Starting phenix.real_space_refine on Thu Jun 26 03:41:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wra_32720/06_2025/7wra_32720.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wra_32720/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wra_32720/06_2025/7wra_32720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wra_32720/06_2025/7wra_32720.map" model { file = "/net/cci-nas-00/data/ceres_data/7wra_32720/06_2025/7wra_32720.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wra_32720/06_2025/7wra_32720.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 20.90, per 1000 atoms: 0.69 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: 6.76 Conformation dependent library (CDL) restraints added in 3.6 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: 3.27 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: 11.14 Time building geometry restraints manager: 8.08 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.380 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 68.450 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.860 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.024 0.003 TRP A 651 HIS 0.006 0.002 HIS D 257 PHE 0.030 0.003 PHE C 832 TYR 0.030 0.003 TYR B 808 ARG 0.006 0.001 ARG C 816 Details of bonding type rmsd hydrogen bonds : bond 0.14987 ( 1774) hydrogen bonds : angle 6.70817 ( 5262) SS BOND : bond 0.02419 ( 4) SS BOND : angle 4.31654 ( 8) covalent geometry : bond 0.00608 (31088) covalent geometry : angle 0.99283 (42112) *********************** 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 : 3.534 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: 0.7271 (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: 0.8639 (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: 0.7285 (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: 1.6466 time to fit residues: 1505.2867 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 : 3.328 ------------------------------------------------------------------------------- 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 314 optimal weight: 7.9990 chunk 281 optimal weight: 8.9990 chunk 156 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 190 optimal weight: 30.0000 chunk 150 optimal weight: 2.9990 chunk 291 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 chunk 177 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 337 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 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 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: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.146589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.105379 restraints weight = 62167.273| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.69 r_work: 0.3404 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 31092 Z= 0.200 Angle : 0.726 10.341 42120 Z= 0.381 Chirality : 0.043 0.181 4708 Planarity : 0.006 0.067 5264 Dihedral : 5.728 35.548 4020 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.61 % Allowed : 13.34 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.12), residues: 3656 helix: -0.53 (0.10), residues: 2460 sheet: -1.61 (0.34), residues: 188 loop : -3.21 (0.15), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 453 HIS 0.004 0.001 HIS C 559 PHE 0.014 0.002 PHE D1082 TYR 0.017 0.002 TYR C1005 ARG 0.005 0.001 ARG A 507 Details of bonding type rmsd hydrogen bonds : bond 0.05611 ( 1774) hydrogen bonds : angle 4.90951 ( 5262) SS BOND : bond 0.00733 ( 4) SS BOND : angle 2.11650 ( 8) covalent geometry : bond 0.00463 (31088) covalent geometry : angle 0.72543 (42112) *********************** 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 542 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 455 time to evaluate : 3.591 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: A 185 HIS cc_start: 0.7799 (OUTLIER) cc_final: 0.7410 (t-90) REVERT: A 189 MET cc_start: 0.7727 (mpp) cc_final: 0.6914 (mtt) REVERT: A 353 MET cc_start: 0.6847 (mpt) cc_final: 0.6544 (mpp) REVERT: A 396 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7609 (mpm) REVERT: A 479 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8137 (tp30) REVERT: A 518 ASP cc_start: 0.7613 (m-30) cc_final: 0.7247 (m-30) REVERT: A 615 GLU cc_start: 0.8392 (tm-30) cc_final: 0.7996 (tm-30) REVERT: A 622 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8087 (pt0) REVERT: A 731 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.6664 (t80) REVERT: A 779 PHE cc_start: 0.8864 (t80) cc_final: 0.8576 (t80) REVERT: A 920 ASP cc_start: 0.8551 (t0) cc_final: 0.8159 (t0) REVERT: B 185 HIS cc_start: 0.7811 (OUTLIER) cc_final: 0.7423 (t-90) REVERT: B 189 MET cc_start: 0.7747 (mpp) cc_final: 0.6906 (mtt) REVERT: B 353 MET cc_start: 0.6841 (mpt) cc_final: 0.6543 (mpp) REVERT: B 396 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7602 (mpm) REVERT: B 518 ASP cc_start: 0.7617 (m-30) cc_final: 0.7252 (m-30) REVERT: B 615 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7790 (tp30) REVERT: B 622 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8098 (pt0) REVERT: B 731 PHE cc_start: 0.7134 (OUTLIER) cc_final: 0.6665 (t80) REVERT: B 779 PHE cc_start: 0.8865 (t80) cc_final: 0.8576 (t80) REVERT: B 920 ASP cc_start: 0.8560 (t0) cc_final: 0.8168 (t0) REVERT: C 185 HIS cc_start: 0.7816 (OUTLIER) cc_final: 0.7426 (t-90) REVERT: C 189 MET cc_start: 0.7721 (mpp) cc_final: 0.6898 (mtt) REVERT: C 353 MET cc_start: 0.6854 (mpt) cc_final: 0.6549 (mpp) REVERT: C 396 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7600 (mpm) REVERT: C 518 ASP cc_start: 0.7624 (m-30) cc_final: 0.7256 (m-30) REVERT: C 615 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7982 (tm-30) REVERT: C 622 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8092 (pt0) REVERT: C 731 PHE cc_start: 0.7136 (OUTLIER) cc_final: 0.6670 (t80) REVERT: C 779 PHE cc_start: 0.8868 (t80) cc_final: 0.8580 (t80) REVERT: C 920 ASP cc_start: 0.8553 (t0) cc_final: 0.8158 (t0) REVERT: D 157 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7256 (mt) REVERT: D 185 HIS cc_start: 0.7825 (OUTLIER) cc_final: 0.7441 (t-90) REVERT: D 189 MET cc_start: 0.7799 (mpp) cc_final: 0.6900 (mtt) REVERT: D 353 MET cc_start: 0.6835 (mpt) cc_final: 0.6538 (mpp) REVERT: D 396 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7604 (mpm) REVERT: D 518 ASP cc_start: 0.7624 (m-30) cc_final: 0.7263 (m-30) REVERT: D 615 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7790 (tp30) REVERT: D 622 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8094 (pt0) REVERT: D 731 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.6662 (t80) REVERT: D 779 PHE cc_start: 0.8866 (t80) cc_final: 0.8575 (t80) REVERT: D 920 ASP cc_start: 0.8554 (t0) cc_final: 0.8148 (t0) outliers start: 87 outliers final: 8 residues processed: 525 average time/residue: 1.3338 time to fit residues: 825.8203 Evaluate side-chains 383 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 357 time to evaluate : 3.357 ------------------------------------------------------------------------------- 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 479 GLU 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 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 516 TYR Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 731 PHE Chi-restraints excluded: chain D residue 157 LEU 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 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 240 optimal weight: 0.7980 chunk 210 optimal weight: 20.0000 chunk 15 optimal weight: 7.9990 chunk 288 optimal weight: 10.0000 chunk 260 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 353 optimal weight: 0.9990 chunk 203 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 312 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 438 GLN A 500 HIS ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN B 619 ASN ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 438 GLN C 500 HIS ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN D 500 HIS D 619 ASN D 635 ASN ** D 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.148301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.107375 restraints weight = 62208.917| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.69 r_work: 0.3441 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31092 Z= 0.132 Angle : 0.653 9.073 42120 Z= 0.342 Chirality : 0.042 0.181 4708 Planarity : 0.005 0.062 5264 Dihedral : 5.244 29.918 4000 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.06 % Allowed : 15.78 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.13), residues: 3656 helix: 0.07 (0.10), residues: 2472 sheet: -1.51 (0.34), residues: 188 loop : -3.10 (0.16), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 453 HIS 0.002 0.001 HIS B 257 PHE 0.024 0.001 PHE A 487 TYR 0.021 0.002 TYR D 727 ARG 0.005 0.001 ARG B 507 Details of bonding type rmsd hydrogen bonds : bond 0.04571 ( 1774) hydrogen bonds : angle 4.44654 ( 5262) SS BOND : bond 0.00757 ( 4) SS BOND : angle 2.17692 ( 8) covalent geometry : bond 0.00284 (31088) covalent geometry : angle 0.65233 (42112) *********************** 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 532 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 430 time to evaluate : 3.420 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 189 MET cc_start: 0.7638 (mpp) cc_final: 0.6679 (mtt) REVERT: A 353 MET cc_start: 0.6851 (mpt) cc_final: 0.6399 (mpp) REVERT: A 396 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7622 (mpm) REVERT: A 615 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7663 (tp30) REVERT: A 622 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7972 (pt0) REVERT: A 680 LYS cc_start: 0.8327 (mtpt) cc_final: 0.8113 (mtpp) REVERT: A 731 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.6773 (t80) REVERT: A 779 PHE cc_start: 0.8860 (t80) cc_final: 0.8547 (t80) REVERT: A 920 ASP cc_start: 0.8398 (t0) cc_final: 0.8112 (t0) REVERT: B 189 MET cc_start: 0.7622 (mpp) cc_final: 0.6685 (mtt) REVERT: B 353 MET cc_start: 0.6833 (mpt) cc_final: 0.6393 (mpp) REVERT: B 396 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7632 (mpm) REVERT: B 462 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8309 (tpp) REVERT: B 615 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7670 (tp30) REVERT: B 622 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7975 (pt0) REVERT: B 680 LYS cc_start: 0.8321 (mtpt) cc_final: 0.8108 (mtpp) REVERT: B 731 PHE cc_start: 0.7274 (OUTLIER) cc_final: 0.6769 (t80) REVERT: B 779 PHE cc_start: 0.8863 (t80) cc_final: 0.8554 (t80) REVERT: B 920 ASP cc_start: 0.8406 (t0) cc_final: 0.8119 (t0) REVERT: C 189 MET cc_start: 0.7630 (mpp) cc_final: 0.6673 (mtt) REVERT: C 353 MET cc_start: 0.6867 (mpt) cc_final: 0.6407 (mpp) REVERT: C 396 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7628 (mpm) REVERT: C 615 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7654 (tp30) REVERT: C 616 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7484 (tm-30) REVERT: C 622 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7990 (pt0) REVERT: C 680 LYS cc_start: 0.8319 (mtpt) cc_final: 0.8105 (mtpp) REVERT: C 731 PHE cc_start: 0.7282 (OUTLIER) cc_final: 0.6779 (t80) REVERT: C 779 PHE cc_start: 0.8868 (t80) cc_final: 0.8557 (t80) REVERT: C 920 ASP cc_start: 0.8406 (t0) cc_final: 0.8119 (t0) REVERT: D 189 MET cc_start: 0.7616 (mpp) cc_final: 0.6643 (mtt) REVERT: D 353 MET cc_start: 0.6836 (mpt) cc_final: 0.6392 (mpp) REVERT: D 396 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7621 (mpm) REVERT: D 615 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7663 (tp30) REVERT: D 622 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7967 (pt0) REVERT: D 731 PHE cc_start: 0.7275 (OUTLIER) cc_final: 0.6772 (t80) REVERT: D 779 PHE cc_start: 0.8865 (t80) cc_final: 0.8553 (t80) REVERT: D 920 ASP cc_start: 0.8408 (t0) cc_final: 0.8122 (t0) outliers start: 102 outliers final: 22 residues processed: 498 average time/residue: 1.5264 time to fit residues: 907.6562 Evaluate side-chains 372 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 336 time to evaluate : 5.035 ------------------------------------------------------------------------------- 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 516 TYR Chi-restraints excluded: chain A residue 584 THR 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 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 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 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 69 optimal weight: 6.9990 chunk 176 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 224 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 150 optimal weight: 0.9980 chunk 361 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 203 optimal weight: 5.9990 chunk 199 optimal weight: 20.0000 chunk 243 optimal weight: 0.0770 overall best weight: 1.2144 ------------------------------------------------------------------------------- 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 635 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 619 ASN C 635 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.148343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.107369 restraints weight = 61985.910| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.67 r_work: 0.3431 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31092 Z= 0.132 Angle : 0.640 8.962 42120 Z= 0.335 Chirality : 0.041 0.182 4708 Planarity : 0.004 0.063 5264 Dihedral : 4.985 29.243 4000 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.19 % Allowed : 16.41 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.13), residues: 3656 helix: 0.37 (0.10), residues: 2488 sheet: -1.20 (0.36), residues: 184 loop : -3.00 (0.16), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 453 HIS 0.003 0.001 HIS A 138 PHE 0.020 0.001 PHE D 487 TYR 0.019 0.002 TYR B 727 ARG 0.005 0.001 ARG A 288 Details of bonding type rmsd hydrogen bonds : bond 0.04263 ( 1774) hydrogen bonds : angle 4.33798 ( 5262) SS BOND : bond 0.00138 ( 4) SS BOND : angle 2.39630 ( 8) covalent geometry : bond 0.00290 (31088) covalent geometry : angle 0.63957 (42112) *********************** 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 476 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 370 time to evaluate : 5.810 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 189 MET cc_start: 0.7527 (mpp) cc_final: 0.6636 (mtt) REVERT: A 385 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7428 (mm) REVERT: A 396 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7623 (mpm) REVERT: A 615 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7669 (tp30) REVERT: A 616 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7523 (tm-30) REVERT: A 622 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7951 (pt0) REVERT: A 680 LYS cc_start: 0.8342 (mtpt) cc_final: 0.8124 (mtpp) REVERT: A 731 PHE cc_start: 0.7434 (OUTLIER) cc_final: 0.6910 (t80) REVERT: A 779 PHE cc_start: 0.8883 (t80) cc_final: 0.8573 (t80) REVERT: A 801 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7779 (ptt) REVERT: A 920 ASP cc_start: 0.8412 (t0) cc_final: 0.8116 (t0) REVERT: B 189 MET cc_start: 0.7539 (mpp) cc_final: 0.6594 (mtt) REVERT: B 385 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7427 (mm) REVERT: B 396 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7631 (mpm) REVERT: B 615 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7532 (tp30) REVERT: B 616 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7484 (tm-30) REVERT: B 622 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7986 (pt0) REVERT: B 680 LYS cc_start: 0.8338 (mtpt) cc_final: 0.8122 (mtpp) REVERT: B 731 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.6908 (t80) REVERT: B 779 PHE cc_start: 0.8883 (t80) cc_final: 0.8568 (t80) REVERT: B 801 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7780 (ptt) REVERT: B 920 ASP cc_start: 0.8425 (t0) cc_final: 0.8126 (t0) REVERT: C 189 MET cc_start: 0.7525 (mpp) cc_final: 0.6631 (mtt) REVERT: C 385 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7430 (mm) REVERT: C 396 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7628 (mpm) REVERT: C 615 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7664 (tp30) REVERT: C 622 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7959 (pt0) REVERT: C 680 LYS cc_start: 0.8340 (mtpt) cc_final: 0.8119 (mtpp) REVERT: C 731 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.6909 (t80) REVERT: C 779 PHE cc_start: 0.8885 (t80) cc_final: 0.8577 (t80) REVERT: C 801 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7765 (ptt) REVERT: C 920 ASP cc_start: 0.8415 (t0) cc_final: 0.8117 (t0) REVERT: D 189 MET cc_start: 0.7540 (mpp) cc_final: 0.6614 (mtt) REVERT: D 385 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7428 (mm) REVERT: D 396 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7637 (mpm) REVERT: D 615 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7539 (tp30) REVERT: D 616 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7482 (tm-30) REVERT: D 622 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7998 (pt0) REVERT: D 731 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.6911 (t80) REVERT: D 779 PHE cc_start: 0.8883 (t80) cc_final: 0.8574 (t80) REVERT: D 801 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7777 (ptt) REVERT: D 920 ASP cc_start: 0.8412 (t0) cc_final: 0.8094 (t0) outliers start: 106 outliers final: 28 residues processed: 453 average time/residue: 1.6197 time to fit residues: 907.3621 Evaluate side-chains 395 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 344 time to evaluate : 3.755 ------------------------------------------------------------------------------- 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 396 MET 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 801 MET 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 396 MET 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 797 LEU Chi-restraints excluded: chain B residue 801 MET 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 396 MET Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 584 THR 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 801 MET 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 396 MET 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 797 LEU Chi-restraints excluded: chain D residue 801 MET 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 141 optimal weight: 10.0000 chunk 341 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 191 optimal weight: 4.9990 chunk 276 optimal weight: 10.0000 chunk 252 optimal weight: 10.0000 chunk 335 optimal weight: 4.9990 chunk 254 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 238 optimal weight: 4.9990 chunk 336 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 619 ASN ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 ASN ** C 257 HIS ** 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 619 ASN ** D 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1101 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.145196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.103462 restraints weight = 62401.445| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.67 r_work: 0.3387 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 31092 Z= 0.205 Angle : 0.681 8.204 42120 Z= 0.358 Chirality : 0.044 0.172 4708 Planarity : 0.005 0.064 5264 Dihedral : 4.991 28.285 4000 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.88 % Allowed : 17.55 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.13), residues: 3656 helix: 0.52 (0.10), residues: 2480 sheet: -1.36 (0.36), residues: 188 loop : -3.02 (0.16), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 453 HIS 0.004 0.001 HIS A 765 PHE 0.014 0.002 PHE B1082 TYR 0.020 0.002 TYR A 787 ARG 0.008 0.001 ARG D 507 Details of bonding type rmsd hydrogen bonds : bond 0.04758 ( 1774) hydrogen bonds : angle 4.43557 ( 5262) SS BOND : bond 0.00265 ( 4) SS BOND : angle 2.71551 ( 8) covalent geometry : bond 0.00481 (31088) covalent geometry : angle 0.68034 (42112) *********************** 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 464 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 368 time to evaluate : 3.344 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: A 179 ILE cc_start: 0.8908 (mt) cc_final: 0.8548 (pt) REVERT: A 314 LYS cc_start: 0.8431 (mttt) cc_final: 0.8095 (mmmm) REVERT: A 385 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7504 (mm) REVERT: A 615 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7669 (tp30) REVERT: A 616 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7518 (tm-30) REVERT: A 622 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7955 (pt0) REVERT: A 680 LYS cc_start: 0.8416 (mtpt) cc_final: 0.8194 (mtpp) REVERT: A 731 PHE cc_start: 0.7355 (OUTLIER) cc_final: 0.6890 (t80) REVERT: A 779 PHE cc_start: 0.8922 (t80) cc_final: 0.8614 (t80) REVERT: A 920 ASP cc_start: 0.8516 (t0) cc_final: 0.8153 (t0) REVERT: B 189 MET cc_start: 0.7468 (mpp) cc_final: 0.6634 (mtt) REVERT: B 314 LYS cc_start: 0.8435 (mttt) cc_final: 0.8100 (mmmm) REVERT: B 385 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7504 (mm) REVERT: B 615 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8065 (tm-30) REVERT: B 616 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7432 (tm-30) REVERT: B 622 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7964 (pt0) REVERT: B 680 LYS cc_start: 0.8417 (mtpt) cc_final: 0.8196 (mtpp) REVERT: B 731 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.6886 (t80) REVERT: B 779 PHE cc_start: 0.8918 (t80) cc_final: 0.8613 (t80) REVERT: B 920 ASP cc_start: 0.8523 (t0) cc_final: 0.8156 (t0) REVERT: C 179 ILE cc_start: 0.8885 (mt) cc_final: 0.8522 (pt) REVERT: C 314 LYS cc_start: 0.8434 (mttt) cc_final: 0.8097 (mmmm) REVERT: C 385 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7501 (mm) REVERT: C 615 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7709 (tp30) REVERT: C 616 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7531 (tm-30) REVERT: C 622 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7969 (pt0) REVERT: C 680 LYS cc_start: 0.8419 (mtpt) cc_final: 0.8197 (mtpp) REVERT: C 731 PHE cc_start: 0.7424 (OUTLIER) cc_final: 0.6953 (t80) REVERT: C 779 PHE cc_start: 0.8925 (t80) cc_final: 0.8619 (t80) REVERT: C 920 ASP cc_start: 0.8517 (t0) cc_final: 0.8151 (t0) REVERT: D 189 MET cc_start: 0.7541 (mpp) cc_final: 0.6638 (mtt) REVERT: D 314 LYS cc_start: 0.8437 (mttt) cc_final: 0.8099 (mmmm) REVERT: D 385 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7504 (mm) REVERT: D 615 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8068 (tm-30) REVERT: D 616 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7421 (tm-30) REVERT: D 622 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7965 (pt0) REVERT: D 731 PHE cc_start: 0.7357 (OUTLIER) cc_final: 0.6894 (t80) REVERT: D 779 PHE cc_start: 0.8926 (t80) cc_final: 0.8619 (t80) REVERT: D 920 ASP cc_start: 0.8498 (t0) cc_final: 0.8132 (t0) outliers start: 96 outliers final: 36 residues processed: 439 average time/residue: 1.2172 time to fit residues: 645.4341 Evaluate side-chains 386 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 334 time to evaluate : 3.733 ------------------------------------------------------------------------------- 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 731 PHE Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 801 MET 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 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 801 MET 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 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 801 MET 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 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 801 MET Chi-restraints excluded: chain D residue 940 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 4.9990 chunk 209 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 314 optimal weight: 2.9990 chunk 328 optimal weight: 8.9990 chunk 139 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 302 optimal weight: 2.9990 chunk 243 optimal weight: 0.8980 chunk 319 optimal weight: 6.9990 chunk 90 optimal weight: 20.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 A1101 ASN ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 973 ASN B 990 ASN 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 C1101 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 973 ASN D 990 ASN D1101 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.147163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.105601 restraints weight = 62017.473| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.72 r_work: 0.3413 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31092 Z= 0.140 Angle : 0.651 8.824 42120 Z= 0.342 Chirality : 0.042 0.170 4708 Planarity : 0.005 0.082 5264 Dihedral : 4.850 27.730 4000 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.00 % Allowed : 18.75 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3656 helix: 0.68 (0.10), residues: 2480 sheet: -1.20 (0.37), residues: 188 loop : -2.95 (0.16), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 453 HIS 0.002 0.001 HIS D 257 PHE 0.028 0.001 PHE B 487 TYR 0.020 0.001 TYR B 727 ARG 0.007 0.000 ARG B 507 Details of bonding type rmsd hydrogen bonds : bond 0.04324 ( 1774) hydrogen bonds : angle 4.30194 ( 5262) SS BOND : bond 0.00151 ( 4) SS BOND : angle 2.19843 ( 8) covalent geometry : bond 0.00313 (31088) covalent geometry : angle 0.65054 (42112) *********************** 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 464 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 364 time to evaluate : 3.411 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: A 179 ILE cc_start: 0.8881 (mt) cc_final: 0.8521 (pt) REVERT: A 189 MET cc_start: 0.7898 (mpm) cc_final: 0.6730 (mmt) REVERT: A 314 LYS cc_start: 0.8415 (mttt) cc_final: 0.8077 (mmmm) REVERT: A 385 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7485 (mm) REVERT: A 479 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8358 (tp30) REVERT: A 605 LYS cc_start: 0.8481 (tppp) cc_final: 0.8039 (tppp) REVERT: A 615 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7700 (tp30) REVERT: A 616 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7524 (tm-30) REVERT: A 622 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7974 (pt0) REVERT: A 731 PHE cc_start: 0.7321 (OUTLIER) cc_final: 0.7069 (t80) REVERT: A 779 PHE cc_start: 0.8910 (t80) cc_final: 0.8610 (t80) REVERT: A 920 ASP cc_start: 0.8444 (t0) cc_final: 0.8092 (t0) REVERT: B 189 MET cc_start: 0.7311 (mpp) cc_final: 0.6582 (mtt) REVERT: B 314 LYS cc_start: 0.8440 (mttt) cc_final: 0.8114 (mmmm) REVERT: B 385 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7480 (mm) REVERT: B 605 LYS cc_start: 0.8481 (tppp) cc_final: 0.8035 (tppp) REVERT: B 615 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7693 (tp30) REVERT: B 616 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7548 (tm-30) REVERT: B 731 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.7068 (t80) REVERT: B 779 PHE cc_start: 0.8912 (t80) cc_final: 0.8615 (t80) REVERT: B 920 ASP cc_start: 0.8442 (t0) cc_final: 0.8082 (t0) REVERT: C 179 ILE cc_start: 0.8873 (mt) cc_final: 0.8514 (pt) REVERT: C 314 LYS cc_start: 0.8440 (mttt) cc_final: 0.8114 (mmmm) REVERT: C 385 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7482 (mm) REVERT: C 605 LYS cc_start: 0.8463 (tppp) cc_final: 0.8021 (tppp) REVERT: C 615 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7611 (tp30) REVERT: C 616 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7528 (tm-30) REVERT: C 622 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7977 (pt0) REVERT: C 731 PHE cc_start: 0.7330 (OUTLIER) cc_final: 0.7079 (t80) REVERT: C 779 PHE cc_start: 0.8916 (t80) cc_final: 0.8617 (t80) REVERT: C 920 ASP cc_start: 0.8435 (t0) cc_final: 0.8075 (t0) REVERT: D 314 LYS cc_start: 0.8426 (mttt) cc_final: 0.8087 (mmmm) REVERT: D 385 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7482 (mm) REVERT: D 605 LYS cc_start: 0.8476 (tppp) cc_final: 0.8032 (tppp) REVERT: D 615 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7692 (tp30) REVERT: D 616 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7536 (tm-30) REVERT: D 731 PHE cc_start: 0.7325 (OUTLIER) cc_final: 0.7075 (t80) REVERT: D 779 PHE cc_start: 0.8911 (t80) cc_final: 0.8612 (t80) REVERT: D 920 ASP cc_start: 0.8441 (t0) cc_final: 0.8091 (t0) outliers start: 100 outliers final: 40 residues processed: 429 average time/residue: 1.0969 time to fit residues: 580.0043 Evaluate side-chains 386 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 331 time to evaluate : 3.313 ------------------------------------------------------------------------------- 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 479 GLU 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 393 VAL Chi-restraints excluded: chain B residue 441 LEU 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 330 optimal weight: 0.0000 chunk 186 optimal weight: 30.0000 chunk 202 optimal weight: 9.9990 chunk 100 optimal weight: 20.0000 chunk 272 optimal weight: 0.0970 chunk 232 optimal weight: 0.9990 chunk 180 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 chunk 324 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 146 optimal weight: 10.0000 overall best weight: 3.4188 ------------------------------------------------------------------------------- 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 A1101 ASN ** B 257 HIS ** 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** C1101 ASN D1101 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.144977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.103219 restraints weight = 62608.607| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.68 r_work: 0.3376 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 31092 Z= 0.193 Angle : 0.699 9.130 42120 Z= 0.364 Chirality : 0.044 0.195 4708 Planarity : 0.005 0.066 5264 Dihedral : 4.861 23.767 4000 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.64 % Allowed : 19.83 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3656 helix: 0.66 (0.10), residues: 2476 sheet: -1.30 (0.37), residues: 192 loop : -2.92 (0.17), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 453 HIS 0.004 0.001 HIS D1080 PHE 0.018 0.001 PHE C 752 TYR 0.021 0.002 TYR C 787 ARG 0.012 0.001 ARG D1079 Details of bonding type rmsd hydrogen bonds : bond 0.04705 ( 1774) hydrogen bonds : angle 4.38960 ( 5262) SS BOND : bond 0.00315 ( 4) SS BOND : angle 2.47313 ( 8) covalent geometry : bond 0.00454 (31088) covalent geometry : angle 0.69774 (42112) *********************** 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 429 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 341 time to evaluate : 3.361 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: A 179 ILE cc_start: 0.8900 (mt) cc_final: 0.8540 (pt) REVERT: A 314 LYS cc_start: 0.8427 (mttt) cc_final: 0.8105 (mmmm) REVERT: A 385 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7582 (mm) REVERT: A 605 LYS cc_start: 0.8567 (tppp) cc_final: 0.8083 (tppp) REVERT: A 615 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7627 (tp30) REVERT: A 616 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7513 (tm-30) REVERT: A 622 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7952 (pt0) REVERT: A 731 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.7099 (t80) REVERT: A 779 PHE cc_start: 0.8916 (t80) cc_final: 0.8594 (t80) REVERT: A 808 TYR cc_start: 0.8737 (m-80) cc_final: 0.8522 (m-10) REVERT: A 920 ASP cc_start: 0.8480 (t0) cc_final: 0.8105 (t0) REVERT: B 179 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8352 (pt) REVERT: B 189 MET cc_start: 0.7368 (mpp) cc_final: 0.6661 (mtt) REVERT: B 314 LYS cc_start: 0.8433 (mttt) cc_final: 0.8109 (mmmm) REVERT: B 385 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7583 (mm) REVERT: B 605 LYS cc_start: 0.8567 (tppp) cc_final: 0.8078 (tppp) REVERT: B 615 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7704 (tp30) REVERT: B 616 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: B 731 PHE cc_start: 0.7334 (OUTLIER) cc_final: 0.7090 (t80) REVERT: B 779 PHE cc_start: 0.8921 (t80) cc_final: 0.8602 (t80) REVERT: B 920 ASP cc_start: 0.8482 (t0) cc_final: 0.8104 (t0) REVERT: C 179 ILE cc_start: 0.8906 (mt) cc_final: 0.8557 (pt) REVERT: C 189 MET cc_start: 0.7757 (mpm) cc_final: 0.6711 (mmt) REVERT: C 314 LYS cc_start: 0.8432 (mttt) cc_final: 0.8108 (mmmm) REVERT: C 385 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7581 (mm) REVERT: C 605 LYS cc_start: 0.8562 (tppp) cc_final: 0.8080 (tppp) REVERT: C 615 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7717 (tp30) REVERT: C 616 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: C 622 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7967 (pt0) REVERT: C 731 PHE cc_start: 0.7347 (OUTLIER) cc_final: 0.7102 (t80) REVERT: C 779 PHE cc_start: 0.8918 (t80) cc_final: 0.8597 (t80) REVERT: C 808 TYR cc_start: 0.8753 (m-80) cc_final: 0.8540 (m-10) REVERT: C 920 ASP cc_start: 0.8481 (t0) cc_final: 0.8104 (t0) REVERT: D 179 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8355 (pt) REVERT: D 194 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8307 (mt-10) REVERT: D 314 LYS cc_start: 0.8451 (mttt) cc_final: 0.8109 (mmmm) REVERT: D 385 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7584 (mm) REVERT: D 605 LYS cc_start: 0.8559 (tppp) cc_final: 0.8078 (tppp) REVERT: D 615 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7707 (tp30) REVERT: D 616 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7553 (tm-30) REVERT: D 731 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.7035 (t80) REVERT: D 779 PHE cc_start: 0.8909 (t80) cc_final: 0.8586 (t80) REVERT: D 808 TYR cc_start: 0.8735 (m-80) cc_final: 0.8520 (m-10) REVERT: D 920 ASP cc_start: 0.8472 (t0) cc_final: 0.8099 (t0) outliers start: 88 outliers final: 38 residues processed: 401 average time/residue: 1.0778 time to fit residues: 531.7030 Evaluate side-chains 370 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 316 time to evaluate : 3.643 ------------------------------------------------------------------------------- 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 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 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 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 B residue 985 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 333 optimal weight: 6.9990 chunk 361 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 369 optimal weight: 5.9990 chunk 338 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 218 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 167 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 ASN B 619 ASN ** B 655 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** C1101 ASN D 619 ASN D1101 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.146792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.105094 restraints weight = 62240.460| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.73 r_work: 0.3408 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31092 Z= 0.138 Angle : 0.660 9.778 42120 Z= 0.344 Chirality : 0.042 0.166 4708 Planarity : 0.004 0.065 5264 Dihedral : 4.751 25.860 4000 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.19 % Allowed : 19.89 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3656 helix: 0.80 (0.10), residues: 2476 sheet: -0.99 (0.38), residues: 188 loop : -2.83 (0.17), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 453 HIS 0.003 0.001 HIS A 257 PHE 0.028 0.001 PHE B 487 TYR 0.024 0.002 TYR C 251 ARG 0.008 0.001 ARG C 507 Details of bonding type rmsd hydrogen bonds : bond 0.04228 ( 1774) hydrogen bonds : angle 4.20436 ( 5262) SS BOND : bond 0.00186 ( 4) SS BOND : angle 1.99774 ( 8) covalent geometry : bond 0.00312 (31088) covalent geometry : angle 0.65925 (42112) *********************** 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 411 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 338 time to evaluate : 3.578 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: A 179 ILE cc_start: 0.8861 (mt) cc_final: 0.8488 (pt) REVERT: A 385 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7556 (mm) REVERT: A 444 ASP cc_start: 0.8611 (m-30) cc_final: 0.8388 (m-30) REVERT: A 605 LYS cc_start: 0.8527 (tppp) cc_final: 0.8209 (tppp) REVERT: A 615 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7640 (tp30) REVERT: A 616 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7517 (tm-30) REVERT: A 622 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7959 (pt0) REVERT: A 731 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.7103 (t80) REVERT: A 779 PHE cc_start: 0.8918 (t80) cc_final: 0.8601 (t80) REVERT: B 179 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8343 (pt) REVERT: B 189 MET cc_start: 0.7362 (mpp) cc_final: 0.6658 (mtt) REVERT: B 385 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7560 (mm) REVERT: B 444 ASP cc_start: 0.8604 (m-30) cc_final: 0.8380 (m-30) REVERT: B 605 LYS cc_start: 0.8526 (tppp) cc_final: 0.8204 (tppp) REVERT: B 615 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8047 (tm-30) REVERT: B 616 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7438 (tm-30) REVERT: B 731 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.7103 (t80) REVERT: B 779 PHE cc_start: 0.8909 (t80) cc_final: 0.8579 (t80) REVERT: C 179 ILE cc_start: 0.8870 (mt) cc_final: 0.8502 (pt) REVERT: C 385 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7555 (mm) REVERT: C 605 LYS cc_start: 0.8512 (tppp) cc_final: 0.8194 (tppp) REVERT: C 615 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7608 (tp30) REVERT: C 616 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7548 (tm-30) REVERT: C 622 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7982 (pt0) REVERT: C 731 PHE cc_start: 0.7345 (OUTLIER) cc_final: 0.7128 (t80) REVERT: C 779 PHE cc_start: 0.8922 (t80) cc_final: 0.8607 (t80) REVERT: D 179 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8348 (pt) REVERT: D 189 MET cc_start: 0.7613 (mpm) cc_final: 0.6597 (mmt) REVERT: D 385 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7540 (mm) REVERT: D 444 ASP cc_start: 0.8604 (m-30) cc_final: 0.8381 (m-30) REVERT: D 605 LYS cc_start: 0.8522 (tppp) cc_final: 0.8207 (tppp) REVERT: D 615 GLU cc_start: 0.8387 (tm-30) cc_final: 0.8061 (tm-30) REVERT: D 616 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7419 (tm-30) REVERT: D 731 PHE cc_start: 0.7335 (OUTLIER) cc_final: 0.7104 (t80) REVERT: D 779 PHE cc_start: 0.8910 (t80) cc_final: 0.8594 (t80) REVERT: D 808 TYR cc_start: 0.8705 (m-80) cc_final: 0.8486 (m-80) outliers start: 73 outliers final: 31 residues processed: 373 average time/residue: 1.1948 time to fit residues: 566.2302 Evaluate side-chains 351 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 304 time to evaluate : 3.851 ------------------------------------------------------------------------------- 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 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 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 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 616 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 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 849 VAL Chi-restraints excluded: chain C residue 940 CYS Chi-restraints excluded: chain D residue 179 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 516 TYR Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 616 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 322 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 339 optimal weight: 0.1980 chunk 205 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 106 optimal weight: 8.9990 chunk 350 optimal weight: 4.9990 chunk 231 optimal weight: 8.9990 chunk 120 optimal weight: 0.0870 chunk 3 optimal weight: 9.9990 chunk 219 optimal weight: 5.9990 overall best weight: 1.5962 ------------------------------------------------------------------------------- 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 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 ASN ** B 655 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** C1101 ASN D1101 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.147010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.105410 restraints weight = 62215.045| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.70 r_work: 0.3416 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31092 Z= 0.137 Angle : 0.661 11.489 42120 Z= 0.343 Chirality : 0.043 0.185 4708 Planarity : 0.004 0.065 5264 Dihedral : 4.675 23.584 4000 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.28 % Allowed : 21.03 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.14), residues: 3656 helix: 0.83 (0.10), residues: 2476 sheet: -0.99 (0.38), residues: 188 loop : -2.76 (0.17), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 426 HIS 0.002 0.001 HIS A 257 PHE 0.029 0.001 PHE A1082 TYR 0.027 0.001 TYR C 808 ARG 0.009 0.001 ARG B 507 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 1774) hydrogen bonds : angle 4.22107 ( 5262) SS BOND : bond 0.00180 ( 4) SS BOND : angle 1.87340 ( 8) covalent geometry : bond 0.00311 (31088) covalent geometry : angle 0.66106 (42112) *********************** 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 418 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 342 time to evaluate : 3.413 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: A 179 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8491 (pt) REVERT: A 314 LYS cc_start: 0.8459 (mttt) cc_final: 0.8140 (mmmm) REVERT: A 385 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7551 (mm) REVERT: A 444 ASP cc_start: 0.8608 (m-30) cc_final: 0.8384 (m-30) REVERT: A 605 LYS cc_start: 0.8468 (tppp) cc_final: 0.8172 (tppp) REVERT: A 615 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7578 (tp30) REVERT: A 616 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7458 (tm-30) REVERT: A 622 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7947 (pt0) REVERT: A 731 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.7055 (t80) REVERT: A 779 PHE cc_start: 0.8925 (t80) cc_final: 0.8590 (t80) REVERT: B 179 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8297 (pt) REVERT: B 189 MET cc_start: 0.7355 (mpp) cc_final: 0.6574 (mtt) REVERT: B 314 LYS cc_start: 0.8468 (mttt) cc_final: 0.8143 (mmmm) REVERT: B 385 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7505 (mm) REVERT: B 444 ASP cc_start: 0.8605 (m-30) cc_final: 0.8381 (m-30) REVERT: B 605 LYS cc_start: 0.8469 (tppp) cc_final: 0.8168 (tppp) REVERT: B 615 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7593 (tp30) REVERT: B 616 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7538 (tm-30) REVERT: B 631 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7855 (mm-30) REVERT: B 731 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.7049 (t80) REVERT: B 779 PHE cc_start: 0.8912 (t80) cc_final: 0.8581 (t80) REVERT: B 808 TYR cc_start: 0.8628 (m-10) cc_final: 0.8411 (m-10) REVERT: C 179 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8479 (pt) REVERT: C 314 LYS cc_start: 0.8470 (mttt) cc_final: 0.8151 (mmmm) REVERT: C 385 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7551 (mm) REVERT: C 605 LYS cc_start: 0.8456 (tppp) cc_final: 0.8157 (tppp) REVERT: C 615 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7634 (tp30) REVERT: C 616 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7526 (tm-30) REVERT: C 622 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7977 (pt0) REVERT: C 731 PHE cc_start: 0.7262 (OUTLIER) cc_final: 0.7038 (t80) REVERT: C 779 PHE cc_start: 0.8932 (t80) cc_final: 0.8599 (t80) REVERT: D 166 SER cc_start: 0.8951 (t) cc_final: 0.8436 (p) REVERT: D 179 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8320 (pt) REVERT: D 189 MET cc_start: 0.7674 (mpm) cc_final: 0.6599 (mmt) REVERT: D 314 LYS cc_start: 0.8465 (mttt) cc_final: 0.8147 (mmmm) REVERT: D 385 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7554 (mm) REVERT: D 444 ASP cc_start: 0.8603 (m-30) cc_final: 0.8381 (m-30) REVERT: D 605 LYS cc_start: 0.8456 (tppp) cc_final: 0.8162 (tppp) REVERT: D 615 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7597 (tp30) REVERT: D 616 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7524 (tm-30) REVERT: D 631 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7852 (mm-30) REVERT: D 731 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.7062 (t80) REVERT: D 779 PHE cc_start: 0.8913 (t80) cc_final: 0.8581 (t80) REVERT: D 808 TYR cc_start: 0.8709 (m-80) cc_final: 0.8506 (m-80) outliers start: 76 outliers final: 34 residues processed: 383 average time/residue: 1.3779 time to fit residues: 653.4201 Evaluate side-chains 375 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 323 time to evaluate : 4.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 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 645 VAL 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 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 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 616 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 179 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 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 849 VAL Chi-restraints excluded: chain C residue 940 CYS Chi-restraints excluded: chain D residue 179 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 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 Chi-restraints excluded: chain D residue 1091 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 148 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 303 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 310 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 335 optimal weight: 9.9990 chunk 351 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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** A1101 ASN B1101 ASN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN ** C 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 ASN D1101 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.145762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.104275 restraints weight = 62546.684| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.67 r_work: 0.3388 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 31092 Z= 0.185 Angle : 0.694 10.871 42120 Z= 0.362 Chirality : 0.044 0.215 4708 Planarity : 0.005 0.065 5264 Dihedral : 4.700 22.988 4000 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.95 % Allowed : 21.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3656 helix: 0.78 (0.10), residues: 2476 sheet: -1.03 (0.38), residues: 188 loop : -2.79 (0.17), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 453 HIS 0.003 0.001 HIS B 765 PHE 0.029 0.001 PHE A1082 TYR 0.026 0.002 TYR A 808 ARG 0.011 0.001 ARG B1046 Details of bonding type rmsd hydrogen bonds : bond 0.04502 ( 1774) hydrogen bonds : angle 4.31728 ( 5262) SS BOND : bond 0.00344 ( 4) SS BOND : angle 2.18227 ( 8) covalent geometry : bond 0.00439 (31088) covalent geometry : angle 0.69301 (42112) ********************** 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 397 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 332 time to evaluate : 3.631 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: A 179 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8487 (pt) REVERT: A 189 MET cc_start: 0.7588 (mpm) cc_final: 0.6584 (mmt) REVERT: A 314 LYS cc_start: 0.8446 (mttt) cc_final: 0.8131 (mmmm) REVERT: A 353 MET cc_start: 0.5753 (mpp) cc_final: 0.5512 (mpp) REVERT: A 385 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7536 (mm) REVERT: A 444 ASP cc_start: 0.8603 (m-30) cc_final: 0.8380 (m-30) REVERT: A 605 LYS cc_start: 0.8514 (tppp) cc_final: 0.8211 (tppp) REVERT: A 615 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7624 (tp30) REVERT: A 616 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7454 (tm-30) REVERT: A 731 PHE cc_start: 0.7227 (OUTLIER) cc_final: 0.7020 (t80) REVERT: A 920 ASP cc_start: 0.8476 (t0) cc_final: 0.8062 (t0) REVERT: B 179 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8309 (pt) REVERT: B 314 LYS cc_start: 0.8457 (mttt) cc_final: 0.8138 (mmmm) REVERT: B 353 MET cc_start: 0.5750 (mpp) cc_final: 0.5511 (mpp) REVERT: B 385 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7533 (mm) REVERT: B 444 ASP cc_start: 0.8622 (m-30) cc_final: 0.8398 (m-30) REVERT: B 605 LYS cc_start: 0.8515 (tppp) cc_final: 0.8209 (tppp) REVERT: B 615 GLU cc_start: 0.8357 (tm-30) cc_final: 0.7691 (tp30) REVERT: B 616 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7562 (tm-30) REVERT: B 631 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7864 (mm-30) REVERT: B 731 PHE cc_start: 0.7222 (OUTLIER) cc_final: 0.7015 (t80) REVERT: C 179 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8502 (pt) REVERT: C 314 LYS cc_start: 0.8459 (mttt) cc_final: 0.8146 (mmmm) REVERT: C 353 MET cc_start: 0.5752 (mpp) cc_final: 0.5511 (mpp) REVERT: C 385 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7533 (mm) REVERT: C 444 ASP cc_start: 0.8615 (m-30) cc_final: 0.8397 (m-30) REVERT: C 605 LYS cc_start: 0.8494 (tppp) cc_final: 0.8191 (tppp) REVERT: C 615 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7616 (tp30) REVERT: C 616 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7556 (tm-30) REVERT: C 622 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7941 (pt0) REVERT: C 631 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7872 (mm-30) REVERT: C 731 PHE cc_start: 0.7224 (OUTLIER) cc_final: 0.7002 (t80) REVERT: C 920 ASP cc_start: 0.8468 (t0) cc_final: 0.8045 (t0) REVERT: D 179 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8317 (pt) REVERT: D 314 LYS cc_start: 0.8452 (mttt) cc_final: 0.8141 (mmmm) REVERT: D 353 MET cc_start: 0.5758 (mpp) cc_final: 0.5520 (mpp) REVERT: D 385 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7537 (mm) REVERT: D 444 ASP cc_start: 0.8611 (m-30) cc_final: 0.8389 (m-30) REVERT: D 605 LYS cc_start: 0.8498 (tppp) cc_final: 0.8195 (tppp) REVERT: D 615 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7687 (tp30) REVERT: D 616 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7551 (tm-30) REVERT: D 631 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7855 (mm-30) REVERT: D 731 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.7023 (t80) REVERT: D 808 TYR cc_start: 0.8724 (m-80) cc_final: 0.8498 (m-10) REVERT: D 1078 MET cc_start: 0.5784 (OUTLIER) cc_final: 0.5494 (mpt) outliers start: 65 outliers final: 36 residues processed: 371 average time/residue: 1.0095 time to fit residues: 467.9911 Evaluate side-chains 372 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 318 time to evaluate : 5.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 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 645 VAL 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 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 516 TYR Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 616 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 B residue 1091 ASP Chi-restraints excluded: chain C residue 179 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 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 C residue 1091 ASP Chi-restraints excluded: chain D residue 179 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 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 Chi-restraints excluded: chain D residue 1078 MET Chi-restraints excluded: chain D residue 1091 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 265 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 158 optimal weight: 4.9990 chunk 144 optimal weight: 0.6980 chunk 236 optimal weight: 8.9990 chunk 175 optimal weight: 0.9990 chunk 235 optimal weight: 6.9990 chunk 336 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 A1101 ASN B1101 ASN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 ASN D1101 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.145920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.104453 restraints weight = 62066.947| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.67 r_work: 0.3396 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 31092 Z= 0.174 Angle : 0.686 12.660 42120 Z= 0.359 Chirality : 0.043 0.219 4708 Planarity : 0.005 0.092 5264 Dihedral : 4.699 24.170 4000 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.19 % Allowed : 21.97 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3656 helix: 0.81 (0.10), residues: 2476 sheet: -1.05 (0.38), residues: 188 loop : -2.77 (0.17), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP B 453 HIS 0.003 0.001 HIS D 257 PHE 0.035 0.001 PHE B1082 TYR 0.028 0.002 TYR B 646 ARG 0.009 0.001 ARG B1046 Details of bonding type rmsd hydrogen bonds : bond 0.04435 ( 1774) hydrogen bonds : angle 4.30435 ( 5262) SS BOND : bond 0.00309 ( 4) SS BOND : angle 2.09803 ( 8) covalent geometry : bond 0.00415 (31088) covalent geometry : angle 0.68522 (42112) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25051.42 seconds wall clock time: 438 minutes 20.07 seconds (26300.07 seconds total)