 ASN ** D 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.148209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.107132 restraints weight = 62387.187| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.71 r_work: 0.3445 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31092 Z= 0.136 Angle : 0.656 8.679 42120 Z= 0.344 Chirality : 0.042 0.187 4708 Planarity : 0.005 0.064 5264 Dihedral : 5.247 29.721 4000 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.79 % Allowed : 15.78 % Favored : 81.43 % 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: -1.34 (0.13), residues: 3656 helix: 0.07 (0.10), residues: 2472 sheet: -1.49 (0.34), residues: 188 loop : -3.11 (0.16), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 288 TYR 0.021 0.002 TYR D 727 PHE 0.023 0.001 PHE C 487 TRP 0.036 0.002 TRP B 426 HIS 0.002 0.001 HIS D 257 Details of bonding type rmsd covalent geometry : bond 0.00298 (31088) covalent geometry : angle 0.65577 (42112) SS BOND : bond 0.00238 ( 4) SS BOND : angle 1.43980 ( 8) hydrogen bonds : bond 0.04590 ( 1774) hydrogen bonds : angle 4.45275 ( 5262) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 440 time to evaluate : 1.192 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 MET cc_start: 0.7635 (mpp) cc_final: 0.6705 (mtt) REVERT: A 353 MET cc_start: 0.6862 (mpt) cc_final: 0.6560 (mpp) REVERT: A 396 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7623 (mpm) REVERT: A 615 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7653 (tp30) REVERT: A 616 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7489 (tm-30) REVERT: A 622 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7968 (pt0) REVERT: A 680 LYS cc_start: 0.8330 (mtpt) cc_final: 0.8111 (mtpp) REVERT: A 731 PHE cc_start: 0.7272 (OUTLIER) cc_final: 0.6771 (t80) REVERT: A 779 PHE cc_start: 0.8871 (t80) cc_final: 0.8557 (t80) REVERT: A 920 ASP cc_start: 0.8424 (t0) cc_final: 0.8131 (t0) REVERT: B 189 MET cc_start: 0.7626 (mpp) cc_final: 0.6671 (mtt) REVERT: B 353 MET cc_start: 0.6843 (mpt) cc_final: 0.6409 (mpp) REVERT: B 396 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7632 (mpm) REVERT: B 462 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8320 (tpp) REVERT: B 615 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7662 (tp30) REVERT: B 622 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7980 (pt0) REVERT: B 680 LYS cc_start: 0.8320 (mtpt) cc_final: 0.8102 (mtpp) REVERT: B 731 PHE cc_start: 0.7272 (OUTLIER) cc_final: 0.6771 (t80) REVERT: B 779 PHE cc_start: 0.8869 (t80) cc_final: 0.8559 (t80) REVERT: B 920 ASP cc_start: 0.8430 (t0) cc_final: 0.8134 (t0) REVERT: C 189 MET cc_start: 0.7632 (mpp) cc_final: 0.6700 (mtt) REVERT: C 353 MET cc_start: 0.6876 (mpt) cc_final: 0.6567 (mpp) REVERT: C 396 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7629 (mpm) REVERT: C 615 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7646 (tp30) REVERT: C 616 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7498 (tm-30) REVERT: C 622 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7985 (pt0) REVERT: C 680 LYS cc_start: 0.8322 (mtpt) cc_final: 0.8103 (mtpp) REVERT: C 731 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.6773 (t80) REVERT: C 779 PHE cc_start: 0.8867 (t80) cc_final: 0.8551 (t80) REVERT: C 920 ASP cc_start: 0.8428 (t0) cc_final: 0.8135 (t0) REVERT: D 353 MET cc_start: 0.6848 (mpt) cc_final: 0.6407 (mpp) REVERT: D 396 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7627 (mpm) REVERT: D 615 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7653 (tp30) REVERT: D 622 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7969 (pt0) REVERT: D 731 PHE cc_start: 0.7270 (OUTLIER) cc_final: 0.6772 (t80) REVERT: D 779 PHE cc_start: 0.8868 (t80) cc_final: 0.8554 (t80) REVERT: D 920 ASP cc_start: 0.8424 (t0) cc_final: 0.8132 (t0) outliers start: 93 outliers final: 26 residues processed: 500 average time/residue: 0.6754 time to fit residues: 397.8033 Evaluate side-chains 381 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 340 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 731 PHE Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 940 CYS Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 464 THR Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 622 GLU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 731 PHE Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 940 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 180 optimal weight: 9.9990 chunk 243 optimal weight: 0.9990 chunk 235 optimal weight: 10.0000 chunk 349 optimal weight: 0.8980 chunk 218 optimal weight: 0.0050 chunk 268 optimal weight: 0.5980 chunk 0 optimal weight: 30.0000 chunk 256 optimal weight: 2.9990 chunk 368 optimal weight: 7.9990 chunk 55 optimal weight: 0.0070 chunk 88 optimal weight: 9.9990 overall best weight: 0.5014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 HIS A 619 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 ASN ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 500 HIS B 635 ASN ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 ASN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 500 HIS C 619 ASN ** C 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 500 HIS ** D 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1101 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.149175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.108272 restraints weight = 61485.256| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.69 r_work: 0.3455 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31092 Z= 0.125 Angle : 0.643 9.441 42120 Z= 0.335 Chirality : 0.041 0.176 4708 Planarity : 0.004 0.065 5264 Dihedral : 4.929 29.237 4000 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.37 % Allowed : 16.71 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.13), residues: 3656 helix: 0.42 (0.10), residues: 2480 sheet: -1.17 (0.36), residues: 184 loop : -2.96 (0.16), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 688 TYR 0.020 0.001 TYR B 727 PHE 0.024 0.001 PHE C 487 TRP 0.035 0.002 TRP C 453 HIS 0.003 0.000 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00260 (31088) covalent geometry : angle 0.64247 (42112) SS BOND : bond 0.00131 ( 4) SS BOND : angle 2.15627 ( 8) hydrogen bonds : bond 0.04031 ( 1774) hydrogen bonds : angle 4.26024 ( 5262) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 405 time to evaluate : 1.153 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 MET cc_start: 0.7547 (mpp) cc_final: 0.6683 (mtt) REVERT: A 353 MET cc_start: 0.6917 (mpt) cc_final: 0.6625 (mpp) REVERT: A 385 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7402 (mm) REVERT: A 396 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7635 (mpm) REVERT: A 615 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7667 (tp30) REVERT: A 680 LYS cc_start: 0.8346 (mtpt) cc_final: 0.8136 (mtpp) REVERT: A 731 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.6815 (t80) REVERT: A 779 PHE cc_start: 0.8890 (t80) cc_final: 0.8557 (t80) REVERT: A 920 ASP cc_start: 0.8406 (t0) cc_final: 0.8116 (t0) REVERT: B 189 MET cc_start: 0.7587 (mpp) cc_final: 0.6699 (mtt) REVERT: B 385 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7406 (mm) REVERT: B 396 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7637 (mpm) REVERT: B 615 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7530 (tp30) REVERT: B 680 LYS cc_start: 0.8344 (mtpt) cc_final: 0.8133 (mtpp) REVERT: B 731 PHE cc_start: 0.7341 (OUTLIER) cc_final: 0.6813 (t80) REVERT: B 779 PHE cc_start: 0.8891 (t80) cc_final: 0.8572 (t80) REVERT: B 920 ASP cc_start: 0.8419 (t0) cc_final: 0.8124 (t0) REVERT: C 189 MET cc_start: 0.7538 (mpp) cc_final: 0.6675 (mtt) REVERT: C 353 MET cc_start: 0.6914 (mpt) cc_final: 0.6623 (mpp) REVERT: C 385 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7397 (mm) REVERT: C 396 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7603 (mpm) REVERT: C 615 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7640 (tp30) REVERT: C 680 LYS cc_start: 0.8346 (mtpt) cc_final: 0.8138 (mtpp) REVERT: C 731 PHE cc_start: 0.7342 (OUTLIER) cc_final: 0.6813 (t80) REVERT: C 779 PHE cc_start: 0.8899 (t80) cc_final: 0.8571 (t80) REVERT: C 840 THR cc_start: 0.9114 (m) cc_final: 0.8828 (m) REVERT: C 920 ASP cc_start: 0.8410 (t0) cc_final: 0.8114 (t0) REVERT: D 188 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8158 (tm) REVERT: D 385 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7399 (mm) REVERT: D 396 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7607 (mpm) REVERT: D 615 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7536 (tp30) REVERT: D 731 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.6819 (t80) REVERT: D 779 PHE cc_start: 0.8888 (t80) cc_final: 0.8555 (t80) REVERT: D 920 ASP cc_start: 0.8405 (t0) cc_final: 0.8115 (t0) outliers start: 112 outliers final: 31 residues processed: 493 average time/residue: 0.5698 time to fit residues: 337.9526 Evaluate side-chains 383 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 339 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 787 TYR Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 731 PHE Chi-restraints excluded: chain C residue 787 TYR Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 940 CYS Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 731 PHE Chi-restraints excluded: chain D residue 787 TYR Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 846 ILE Chi-restraints excluded: chain D residue 940 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 136 optimal weight: 9.9990 chunk 313 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 276 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 326 optimal weight: 0.7980 chunk 324 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 269 optimal weight: 0.8980 chunk 295 optimal weight: 6.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 ASN ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 ASN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.146688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.104892 restraints weight = 62142.764| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.70 r_work: 0.3399 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 31092 Z= 0.167 Angle : 0.658 8.316 42120 Z= 0.343 Chirality : 0.043 0.171 4708 Planarity : 0.004 0.066 5264 Dihedral : 4.819 28.174 4000 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.52 % Allowed : 18.45 % Favored : 79.03 % 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: -0.63 (0.14), residues: 3656 helix: 0.60 (0.10), residues: 2488 sheet: -1.27 (0.36), residues: 188 loop : -2.86 (0.17), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 507 TYR 0.020 0.002 TYR A 787 PHE 0.015 0.001 PHE D1082 TRP 0.035 0.002 TRP B 453 HIS 0.003 0.001 HIS A 765 Details of bonding type rmsd covalent geometry : bond 0.00387 (31088) covalent geometry : angle 0.65748 (42112) SS BOND : bond 0.00205 ( 4) SS BOND : angle 2.34112 ( 8) hydrogen bonds : bond 0.04467 ( 1774) hydrogen bonds : angle 4.25670 ( 5262) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 363 time to evaluate : 1.363 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 ILE cc_start: 0.8896 (mt) cc_final: 0.8529 (pt) REVERT: A 353 MET cc_start: 0.6928 (mpt) cc_final: 0.6667 (mpp) REVERT: A 385 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7464 (mm) REVERT: A 615 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7711 (tp30) REVERT: A 616 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7474 (tm-30) REVERT: A 622 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7948 (pt0) REVERT: A 731 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.6886 (t80) REVERT: A 779 PHE cc_start: 0.8903 (t80) cc_final: 0.8607 (t80) REVERT: A 920 ASP cc_start: 0.8471 (t0) cc_final: 0.8148 (t0) REVERT: B 189 MET cc_start: 0.7456 (mpp) cc_final: 0.6541 (mtt) REVERT: B 385 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7472 (mm) REVERT: B 615 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7685 (tp30) REVERT: B 616 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7481 (tm-30) REVERT: B 622 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7949 (pt0) REVERT: B 731 PHE cc_start: 0.7330 (OUTLIER) cc_final: 0.6883 (t80) REVERT: B 779 PHE cc_start: 0.8908 (t80) cc_final: 0.8615 (t80) REVERT: B 920 ASP cc_start: 0.8464 (t0) cc_final: 0.8127 (t0) REVERT: C 179 ILE cc_start: 0.8893 (mt) cc_final: 0.8543 (pt) REVERT: C 353 MET cc_start: 0.6920 (mpt) cc_final: 0.6663 (mpp) REVERT: C 385 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7467 (mm) REVERT: C 396 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7688 (mpm) REVERT: C 615 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7697 (tp30) REVERT: C 616 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7507 (tm-30) REVERT: C 622 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7956 (pt0) REVERT: C 731 PHE cc_start: 0.7329 (OUTLIER) cc_final: 0.6885 (t80) REVERT: C 779 PHE cc_start: 0.8914 (t80) cc_final: 0.8621 (t80) REVERT: C 920 ASP cc_start: 0.8470 (t0) cc_final: 0.8145 (t0) REVERT: D 189 MET cc_start: 0.7797 (mpm) cc_final: 0.6559 (mmt) REVERT: D 385 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7449 (mm) REVERT: D 615 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7693 (tp30) REVERT: D 616 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7459 (tm-30) REVERT: D 622 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7948 (pt0) REVERT: D 731 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.6898 (t80) REVERT: D 779 PHE cc_start: 0.8910 (t80) cc_final: 0.8616 (t80) REVERT: D 920 ASP cc_start: 0.8467 (t0) cc_final: 0.8133 (t0) outliers start: 84 outliers final: 39 residues processed: 425 average time/residue: 0.5582 time to fit residues: 289.3358 Evaluate side-chains 373 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 317 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 787 TYR Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 731 PHE Chi-restraints excluded: chain C residue 787 TYR Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 940 CYS Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 616 GLU Chi-restraints excluded: chain D residue 622 GLU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 731 PHE Chi-restraints excluded: chain D residue 787 TYR Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 985 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 32 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 255 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 339 optimal weight: 8.9990 chunk 253 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 277 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN A 973 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 ASN ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 973 ASN ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 ASN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN ** C 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 973 ASN ** C 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1101 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.145044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.103120 restraints weight = 62428.819| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.73 r_work: 0.3373 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 31092 Z= 0.209 Angle : 0.696 7.957 42120 Z= 0.367 Chirality : 0.045 0.169 4708 Planarity : 0.005 0.067 5264 Dihedral : 4.920 27.384 4000 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.00 % Allowed : 19.02 % Favored : 77.97 % 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: 3656 helix: 0.58 (0.10), residues: 2480 sheet: -1.24 (0.36), residues: 188 loop : -2.96 (0.16), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 507 TYR 0.020 0.002 TYR C 787 PHE 0.024 0.002 PHE B 487 TRP 0.039 0.002 TRP B 453 HIS 0.004 0.001 HIS C 765 Details of bonding type rmsd covalent geometry : bond 0.00495 (31088) covalent geometry : angle 0.69488 (42112) SS BOND : bond 0.00328 ( 4) SS BOND : angle 2.61507 ( 8) hydrogen bonds : bond 0.04745 ( 1774) hydrogen bonds : angle 4.42173 ( 5262) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 340 time to evaluate : 1.312 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 ILE cc_start: 0.8897 (mt) cc_final: 0.8531 (pt) REVERT: A 353 MET cc_start: 0.6935 (mpt) cc_final: 0.6690 (mpp) REVERT: A 385 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7669 (mm) REVERT: A 518 ASP cc_start: 0.7677 (t0) cc_final: 0.7461 (t70) REVERT: A 615 GLU cc_start: 0.8377 (tm-30) cc_final: 0.7746 (tp30) REVERT: A 616 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7543 (tm-30) REVERT: A 622 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7927 (pt0) REVERT: A 731 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.6830 (t80) REVERT: A 779 PHE cc_start: 0.8922 (t80) cc_final: 0.8613 (t80) REVERT: A 920 ASP cc_start: 0.8495 (t0) cc_final: 0.8115 (t0) REVERT: B 179 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8388 (pt) REVERT: B 189 MET cc_start: 0.7322 (mpp) cc_final: 0.6651 (mtt) REVERT: B 353 MET cc_start: 0.5398 (mpp) cc_final: 0.4917 (mpp) REVERT: B 385 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7669 (mm) REVERT: B 518 ASP cc_start: 0.7669 (t0) cc_final: 0.7448 (t70) REVERT: B 615 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7727 (tp30) REVERT: B 616 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7554 (tm-30) REVERT: B 622 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7933 (pt0) REVERT: B 731 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.6829 (t80) REVERT: B 779 PHE cc_start: 0.8925 (t80) cc_final: 0.8603 (t80) REVERT: B 920 ASP cc_start: 0.8499 (t0) cc_final: 0.8121 (t0) REVERT: C 179 ILE cc_start: 0.8893 (mt) cc_final: 0.8524 (pt) REVERT: C 353 MET cc_start: 0.6934 (mpt) cc_final: 0.6689 (mpp) REVERT: C 385 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7698 (mm) REVERT: C 518 ASP cc_start: 0.7663 (t0) cc_final: 0.7444 (t70) REVERT: C 615 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7754 (tp30) REVERT: C 616 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7557 (tm-30) REVERT: C 622 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7990 (pt0) REVERT: C 731 PHE cc_start: 0.7263 (OUTLIER) cc_final: 0.6825 (t80) REVERT: C 779 PHE cc_start: 0.8931 (t80) cc_final: 0.8627 (t80) REVERT: C 808 TYR cc_start: 0.8737 (m-80) cc_final: 0.8534 (m-10) REVERT: C 920 ASP cc_start: 0.8493 (t0) cc_final: 0.8109 (t0) REVERT: D 179 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8386 (pt) REVERT: D 353 MET cc_start: 0.5409 (mpp) cc_final: 0.4920 (mpp) REVERT: D 385 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7698 (mm) REVERT: D 518 ASP cc_start: 0.7667 (t0) cc_final: 0.7449 (t70) REVERT: D 615 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7732 (tp30) REVERT: D 616 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7537 (tm-30) REVERT: D 622 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7935 (pt0) REVERT: D 731 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.6834 (t80) REVERT: D 779 PHE cc_start: 0.8924 (t80) cc_final: 0.8617 (t80) REVERT: D 920 ASP cc_start: 0.8478 (t0) cc_final: 0.8105 (t0) outliers start: 100 outliers final: 42 residues processed: 416 average time/residue: 0.5442 time to fit residues: 276.9632 Evaluate side-chains 371 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 311 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 787 TYR Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 731 PHE Chi-restraints excluded: chain C residue 787 TYR Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 940 CYS Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 616 GLU Chi-restraints excluded: chain D residue 622 GLU Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 731 PHE Chi-restraints excluded: chain D residue 787 TYR Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 940 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 30 optimal weight: 7.9990 chunk 190 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 314 optimal weight: 0.5980 chunk 320 optimal weight: 0.6980 chunk 340 optimal weight: 5.9990 chunk 358 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 204 optimal weight: 8.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 ASN ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 ASN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN ** C 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 ASN D 973 ASN ** D 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1101 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.146868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.105499 restraints weight = 62119.745| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.67 r_work: 0.3416 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31092 Z= 0.139 Angle : 0.655 8.529 42120 Z= 0.344 Chirality : 0.042 0.166 4708 Planarity : 0.004 0.065 5264 Dihedral : 4.727 26.176 4000 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.82 % Allowed : 19.74 % Favored : 77.43 % 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: -0.42 (0.14), residues: 3656 helix: 0.77 (0.10), residues: 2476 sheet: -0.91 (0.38), residues: 184 loop : -2.84 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 451 TYR 0.021 0.001 TYR B 727 PHE 0.023 0.001 PHE D1082 TRP 0.041 0.002 TRP C 453 HIS 0.003 0.001 HIS D 257 Details of bonding type rmsd covalent geometry : bond 0.00314 (31088) covalent geometry : angle 0.65481 (42112) SS BOND : bond 0.00182 ( 4) SS BOND : angle 2.02676 ( 8) hydrogen bonds : bond 0.04171 ( 1774) hydrogen bonds : angle 4.25869 ( 5262) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 360 time to evaluate : 1.116 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 ILE cc_start: 0.8846 (mt) cc_final: 0.8477 (pt) REVERT: A 385 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7645 (mm) REVERT: A 518 ASP cc_start: 0.7681 (t0) cc_final: 0.7456 (t70) REVERT: A 605 LYS cc_start: 0.8531 (tppp) cc_final: 0.8063 (tppp) REVERT: A 615 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7592 (tp30) REVERT: A 616 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7486 (tm-30) REVERT: A 622 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7902 (pt0) REVERT: A 731 PHE cc_start: 0.7270 (OUTLIER) cc_final: 0.7048 (t80) REVERT: A 779 PHE cc_start: 0.8921 (t80) cc_final: 0.8604 (t80) REVERT: A 920 ASP cc_start: 0.8414 (t0) cc_final: 0.8048 (t0) REVERT: B 189 MET cc_start: 0.7271 (mpp) cc_final: 0.6530 (mtt) REVERT: B 385 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7646 (mm) REVERT: B 518 ASP cc_start: 0.7668 (t0) cc_final: 0.7444 (t70) REVERT: B 605 LYS cc_start: 0.8533 (tppp) cc_final: 0.8062 (tppp) REVERT: B 615 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7617 (tp30) REVERT: B 616 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: B 622 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7918 (pt0) REVERT: B 731 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.7041 (t80) REVERT: B 779 PHE cc_start: 0.8905 (t80) cc_final: 0.8580 (t80) REVERT: B 920 ASP cc_start: 0.8422 (t0) cc_final: 0.8050 (t0) REVERT: C 179 ILE cc_start: 0.8834 (mt) cc_final: 0.8477 (pt) REVERT: C 385 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7644 (mm) REVERT: C 451 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6751 (pmt-80) REVERT: C 518 ASP cc_start: 0.7669 (t0) cc_final: 0.7446 (t70) REVERT: C 605 LYS cc_start: 0.8530 (tppp) cc_final: 0.8060 (tppp) REVERT: C 615 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7597 (tp30) REVERT: C 616 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7513 (tm-30) REVERT: C 622 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7930 (pt0) REVERT: C 731 PHE cc_start: 0.7263 (OUTLIER) cc_final: 0.7044 (t80) REVERT: C 779 PHE cc_start: 0.8930 (t80) cc_final: 0.8615 (t80) REVERT: C 808 TYR cc_start: 0.8719 (m-80) cc_final: 0.8516 (m-80) REVERT: C 920 ASP cc_start: 0.8416 (t0) cc_final: 0.8043 (t0) REVERT: D 385 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7647 (mm) REVERT: D 518 ASP cc_start: 0.7666 (t0) cc_final: 0.7439 (t70) REVERT: D 605 LYS cc_start: 0.8520 (tppp) cc_final: 0.8051 (tppp) REVERT: D 615 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7629 (tp30) REVERT: D 616 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7519 (tm-30) REVERT: D 622 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7915 (pt0) REVERT: D 731 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.7045 (t80) REVERT: D 779 PHE cc_start: 0.8923 (t80) cc_final: 0.8606 (t80) REVERT: D 920 ASP cc_start: 0.8410 (t0) cc_final: 0.8040 (t0) outliers start: 94 outliers final: 38 residues processed: 427 average time/residue: 0.5528 time to fit residues: 286.5840 Evaluate side-chains 381 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 326 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 787 TYR Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 731 PHE Chi-restraints excluded: chain C residue 787 TYR Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 940 CYS Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 616 GLU Chi-restraints excluded: chain D residue 622 GLU Chi-restraints excluded: chain D residue 731 PHE Chi-restraints excluded: chain D residue 787 TYR Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 940 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 317 optimal weight: 10.0000 chunk 192 optimal weight: 1.9990 chunk 196 optimal weight: 7.9990 chunk 209 optimal weight: 0.0980 chunk 190 optimal weight: 0.0980 chunk 6 optimal weight: 1.9990 chunk 308 optimal weight: 8.9990 chunk 302 optimal weight: 7.9990 chunk 307 optimal weight: 8.9990 chunk 232 optimal weight: 3.9990 chunk 221 optimal weight: 7.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 ASN B 619 ASN ** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 ASN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 973 ASN ** C 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 ASN D 619 ASN ** D 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1101 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.146962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.105420 restraints weight = 62465.098| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.71 r_work: 0.3418 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31092 Z= 0.137 Angle : 0.662 10.231 42120 Z= 0.343 Chirality : 0.042 0.167 4708 Planarity : 0.004 0.066 5264 Dihedral : 4.637 23.745 4000 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.28 % Allowed : 20.67 % Favored : 77.04 % 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: -0.36 (0.14), residues: 3656 helix: 0.79 (0.10), residues: 2476 sheet: -0.87 (0.38), residues: 184 loop : -2.75 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 452 TYR 0.024 0.002 TYR B 251 PHE 0.027 0.001 PHE A 487 TRP 0.031 0.002 TRP C 453 HIS 0.002 0.001 HIS D 257 Details of bonding type rmsd covalent geometry : bond 0.00310 (31088) covalent geometry : angle 0.66185 (42112) SS BOND : bond 0.00183 ( 4) SS BOND : angle 1.93457 ( 8) hydrogen bonds : bond 0.04134 ( 1774) hydrogen bonds : angle 4.26457 ( 5262) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 366 time to evaluate : 1.242 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 ILE cc_start: 0.8836 (mt) cc_final: 0.8455 (pt) REVERT: A 385 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7640 (mm) REVERT: A 605 LYS cc_start: 0.8460 (tppp) cc_final: 0.8149 (tppp) REVERT: A 615 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7591 (tp30) REVERT: A 616 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7494 (tm-30) REVERT: A 622 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7869 (pt0) REVERT: A 731 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.7072 (t80) REVERT: A 779 PHE cc_start: 0.8905 (t80) cc_final: 0.8581 (t80) REVERT: A 920 ASP cc_start: 0.8421 (t0) cc_final: 0.8041 (t0) REVERT: B 189 MET cc_start: 0.7229 (mpp) cc_final: 0.6488 (mtt) REVERT: B 385 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7641 (mm) REVERT: B 605 LYS cc_start: 0.8457 (tppp) cc_final: 0.8145 (tppp) REVERT: B 615 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7609 (tp30) REVERT: B 616 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7492 (tm-30) REVERT: B 622 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7866 (pt0) REVERT: B 631 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7914 (mm-30) REVERT: B 731 PHE cc_start: 0.7281 (OUTLIER) cc_final: 0.7066 (t80) REVERT: B 779 PHE cc_start: 0.8900 (t80) cc_final: 0.8579 (t80) REVERT: B 920 ASP cc_start: 0.8468 (t0) cc_final: 0.8078 (t0) REVERT: C 179 ILE cc_start: 0.8848 (mt) cc_final: 0.8489 (pt) REVERT: C 189 MET cc_start: 0.7602 (mpm) cc_final: 0.6737 (mmt) REVERT: C 385 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7640 (mm) REVERT: C 451 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6314 (pmt-80) REVERT: C 605 LYS cc_start: 0.8459 (tppp) cc_final: 0.8147 (tppp) REVERT: C 615 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7585 (tp30) REVERT: C 616 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7493 (tm-30) REVERT: C 622 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7886 (pt0) REVERT: C 731 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.7039 (t80) REVERT: C 779 PHE cc_start: 0.8911 (t80) cc_final: 0.8591 (t80) REVERT: C 808 TYR cc_start: 0.8727 (m-80) cc_final: 0.8517 (m-80) REVERT: C 920 ASP cc_start: 0.8431 (t0) cc_final: 0.8048 (t0) REVERT: D 166 SER cc_start: 0.8949 (t) cc_final: 0.8432 (p) REVERT: D 385 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7646 (mm) REVERT: D 605 LYS cc_start: 0.8456 (tppp) cc_final: 0.8145 (tppp) REVERT: D 615 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7616 (tp30) REVERT: D 616 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7470 (tm-30) REVERT: D 622 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7862 (pt0) REVERT: D 631 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7926 (mm-30) REVERT: D 731 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.7072 (t80) REVERT: D 779 PHE cc_start: 0.8907 (t80) cc_final: 0.8584 (t80) REVERT: D 920 ASP cc_start: 0.8456 (t0) cc_final: 0.8067 (t0) outliers start: 76 outliers final: 39 residues processed: 422 average time/residue: 0.5407 time to fit residues: 279.3996 Evaluate side-chains 383 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 327 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 1091 ASP Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain B residue 1091 ASP Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 731 PHE Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 940 CYS Chi-restraints excluded: chain C residue 1091 ASP Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 616 GLU Chi-restraints excluded: chain D residue 622 GLU Chi-restraints excluded: chain D residue 731 PHE Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 1091 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 158 optimal weight: 7.9990 chunk 173 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 252 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 chunk 134 optimal weight: 0.7980 chunk 366 optimal weight: 0.0570 chunk 87 optimal weight: 20.0000 chunk 206 optimal weight: 6.9990 overall best weight: 2.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 973 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1068 ASN A1101 ASN B 973 ASN ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1068 ASN B1101 ASN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 973 ASN ** C 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1068 ASN C1101 ASN D 973 ASN ** D 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1068 ASN D1101 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.146264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.104593 restraints weight = 62362.090| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.70 r_work: 0.3404 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31092 Z= 0.165 Angle : 0.687 11.323 42120 Z= 0.360 Chirality : 0.043 0.171 4708 Planarity : 0.004 0.066 5264 Dihedral : 4.669 26.049 4000 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.46 % Allowed : 20.79 % Favored : 76.74 % 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: 3656 helix: 0.77 (0.10), residues: 2476 sheet: -0.91 (0.38), residues: 184 loop : -2.71 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 507 TYR 0.022 0.002 TYR D 787 PHE 0.024 0.001 PHE C 487 TRP 0.045 0.002 TRP B 453 HIS 0.002 0.001 HIS C 765 Details of bonding type rmsd covalent geometry : bond 0.00383 (31088) covalent geometry : angle 0.68672 (42112) SS BOND : bond 0.00270 ( 4) SS BOND : angle 2.04728 ( 8) hydrogen bonds : bond 0.04353 ( 1774) hydrogen bonds : angle 4.35518 ( 5262) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 341 time to evaluate : 1.199 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 ILE cc_start: 0.8853 (mt) cc_final: 0.8481 (pt) REVERT: A 189 MET cc_start: 0.7435 (mpm) cc_final: 0.6605 (mmt) REVERT: A 353 MET cc_start: 0.5604 (mpp) cc_final: 0.5013 (mpp) REVERT: A 385 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7647 (mm) REVERT: A 605 LYS cc_start: 0.8470 (tppp) cc_final: 0.8167 (tppp) REVERT: A 615 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7561 (tp30) REVERT: A 616 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7445 (tm-30) REVERT: A 622 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7851 (pt0) REVERT: A 631 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7886 (mm-30) REVERT: A 731 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.7007 (t80) REVERT: A 779 PHE cc_start: 0.8911 (t80) cc_final: 0.8584 (t80) REVERT: A 920 ASP cc_start: 0.8420 (t0) cc_final: 0.8040 (t0) REVERT: B 189 MET cc_start: 0.7335 (mpp) cc_final: 0.6593 (mtt) REVERT: B 385 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7643 (mm) REVERT: B 444 ASP cc_start: 0.8611 (m-30) cc_final: 0.8399 (m-30) REVERT: B 605 LYS cc_start: 0.8468 (tppp) cc_final: 0.8162 (tppp) REVERT: B 615 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7594 (tp30) REVERT: B 616 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7440 (tm-30) REVERT: B 622 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7853 (pt0) REVERT: B 631 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7900 (mm-30) REVERT: B 731 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.7000 (t80) REVERT: B 779 PHE cc_start: 0.8915 (t80) cc_final: 0.8591 (t80) REVERT: B 920 ASP cc_start: 0.8422 (t0) cc_final: 0.8037 (t0) REVERT: C 179 ILE cc_start: 0.8863 (mt) cc_final: 0.8505 (pt) REVERT: C 353 MET cc_start: 0.5607 (mpp) cc_final: 0.5014 (mpp) REVERT: C 385 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7676 (mm) REVERT: C 444 ASP cc_start: 0.8595 (m-30) cc_final: 0.8388 (m-30) REVERT: C 451 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6931 (pmt170) REVERT: C 507 ARG cc_start: 0.7780 (mmm160) cc_final: 0.7579 (mmm160) REVERT: C 605 LYS cc_start: 0.8462 (tppp) cc_final: 0.8156 (tppp) REVERT: C 615 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7546 (tp30) REVERT: C 616 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7441 (tm-30) REVERT: C 622 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7868 (pt0) REVERT: C 731 PHE cc_start: 0.7166 (OUTLIER) cc_final: 0.6950 (t80) REVERT: C 779 PHE cc_start: 0.8918 (t80) cc_final: 0.8594 (t80) REVERT: C 808 TYR cc_start: 0.8741 (m-80) cc_final: 0.8530 (m-80) REVERT: C 920 ASP cc_start: 0.8420 (t0) cc_final: 0.8036 (t0) REVERT: D 189 MET cc_start: 0.7485 (mpm) cc_final: 0.6525 (mmt) REVERT: D 385 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7613 (mm) REVERT: D 444 ASP cc_start: 0.8601 (m-30) cc_final: 0.8378 (m-30) REVERT: D 605 LYS cc_start: 0.8458 (tppp) cc_final: 0.8154 (tppp) REVERT: D 615 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7601 (tp30) REVERT: D 616 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7424 (tm-30) REVERT: D 622 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7846 (pt0) REVERT: D 631 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7909 (mm-30) REVERT: D 731 PHE cc_start: 0.7230 (OUTLIER) cc_final: 0.7009 (t80) REVERT: D 779 PHE cc_start: 0.8914 (t80) cc_final: 0.8585 (t80) REVERT: D 920 ASP cc_start: 0.8408 (t0) cc_final: 0.8028 (t0) outliers start: 82 outliers final: 32 residues processed: 392 average time/residue: 0.5378 time to fit residues: 257.9211 Evaluate side-chains 365 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 316 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 731 PHE Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 940 CYS Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 616 GLU Chi-restraints excluded: chain D residue 622 GLU Chi-restraints excluded: chain D residue 731 PHE Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 940 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 24 optimal weight: 7.9990 chunk 347 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 216 optimal weight: 10.0000 chunk 322 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 chunk 168 optimal weight: 0.0370 chunk 269 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 973 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 ASN ** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 973 ASN ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 ASN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN C 438 GLN C 619 ASN ** C 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 ASN D 973 ASN ** D 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1068 ASN D1101 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.146310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.104572 restraints weight = 62108.777| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.71 r_work: 0.3403 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31092 Z= 0.160 Angle : 0.689 10.842 42120 Z= 0.361 Chirality : 0.044 0.169 4708 Planarity : 0.004 0.066 5264 Dihedral : 4.661 23.913 4000 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.77 % Allowed : 21.81 % Favored : 76.41 % 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: -0.35 (0.14), residues: 3656 helix: 0.78 (0.10), residues: 2476 sheet: -0.89 (0.38), residues: 184 loop : -2.68 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1079 TYR 0.023 0.001 TYR C 787 PHE 0.032 0.001 PHE C1082 TRP 0.041 0.002 TRP C 525 HIS 0.002 0.001 HIS D 257 Details of bonding type rmsd covalent geometry : bond 0.00372 (31088) covalent geometry : angle 0.68884 (42112) SS BOND : bond 0.00257 ( 4) SS BOND : angle 1.99912 ( 8) hydrogen bonds : bond 0.04379 ( 1774) hydrogen bonds : angle 4.36483 ( 5262) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 331 time to evaluate : 1.248 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 ILE cc_start: 0.8853 (mt) cc_final: 0.8481 (pt) REVERT: A 189 MET cc_start: 0.7586 (mpm) cc_final: 0.6571 (mmt) REVERT: A 353 MET cc_start: 0.5638 (mpp) cc_final: 0.5086 (mpp) REVERT: A 385 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7618 (mm) REVERT: A 444 ASP cc_start: 0.8596 (m-30) cc_final: 0.8374 (m-30) REVERT: A 605 LYS cc_start: 0.8471 (tppp) cc_final: 0.8172 (tppp) REVERT: A 615 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7893 (tm-30) REVERT: A 622 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7808 (pt0) REVERT: A 731 PHE cc_start: 0.7235 (OUTLIER) cc_final: 0.7025 (t80) REVERT: A 779 PHE cc_start: 0.8927 (t80) cc_final: 0.8598 (t80) REVERT: A 808 TYR cc_start: 0.8689 (m-10) cc_final: 0.8467 (m-10) REVERT: A 920 ASP cc_start: 0.8436 (t0) cc_final: 0.8019 (t0) REVERT: B 385 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7610 (mm) REVERT: B 444 ASP cc_start: 0.8610 (m-30) cc_final: 0.8388 (m-30) REVERT: B 605 LYS cc_start: 0.8463 (tppp) cc_final: 0.8160 (tppp) REVERT: B 615 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7584 (tp30) REVERT: B 616 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7394 (tm-30) REVERT: B 622 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7785 (pt0) REVERT: B 631 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7941 (mm-30) REVERT: B 731 PHE cc_start: 0.7229 (OUTLIER) cc_final: 0.7017 (t80) REVERT: B 779 PHE cc_start: 0.8920 (t80) cc_final: 0.8594 (t80) REVERT: B 808 TYR cc_start: 0.8686 (m-10) cc_final: 0.8460 (m-10) REVERT: C 179 ILE cc_start: 0.8849 (mt) cc_final: 0.8486 (pt) REVERT: C 189 MET cc_start: 0.7533 (mpm) cc_final: 0.6720 (mmt) REVERT: C 353 MET cc_start: 0.5655 (mpp) cc_final: 0.5092 (mpp) REVERT: C 385 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7619 (mm) REVERT: C 444 ASP cc_start: 0.8595 (m-30) cc_final: 0.8383 (m-30) REVERT: C 451 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6671 (pmt170) REVERT: C 605 LYS cc_start: 0.8459 (tppp) cc_final: 0.8158 (tppp) REVERT: C 615 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7564 (tp30) REVERT: C 616 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7382 (tm-30) REVERT: C 622 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7813 (pt0) REVERT: C 631 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7920 (mm-30) REVERT: C 731 PHE cc_start: 0.7209 (OUTLIER) cc_final: 0.6999 (t80) REVERT: C 779 PHE cc_start: 0.8929 (t80) cc_final: 0.8601 (t80) REVERT: C 808 TYR cc_start: 0.8742 (m-80) cc_final: 0.8517 (m-10) REVERT: D 385 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7620 (mm) REVERT: D 444 ASP cc_start: 0.8596 (m-30) cc_final: 0.8373 (m-30) REVERT: D 605 LYS cc_start: 0.8459 (tppp) cc_final: 0.8158 (tppp) REVERT: D 615 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7573 (tp30) REVERT: D 616 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7383 (tm-30) REVERT: D 622 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7785 (pt0) REVERT: D 631 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7935 (mm-30) REVERT: D 731 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.7005 (t80) REVERT: D 779 PHE cc_start: 0.8919 (t80) cc_final: 0.8589 (t80) REVERT: D 808 TYR cc_start: 0.8684 (m-10) cc_final: 0.8456 (m-10) outliers start: 59 outliers final: 33 residues processed: 373 average time/residue: 0.4909 time to fit residues: 227.8106 Evaluate side-chains 362 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 313 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 731 PHE Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 940 CYS Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 616 GLU Chi-restraints excluded: chain D residue 622 GLU Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 731 PHE Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 940 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 247 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 352 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 260 optimal weight: 0.1980 chunk 223 optimal weight: 9.9990 chunk 4 optimal weight: 0.0670 chunk 257 optimal weight: 0.8980 chunk 348 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 321 optimal weight: 4.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1068 ASN A1101 ASN B 619 ASN ** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1068 ASN B1101 ASN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1068 ASN C1101 ASN D 406 ASN D 438 GLN D 619 ASN ** D 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1068 ASN D1101 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.148315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.107107 restraints weight = 62476.010| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.71 r_work: 0.3448 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 31092 Z= 0.129 Angle : 0.674 16.134 42120 Z= 0.348 Chirality : 0.042 0.170 4708 Planarity : 0.005 0.094 5264 Dihedral : 4.518 25.255 4000 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.59 % Allowed : 22.09 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.14), residues: 3656 helix: 0.88 (0.10), residues: 2472 sheet: -0.83 (0.39), residues: 184 loop : -2.60 (0.17), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1079 TYR 0.027 0.001 TYR A 646 PHE 0.034 0.001 PHE C1082 TRP 0.038 0.002 TRP A 453 HIS 0.002 0.000 HIS D 257 Details of bonding type rmsd covalent geometry : bond 0.00284 (31088) covalent geometry : angle 0.67325 (42112) SS BOND : bond 0.00086 ( 4) SS BOND : angle 1.52777 ( 8) hydrogen bonds : bond 0.03890 ( 1774) hydrogen bonds : angle 4.22915 ( 5262) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12276.45 seconds wall clock time: 209 minutes 13.84 seconds (12553.84 seconds total)