Starting phenix.real_space_refine on Sun Jun 29 23:44:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kt3_62556/06_2025/9kt3_62556.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kt3_62556/06_2025/9kt3_62556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kt3_62556/06_2025/9kt3_62556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kt3_62556/06_2025/9kt3_62556.map" model { file = "/net/cci-nas-00/data/ceres_data/9kt3_62556/06_2025/9kt3_62556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kt3_62556/06_2025/9kt3_62556.cif" } resolution = 3.63 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= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 159 5.16 5 C 22260 2.51 5 N 5805 2.21 5 O 6726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34950 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8502 Classifications: {'peptide': 1087} Link IDs: {'PCIS': 1, 'PTRANS': 59, 'TRANS': 1026} Chain breaks: 6 Chain: "K" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1502 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "H" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1646 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "B" Number of atoms: 8502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8502 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 60, 'TRANS': 1026} Chain breaks: 6 Chain: "J" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1502 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "G" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1646 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "L" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1502 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "I" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1646 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "C" Number of atoms: 8502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8502 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 60, 'TRANS': 1026} Chain breaks: 6 Time building chain proxies: 17.64, per 1000 atoms: 0.50 Number of scatterers: 34950 At special positions: 0 Unit cell: (170.17, 179.69, 226.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 159 16.00 O 6726 8.00 N 5805 7.00 C 22260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 104 " distance=2.03 Simple disulfide: pdb=" SG CYS K 155 " - pdb=" SG CYS K 214 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.03 Simple disulfide: pdb=" SG CYS B 132 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 104 " distance=2.03 Simple disulfide: pdb=" SG CYS J 155 " - pdb=" SG CYS J 214 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 104 " distance=2.03 Simple disulfide: pdb=" SG CYS G 155 " - pdb=" SG CYS G 211 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.03 Simple disulfide: pdb=" SG CYS L 155 " - pdb=" SG CYS L 214 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 104 " distance=2.03 Simple disulfide: pdb=" SG CYS I 155 " - pdb=" SG CYS I 211 " distance=2.03 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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: 7.43 Conformation dependent library (CDL) restraints added in 4.0 seconds 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8406 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 78 sheets defined 18.2% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.01 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.755A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.979A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.642A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.709A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 751 through 756 removed outlier: 3.501A pdb=" N LEU A 754 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 783 removed outlier: 3.507A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 837 through 841 removed outlier: 3.669A pdb=" N CYS A 840 " --> pdb=" O TYR A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.894A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 881 removed outlier: 3.730A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.065A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.029A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.876A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.889A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A1010 " --> pdb=" O THR A1006 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 99 Processing helix chain 'K' and resid 202 through 207 Processing helix chain 'H' and resid 95 through 99 removed outlier: 3.935A pdb=" N THR H 99 " --> pdb=" O ALA H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 173 No H-bonds generated for 'chain 'H' and resid 171 through 173' Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.893A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.921A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.779A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 783 removed outlier: 3.576A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.542A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 838 through 842 removed outlier: 3.931A pdb=" N GLY B 842 " --> pdb=" O ASP B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.841A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.688A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.256A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 208 removed outlier: 3.616A pdb=" N TRP J 206 " --> pdb=" O THR J 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 37 removed outlier: 3.791A pdb=" N TYR G 37 " --> pdb=" O PHE G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 72 removed outlier: 3.632A pdb=" N GLN G 72 " --> pdb=" O PRO G 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 69 through 72' Processing helix chain 'G' and resid 95 through 99 removed outlier: 3.933A pdb=" N THR G 99 " --> pdb=" O ALA G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 173 No H-bonds generated for 'chain 'G' and resid 171 through 173' Processing helix chain 'G' and resid 202 through 204 No H-bonds generated for 'chain 'G' and resid 202 through 204' Processing helix chain 'L' and resid 95 through 99 removed outlier: 4.193A pdb=" N GLU L 99 " --> pdb=" O ALA L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 148 Processing helix chain 'L' and resid 202 through 208 Processing helix chain 'I' and resid 95 through 99 removed outlier: 4.107A pdb=" N THR I 99 " --> pdb=" O ALA I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 204 removed outlier: 3.786A pdb=" N LEU I 204 " --> pdb=" O SER I 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 341 removed outlier: 3.703A pdb=" N GLU C 340 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL C 341 " --> pdb=" O PHE C 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 337 through 341' Processing helix chain 'C' and resid 365 through 370 removed outlier: 4.081A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 751 through 755 Processing helix chain 'C' and resid 756 through 783 removed outlier: 3.532A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 815 removed outlier: 3.606A pdb=" N LYS C 814 " --> pdb=" O LYS C 811 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ARG C 815 " --> pdb=" O PRO C 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 811 through 815' Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 836 through 841 Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.731A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.775A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.083A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.682A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.153A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.790A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 32 removed outlier: 3.540A pdb=" N SER A 32 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ASN A 62 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR A 269 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 94 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 52 Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 85 through 86 removed outlier: 3.703A pdb=" N ILE A 106 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY A 104 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A 168 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 143 through 144 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 removed outlier: 4.251A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N VAL A 597 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY A 593 " --> pdb=" O ARG A 319 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 314 removed outlier: 4.251A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N VAL A 597 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.535A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 542 Processing sheet with id=AB2, first strand: chain 'A' and resid 584 through 585 removed outlier: 6.829A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N PHE A 565 " --> pdb=" O PHE B 44 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.275A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 727 removed outlier: 3.601A pdb=" N THR A 716 " --> pdb=" O GLN A1071 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.651A pdb=" N ASN C 703 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'K' and resid 9 through 13 removed outlier: 3.524A pdb=" N GLY K 13 " --> pdb=" O THR K 125 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLN K 43 " --> pdb=" O LEU K 52 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LEU K 52 " --> pdb=" O GLN K 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 9 through 13 removed outlier: 3.524A pdb=" N GLY K 13 " --> pdb=" O THR K 125 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER K 106 " --> pdb=" O VAL K 117 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL K 117 " --> pdb=" O SER K 106 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 19 through 24 Processing sheet with id=AC4, first strand: chain 'K' and resid 137 through 139 removed outlier: 3.746A pdb=" N VAL K 154 " --> pdb=" O PHE K 139 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP K 159 " --> pdb=" O TYR K 193 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR K 193 " --> pdb=" O ASP K 159 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU K 181 " --> pdb=" O TYR K 198 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 174 through 176 removed outlier: 4.248A pdb=" N TRP K 169 " --> pdb=" O VAL K 176 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS K 170 " --> pdb=" O SER K 213 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.485A pdb=" N GLU H 11 " --> pdb=" O THR H 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'H' and resid 62 through 67 removed outlier: 4.929A pdb=" N ASP H 64 " --> pdb=" O TYR H 57 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR H 57 " --> pdb=" O ASP H 64 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TRP H 41 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE H 55 " --> pdb=" O ILE H 39 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE H 39 " --> pdb=" O ILE H 55 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 135 through 139 removed outlier: 6.418A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N SER H 192 " --> pdb=" O ALA H 183 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA H 183 " --> pdb=" O SER H 192 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER H 194 " --> pdb=" O PHE H 181 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 166 through 169 removed outlier: 3.709A pdb=" N LYS H 224 " --> pdb=" O CYS H 211 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL H 222 " --> pdb=" O VAL H 213 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AD3, first strand: chain 'B' and resid 50 through 56 Processing sheet with id=AD4, first strand: chain 'B' and resid 85 through 86 removed outlier: 3.857A pdb=" N GLY B 104 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL B 121 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL B 128 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE B 168 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 224 through 230 removed outlier: 6.200A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 95 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE B 194 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B 91 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 94 " --> pdb=" O TYR B 266 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 142 through 145 removed outlier: 3.990A pdb=" N TYR B 145 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLU B 154 " --> pdb=" O TYR B 145 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 317 through 320 removed outlier: 3.888A pdb=" N ASN B 317 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 326 through 328 removed outlier: 3.523A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.040A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.592A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.308A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 701 through 704 removed outlier: 7.047A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.811A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AE6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE8, first strand: chain 'J' and resid 9 through 13 removed outlier: 6.394A pdb=" N TRP J 41 " --> pdb=" O MET J 53 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 19 through 24 Processing sheet with id=AF1, first strand: chain 'J' and resid 151 through 160 removed outlier: 3.511A pdb=" N CYS J 155 " --> pdb=" O SER J 197 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER J 197 " --> pdb=" O CYS J 155 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE J 157 " --> pdb=" O ALA J 195 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP J 159 " --> pdb=" O TYR J 193 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TYR J 193 " --> pdb=" O ASP J 159 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU J 181 " --> pdb=" O TYR J 198 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 174 through 176 removed outlier: 4.286A pdb=" N TRP J 169 " --> pdb=" O VAL J 176 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS J 170 " --> pdb=" O SER J 213 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AF4, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.543A pdb=" N GLU G 11 " --> pdb=" O THR G 125 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY G 54 " --> pdb=" O TRP G 41 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ARG G 43 " --> pdb=" O TRP G 52 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N TRP G 52 " --> pdb=" O ARG G 43 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.543A pdb=" N GLU G 11 " --> pdb=" O THR G 125 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 135 through 139 removed outlier: 6.255A pdb=" N TYR G 191 " --> pdb=" O ASP G 159 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 135 through 139 removed outlier: 6.255A pdb=" N TYR G 191 " --> pdb=" O ASP G 159 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 166 through 169 removed outlier: 3.507A pdb=" N THR G 166 " --> pdb=" O ASN G 214 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 9 through 11 removed outlier: 3.589A pdb=" N LEU L 124 " --> pdb=" O ALA L 100 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA L 100 " --> pdb=" O LEU L 124 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR L 55 " --> pdb=" O VAL L 39 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N TRP L 41 " --> pdb=" O MET L 53 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 9 through 11 removed outlier: 3.589A pdb=" N LEU L 124 " --> pdb=" O ALA L 100 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA L 100 " --> pdb=" O LEU L 124 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.847A pdb=" N VAL L 19 " --> pdb=" O ILE L 91 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 135 through 139 removed outlier: 3.742A pdb=" N VAL L 154 " --> pdb=" O PHE L 139 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP L 159 " --> pdb=" O TYR L 193 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N TYR L 193 " --> pdb=" O ASP L 159 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 174 through 176 removed outlier: 4.564A pdb=" N TRP L 169 " --> pdb=" O VAL L 176 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS L 170 " --> pdb=" O SER L 213 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 3 through 6 removed outlier: 3.637A pdb=" N GLN I 3 " --> pdb=" O SER I 26 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU I 19 " --> pdb=" O TRP I 91 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 11 through 13 removed outlier: 3.535A pdb=" N VAL I 124 " --> pdb=" O ALA I 100 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA I 105 " --> pdb=" O GLY I 40 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY I 40 " --> pdb=" O ALA I 105 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE I 39 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE I 55 " --> pdb=" O ILE I 39 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TRP I 41 " --> pdb=" O MET I 53 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR I 57 " --> pdb=" O ASP I 64 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ASP I 64 " --> pdb=" O TYR I 57 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 11 through 13 removed outlier: 3.535A pdb=" N VAL I 124 " --> pdb=" O ALA I 100 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 135 through 139 removed outlier: 3.786A pdb=" N GLY I 154 " --> pdb=" O LEU I 139 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR I 191 " --> pdb=" O ASP I 159 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N SER I 192 " --> pdb=" O ALA I 183 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA I 183 " --> pdb=" O SER I 192 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER I 194 " --> pdb=" O PHE I 181 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 166 through 169 removed outlier: 3.558A pdb=" N THR I 166 " --> pdb=" O ASN I 214 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 27 through 32 removed outlier: 3.664A pdb=" N SER C 61 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ASN C 62 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TYR C 269 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR C 64 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER C 95 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.297A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL C 37 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 48 through 56 removed outlier: 3.679A pdb=" N VAL C 48 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP C 54 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG C 273 " --> pdb=" O ASP C 54 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 85 through 86 removed outlier: 4.117A pdb=" N GLY C 104 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ARG C 103 " --> pdb=" O ASN C 122 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE C 168 " --> pdb=" O VAL C 131 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 143 through 145 removed outlier: 3.531A pdb=" N ASP C 143 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU C 156 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N TYR C 145 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLU C 154 " --> pdb=" O TYR C 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'C' and resid 317 through 318 removed outlier: 3.728A pdb=" N ASN C 317 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.415A pdb=" N SER C 325 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ASN C 542 " --> pdb=" O SER C 325 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL C 327 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'C' and resid 354 through 355 removed outlier: 3.725A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA C 435 " --> pdb=" O ALA C 376 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ALA C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.672A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.033A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'C' and resid 711 through 714 Processing sheet with id=AI2, first strand: chain 'C' and resid 717 through 718 removed outlier: 3.840A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'C' and resid 721 through 728 removed outlier: 3.709A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.417A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR C 859 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AI6, first strand: chain 'C' and resid 1094 through 1097 1228 hydrogen bonds defined for protein. 3216 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: 16.04 Time building geometry restraints manager: 9.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7221 1.33 - 1.45: 8779 1.45 - 1.57: 19610 1.57 - 1.70: 0 1.70 - 1.82: 204 Bond restraints: 35814 Sorted by residual: bond pdb=" CA ASP B 420 " pdb=" C ASP B 420 " ideal model delta sigma weight residual 1.521 1.454 0.067 1.27e-02 6.20e+03 2.77e+01 bond pdb=" C ASN B 82 " pdb=" N PRO B 83 " ideal model delta sigma weight residual 1.328 1.386 -0.058 1.26e-02 6.30e+03 2.11e+01 bond pdb=" C SER B 383 " pdb=" N PRO B 384 " ideal model delta sigma weight residual 1.335 1.388 -0.054 1.19e-02 7.06e+03 2.04e+01 bond pdb=" CA GLN A1113 " pdb=" C GLN A1113 " ideal model delta sigma weight residual 1.522 1.468 0.054 1.23e-02 6.61e+03 1.91e+01 bond pdb=" C LYS A 444 " pdb=" N PRO A 445 " ideal model delta sigma weight residual 1.335 1.386 -0.051 1.28e-02 6.10e+03 1.58e+01 ... (remaining 35809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 48212 2.26 - 4.52: 508 4.52 - 6.78: 47 6.78 - 9.04: 12 9.04 - 11.31: 4 Bond angle restraints: 48783 Sorted by residual: angle pdb=" N ASP B 420 " pdb=" CA ASP B 420 " pdb=" C ASP B 420 " ideal model delta sigma weight residual 113.97 105.61 8.36 1.28e+00 6.10e-01 4.26e+01 angle pdb=" N TYR B 265 " pdb=" CA TYR B 265 " pdb=" C TYR B 265 " ideal model delta sigma weight residual 108.34 116.75 -8.41 1.31e+00 5.83e-01 4.12e+01 angle pdb=" N ARG B 246 " pdb=" CA ARG B 246 " pdb=" C ARG B 246 " ideal model delta sigma weight residual 113.97 105.98 7.99 1.28e+00 6.10e-01 3.89e+01 angle pdb=" N VAL B 736 " pdb=" CA VAL B 736 " pdb=" C VAL B 736 " ideal model delta sigma weight residual 108.46 117.75 -9.29 1.49e+00 4.50e-01 3.89e+01 angle pdb=" N HIS B 67 " pdb=" CA HIS B 67 " pdb=" C HIS B 67 " ideal model delta sigma weight residual 109.72 100.57 9.15 1.60e+00 3.91e-01 3.27e+01 ... (remaining 48778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 20604 17.41 - 34.81: 508 34.81 - 52.22: 159 52.22 - 69.63: 68 69.63 - 87.03: 6 Dihedral angle restraints: 21345 sinusoidal: 8223 harmonic: 13122 Sorted by residual: dihedral pdb=" CA GLU J 56 " pdb=" C GLU J 56 " pdb=" N VAL J 57 " pdb=" CA VAL J 57 " ideal model delta harmonic sigma weight residual -180.00 -154.81 -25.19 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA GLU L 56 " pdb=" C GLU L 56 " pdb=" N VAL L 57 " pdb=" CA VAL L 57 " ideal model delta harmonic sigma weight residual -180.00 -157.93 -22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ILE A 312 " pdb=" C ILE A 312 " pdb=" N TYR A 313 " pdb=" CA TYR A 313 " ideal model delta harmonic sigma weight residual -180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 21342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4876 0.074 - 0.147: 570 0.147 - 0.221: 27 0.221 - 0.295: 7 0.295 - 0.369: 4 Chirality restraints: 5484 Sorted by residual: chirality pdb=" CA THR B 259 " pdb=" N THR B 259 " pdb=" C THR B 259 " pdb=" CB THR B 259 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CA ASN B 82 " pdb=" N ASN B 82 " pdb=" C ASN B 82 " pdb=" CB ASN B 82 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CA SER B 47 " pdb=" N SER B 47 " pdb=" C SER B 47 " pdb=" CB SER B 47 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 5481 not shown) Planarity restraints: 6288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 755 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.67e+00 pdb=" C GLN B 755 " -0.041 2.00e-02 2.50e+03 pdb=" O GLN B 755 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR B 756 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 411 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO B 412 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 412 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 412 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 250 " 0.032 5.00e-02 4.00e+02 4.92e-02 3.88e+00 pdb=" N PRO B 251 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 251 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 251 " 0.028 5.00e-02 4.00e+02 ... (remaining 6285 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 2293 2.73 - 3.27: 35888 3.27 - 3.81: 55255 3.81 - 4.36: 68667 4.36 - 4.90: 118579 Nonbonded interactions: 280682 Sorted by model distance: nonbonded pdb=" N GLU B 97 " pdb=" OE1 GLU B 97 " model vdw 2.184 3.120 nonbonded pdb=" O PRO B 812 " pdb=" OG SER B 813 " model vdw 2.196 3.040 nonbonded pdb=" NH2 ARG J 75 " pdb=" O GLY J 93 " model vdw 2.196 3.120 nonbonded pdb=" O PRO A 812 " pdb=" OG SER A 813 " model vdw 2.207 3.040 nonbonded pdb=" OG SER A 530 " pdb=" O ASN A 542 " model vdw 2.211 3.040 ... (remaining 280677 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } 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 group one per residue 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: 14.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.160 Check model and map are aligned: 0.230 Set scattering table: 0.270 Process input model: 76.400 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.160 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 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 : 0.003 0.067 35868 Z= 0.160 Angle : 0.558 11.306 48891 Z= 0.327 Chirality : 0.045 0.369 5484 Planarity : 0.003 0.053 6288 Dihedral : 9.356 87.034 12777 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.00 % Favored : 93.87 % Rotamer: Outliers : 3.33 % Allowed : 4.10 % Favored : 92.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % 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: -3.32 (0.11), residues: 4470 helix: -1.05 (0.18), residues: 674 sheet: -1.88 (0.14), residues: 1040 loop : -2.77 (0.10), residues: 2756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 52 HIS 0.003 0.000 HIS B 50 PHE 0.020 0.001 PHE A1121 TYR 0.016 0.001 TYR B 756 ARG 0.002 0.000 ARG A 158 Details of bonding type rmsd hydrogen bonds : bond 0.24552 ( 1194) hydrogen bonds : angle 9.25526 ( 3216) SS BOND : bond 0.00343 ( 54) SS BOND : angle 0.66614 ( 108) covalent geometry : bond 0.00262 (35814) covalent geometry : angle 0.55784 (48783) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 468 time to evaluate : 3.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6164 (pmm) cc_final: 0.4953 (pmm) REVERT: A 318 PHE cc_start: 0.5814 (m-80) cc_final: 0.5491 (m-80) REVERT: A 441 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7209 (mt) REVERT: K 55 TYR cc_start: 0.8184 (p90) cc_final: 0.7482 (p90) REVERT: H 2 MET cc_start: 0.3901 (mtm) cc_final: 0.2554 (tmm) REVERT: H 132 LYS cc_start: 0.6568 (tmmt) cc_final: 0.6122 (ptpt) REVERT: H 215 HIS cc_start: 0.4219 (t70) cc_final: 0.3395 (t70) REVERT: B 80 PHE cc_start: 0.5755 (OUTLIER) cc_final: 0.5055 (m-10) REVERT: B 152 TRP cc_start: 0.7143 (m100) cc_final: 0.6637 (m100) REVERT: B 249 LEU cc_start: 0.4458 (OUTLIER) cc_final: 0.4255 (tt) REVERT: B 250 THR cc_start: -0.1656 (OUTLIER) cc_final: -0.2104 (m) REVERT: B 367 VAL cc_start: 0.8578 (m) cc_final: 0.8154 (t) REVERT: B 402 ILE cc_start: 0.0232 (OUTLIER) cc_final: 0.0025 (pp) REVERT: B 739 THR cc_start: 0.6541 (OUTLIER) cc_final: 0.5894 (t) REVERT: J 36 TYR cc_start: 0.6567 (m-80) cc_final: 0.6249 (m-80) REVERT: L 20 THR cc_start: 0.6751 (m) cc_final: 0.6422 (p) REVERT: L 53 MET cc_start: 0.4542 (OUTLIER) cc_final: 0.4247 (mmm) REVERT: L 101 ASP cc_start: 0.9019 (m-30) cc_final: 0.8296 (m-30) REVERT: C 34 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.7477 (p) REVERT: C 776 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8232 (tmmt) outliers start: 130 outliers final: 26 residues processed: 577 average time/residue: 0.5087 time to fit residues: 459.6935 Evaluate side-chains 229 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 3.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain K residue 192 LYS Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain J residue 53 MET Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain L residue 53 MET Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 377 optimal weight: 5.9990 chunk 338 optimal weight: 7.9990 chunk 187 optimal weight: 0.9990 chunk 115 optimal weight: 20.0000 chunk 228 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 350 optimal weight: 0.4980 chunk 135 optimal weight: 4.9990 chunk 213 optimal weight: 6.9990 chunk 260 optimal weight: 6.9990 chunk 405 optimal weight: 2.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN A 88 ASN A 188 ASN A 239 GLN A 282 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN A 540 ASN A 542 ASN A 607 GLN A 625 HIS ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 ASN K 95 GLN K 218 HIS H 120 GLN B 122 ASN B 394 ASN B 405 ASN B 437 ASN B 540 ASN B 564 GLN B 690 GLN B 853 GLN J 43 GLN J 218 HIS G 120 GLN ** G 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 GLN I 90 HIS I 120 GLN C 31 ASN C 211 ASN C 239 GLN C 414 GLN C 607 GLN C 690 GLN ** C 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1011 GLN C1058 HIS C1113 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.078005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.054659 restraints weight = 233052.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.055880 restraints weight = 129130.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.056256 restraints weight = 85598.137| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 35868 Z= 0.227 Angle : 0.686 9.652 48891 Z= 0.351 Chirality : 0.047 0.193 5484 Planarity : 0.005 0.072 6288 Dihedral : 5.524 59.426 4911 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.40 % Favored : 93.58 % Rotamer: Outliers : 2.31 % Allowed : 8.92 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % 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: -2.10 (0.12), residues: 4470 helix: 0.54 (0.20), residues: 662 sheet: -1.11 (0.14), residues: 1163 loop : -2.13 (0.11), residues: 2645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 258 HIS 0.013 0.002 HIS A 954 PHE 0.025 0.002 PHE G 30 TYR 0.021 0.002 TYR A 92 ARG 0.008 0.001 ARG B 509 Details of bonding type rmsd hydrogen bonds : bond 0.04587 ( 1194) hydrogen bonds : angle 6.67068 ( 3216) SS BOND : bond 0.00651 ( 54) SS BOND : angle 1.17784 ( 108) covalent geometry : bond 0.00492 (35814) covalent geometry : angle 0.68461 (48783) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 194 time to evaluate : 3.961 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 326 ILE cc_start: 0.6949 (OUTLIER) cc_final: 0.6639 (mm) REVERT: A 441 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7652 (mt) REVERT: A 869 MET cc_start: 0.8561 (mtt) cc_final: 0.8122 (ptp) REVERT: H 132 LYS cc_start: 0.8165 (tmmt) cc_final: 0.7513 (ptpt) REVERT: H 215 HIS cc_start: 0.6016 (t70) cc_final: 0.5082 (t70) REVERT: B 78 LYS cc_start: 0.4256 (OUTLIER) cc_final: 0.3029 (ttpt) REVERT: B 250 THR cc_start: 0.1163 (OUTLIER) cc_final: 0.0214 (m) REVERT: B 367 VAL cc_start: 0.8896 (m) cc_final: 0.8466 (p) REVERT: B 403 ARG cc_start: 0.4846 (ttm-80) cc_final: 0.4646 (mtm180) REVERT: B 437 ASN cc_start: 0.6229 (OUTLIER) cc_final: 0.5942 (m-40) REVERT: B 740 MET cc_start: 0.7468 (mmm) cc_final: 0.7159 (mmp) REVERT: B 741 TYR cc_start: 0.7167 (t80) cc_final: 0.6719 (t80) REVERT: B 869 MET cc_start: 0.9241 (mtt) cc_final: 0.9001 (mtt) REVERT: B 1002 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8447 (mp10) REVERT: G 101 MET cc_start: 0.9286 (tpp) cc_final: 0.8944 (tpp) REVERT: I 112 TRP cc_start: 0.7004 (p-90) cc_final: 0.6280 (p-90) REVERT: I 117 TYR cc_start: 0.6659 (t80) cc_final: 0.6401 (t80) REVERT: C 988 GLU cc_start: 0.8395 (mp0) cc_final: 0.8192 (mp0) outliers start: 90 outliers final: 51 residues processed: 268 average time/residue: 0.4761 time to fit residues: 212.6254 Evaluate side-chains 208 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 151 time to evaluate : 4.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 56 GLU Chi-restraints excluded: chain J residue 69 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 88 SER Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 91 TRP Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 235 optimal weight: 2.9990 chunk 168 optimal weight: 9.9990 chunk 328 optimal weight: 3.9990 chunk 371 optimal weight: 0.3980 chunk 116 optimal weight: 7.9990 chunk 419 optimal weight: 0.9990 chunk 392 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 231 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 418 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 677 GLN A 836 GLN A1002 GLN ** K 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 190 ASN B 50 HIS B 405 ASN B1101 HIS ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 HIS ** G 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.078288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.054749 restraints weight = 233473.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.056177 restraints weight = 130271.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.056259 restraints weight = 92910.101| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 35868 Z= 0.130 Angle : 0.584 9.740 48891 Z= 0.297 Chirality : 0.044 0.168 5484 Planarity : 0.004 0.058 6288 Dihedral : 4.711 58.273 4880 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.97 % Allowed : 9.28 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % 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: -1.48 (0.12), residues: 4470 helix: 1.24 (0.21), residues: 664 sheet: -0.73 (0.14), residues: 1167 loop : -1.76 (0.12), residues: 2639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 633 HIS 0.006 0.001 HIS G 90 PHE 0.026 0.001 PHE A 220 TYR 0.018 0.001 TYR L 55 ARG 0.011 0.000 ARG K 67 Details of bonding type rmsd hydrogen bonds : bond 0.03701 ( 1194) hydrogen bonds : angle 6.06588 ( 3216) SS BOND : bond 0.00226 ( 54) SS BOND : angle 0.75891 ( 108) covalent geometry : bond 0.00280 (35814) covalent geometry : angle 0.58387 (48783) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 164 time to evaluate : 3.607 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 318 PHE cc_start: 0.6912 (m-80) cc_final: 0.6314 (m-80) REVERT: A 326 ILE cc_start: 0.6980 (OUTLIER) cc_final: 0.6725 (mm) REVERT: A 513 LEU cc_start: 0.9519 (tp) cc_final: 0.9172 (pp) REVERT: K 53 MET cc_start: 0.6483 (ptt) cc_final: 0.5993 (ptt) REVERT: K 67 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7397 (ptm-80) REVERT: H 99 THR cc_start: 0.7881 (OUTLIER) cc_final: 0.7490 (p) REVERT: H 132 LYS cc_start: 0.7739 (tmmt) cc_final: 0.7118 (ptpt) REVERT: H 215 HIS cc_start: 0.6484 (t70) cc_final: 0.5678 (t70) REVERT: B 78 LYS cc_start: 0.4514 (OUTLIER) cc_final: 0.3435 (ttpt) REVERT: B 338 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.8750 (t80) REVERT: B 741 TYR cc_start: 0.7190 (t80) cc_final: 0.6755 (t80) REVERT: B 844 ILE cc_start: 0.7180 (OUTLIER) cc_final: 0.6541 (tt) REVERT: G 45 MET cc_start: 0.8404 (mmm) cc_final: 0.8162 (mmm) REVERT: G 53 MET cc_start: 0.8389 (mmm) cc_final: 0.8089 (mmt) REVERT: G 101 MET cc_start: 0.9312 (tpp) cc_final: 0.8987 (tpp) REVERT: I 112 TRP cc_start: 0.7163 (p-90) cc_final: 0.6421 (p-90) REVERT: C 699 LEU cc_start: 0.8553 (mt) cc_final: 0.8194 (mp) outliers start: 77 outliers final: 38 residues processed: 229 average time/residue: 0.4555 time to fit residues: 174.2278 Evaluate side-chains 192 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 3.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain K residue 55 TYR Chi-restraints excluded: chain K residue 67 ARG Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain J residue 56 GLU Chi-restraints excluded: chain J residue 69 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 333 optimal weight: 6.9990 chunk 125 optimal weight: 20.0000 chunk 252 optimal weight: 0.6980 chunk 212 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 204 optimal weight: 0.3980 chunk 384 optimal weight: 0.8980 chunk 442 optimal weight: 3.9990 chunk 224 optimal weight: 0.2980 chunk 151 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 762 GLN J 43 GLN G 72 GLN ** G 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.078108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.054670 restraints weight = 233195.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.056098 restraints weight = 131450.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.056434 restraints weight = 81904.583| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 35868 Z= 0.113 Angle : 0.566 14.428 48891 Z= 0.283 Chirality : 0.044 0.185 5484 Planarity : 0.004 0.054 6288 Dihedral : 4.517 58.083 4872 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.95 % Allowed : 10.05 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.16 (0.12), residues: 4470 helix: 1.40 (0.21), residues: 663 sheet: -0.48 (0.15), residues: 1162 loop : -1.54 (0.12), residues: 2645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 258 HIS 0.004 0.001 HIS G 90 PHE 0.019 0.001 PHE A 220 TYR 0.019 0.001 TYR A 707 ARG 0.011 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.03371 ( 1194) hydrogen bonds : angle 5.73431 ( 3216) SS BOND : bond 0.00214 ( 54) SS BOND : angle 0.66604 ( 108) covalent geometry : bond 0.00248 (35814) covalent geometry : angle 0.56625 (48783) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 159 time to evaluate : 4.310 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 318 PHE cc_start: 0.6874 (m-80) cc_final: 0.6373 (m-80) REVERT: A 326 ILE cc_start: 0.6713 (OUTLIER) cc_final: 0.6347 (mm) REVERT: A 513 LEU cc_start: 0.9472 (tp) cc_final: 0.9118 (pp) REVERT: H 2 MET cc_start: 0.4252 (mtt) cc_final: 0.2812 (tmm) REVERT: H 132 LYS cc_start: 0.7768 (tmmt) cc_final: 0.7277 (ptmt) REVERT: H 215 HIS cc_start: 0.6713 (t70) cc_final: 0.6065 (t70) REVERT: B 338 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8729 (t80) REVERT: B 741 TYR cc_start: 0.7624 (t80) cc_final: 0.7254 (t80) REVERT: B 844 ILE cc_start: 0.7110 (OUTLIER) cc_final: 0.6367 (tt) REVERT: B 912 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8525 (p) REVERT: G 53 MET cc_start: 0.8550 (mmm) cc_final: 0.8329 (mmt) REVERT: G 101 MET cc_start: 0.9343 (tpp) cc_final: 0.9055 (tpp) REVERT: C 699 LEU cc_start: 0.8550 (mt) cc_final: 0.8272 (mp) outliers start: 76 outliers final: 50 residues processed: 221 average time/residue: 0.4730 time to fit residues: 176.5209 Evaluate side-chains 194 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 140 time to evaluate : 3.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain K residue 67 ARG Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain J residue 56 GLU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 91 TRP Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 747 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 352 optimal weight: 0.0370 chunk 374 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 337 optimal weight: 10.0000 chunk 320 optimal weight: 3.9990 chunk 319 optimal weight: 6.9990 chunk 198 optimal weight: 0.6980 chunk 285 optimal weight: 5.9990 chunk 405 optimal weight: 2.9990 chunk 223 optimal weight: 0.7980 chunk 407 optimal weight: 0.0870 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN A1036 GLN ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN B 901 GLN J 85 ASN ** G 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 955 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.078121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.054844 restraints weight = 232479.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.056174 restraints weight = 130228.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.056160 restraints weight = 90136.685| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 35868 Z= 0.102 Angle : 0.550 15.006 48891 Z= 0.275 Chirality : 0.043 0.193 5484 Planarity : 0.004 0.052 6288 Dihedral : 4.409 57.009 4871 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.05 % Allowed : 10.21 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.97 (0.13), residues: 4470 helix: 1.46 (0.21), residues: 663 sheet: -0.25 (0.15), residues: 1167 loop : -1.44 (0.12), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 633 HIS 0.003 0.000 HIS G 90 PHE 0.023 0.001 PHE A 927 TYR 0.019 0.001 TYR A 707 ARG 0.005 0.000 ARG C1107 Details of bonding type rmsd hydrogen bonds : bond 0.03205 ( 1194) hydrogen bonds : angle 5.51953 ( 3216) SS BOND : bond 0.00171 ( 54) SS BOND : angle 0.65258 ( 108) covalent geometry : bond 0.00221 (35814) covalent geometry : angle 0.54991 (48783) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 160 time to evaluate : 3.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.6706 (m-80) cc_final: 0.6338 (m-80) REVERT: A 326 ILE cc_start: 0.6870 (OUTLIER) cc_final: 0.6554 (mm) REVERT: A 513 LEU cc_start: 0.9492 (tp) cc_final: 0.9189 (pp) REVERT: H 2 MET cc_start: 0.4304 (mtt) cc_final: 0.2863 (tmm) REVERT: H 53 MET cc_start: 0.6149 (mpp) cc_final: 0.5223 (mpp) REVERT: H 132 LYS cc_start: 0.7782 (tmmt) cc_final: 0.7357 (ptmt) REVERT: H 215 HIS cc_start: 0.6770 (t70) cc_final: 0.6241 (t70) REVERT: B 741 TYR cc_start: 0.7409 (t80) cc_final: 0.7144 (t80) REVERT: B 844 ILE cc_start: 0.7069 (OUTLIER) cc_final: 0.6316 (tt) REVERT: B 912 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8486 (p) REVERT: B 1002 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8487 (pm20) REVERT: G 45 MET cc_start: 0.8681 (mmm) cc_final: 0.8294 (mmm) REVERT: G 53 MET cc_start: 0.8398 (mmm) cc_final: 0.8026 (mmt) REVERT: L 116 VAL cc_start: 0.7141 (OUTLIER) cc_final: 0.6847 (m) REVERT: C 699 LEU cc_start: 0.8547 (mt) cc_final: 0.8261 (mp) outliers start: 80 outliers final: 53 residues processed: 226 average time/residue: 0.4557 time to fit residues: 176.5900 Evaluate side-chains 201 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 143 time to evaluate : 3.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain K residue 67 ARG Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain J residue 69 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 869 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 230 optimal weight: 0.8980 chunk 318 optimal weight: 3.9990 chunk 325 optimal weight: 0.9990 chunk 197 optimal weight: 0.2980 chunk 8 optimal weight: 4.9990 chunk 39 optimal weight: 20.0000 chunk 349 optimal weight: 7.9990 chunk 45 optimal weight: 0.5980 chunk 436 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 262 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1036 GLN ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 HIS B 677 GLN B 762 GLN B 901 GLN ** G 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.076829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.053354 restraints weight = 234336.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.054495 restraints weight = 132620.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.054812 restraints weight = 95331.455| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 35868 Z= 0.147 Angle : 0.565 13.024 48891 Z= 0.287 Chirality : 0.043 0.181 5484 Planarity : 0.004 0.049 6288 Dihedral : 4.454 57.834 4867 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.03 % Allowed : 10.79 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % 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: -0.94 (0.13), residues: 4470 helix: 1.28 (0.21), residues: 683 sheet: -0.24 (0.15), residues: 1166 loop : -1.36 (0.12), residues: 2621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 633 HIS 0.005 0.001 HIS C 339 PHE 0.029 0.001 PHE B 371 TYR 0.019 0.001 TYR A 707 ARG 0.013 0.000 ARG A 79 Details of bonding type rmsd hydrogen bonds : bond 0.03295 ( 1194) hydrogen bonds : angle 5.50828 ( 3216) SS BOND : bond 0.00179 ( 54) SS BOND : angle 0.65563 ( 108) covalent geometry : bond 0.00319 (35814) covalent geometry : angle 0.56523 (48783) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 141 time to evaluate : 8.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 513 LEU cc_start: 0.9403 (tp) cc_final: 0.9041 (pp) REVERT: A 515 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.7889 (p90) REVERT: K 123 MET cc_start: 0.8686 (ptp) cc_final: 0.8474 (tpt) REVERT: H 2 MET cc_start: 0.4062 (mtt) cc_final: 0.2498 (tmm) REVERT: H 53 MET cc_start: 0.5915 (mpp) cc_final: 0.4882 (mpp) REVERT: H 132 LYS cc_start: 0.7807 (tmmt) cc_final: 0.7375 (ptmt) REVERT: H 215 HIS cc_start: 0.6776 (t70) cc_final: 0.6141 (t70) REVERT: B 741 TYR cc_start: 0.7411 (t80) cc_final: 0.7057 (t80) REVERT: B 844 ILE cc_start: 0.7140 (OUTLIER) cc_final: 0.6344 (tt) REVERT: B 1002 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8493 (pm20) REVERT: G 45 MET cc_start: 0.8539 (mmm) cc_final: 0.8282 (mmm) REVERT: G 53 MET cc_start: 0.8424 (mmm) cc_final: 0.8155 (tpp) REVERT: G 76 VAL cc_start: 0.9026 (OUTLIER) cc_final: 0.8821 (t) REVERT: L 116 VAL cc_start: 0.7086 (OUTLIER) cc_final: 0.6881 (m) REVERT: I 112 TRP cc_start: 0.7344 (p-90) cc_final: 0.6742 (p-90) outliers start: 79 outliers final: 56 residues processed: 205 average time/residue: 0.4716 time to fit residues: 168.2321 Evaluate side-chains 194 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 133 time to evaluate : 3.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain K residue 67 ARG Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain J residue 69 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 91 TRP Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 869 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 281 optimal weight: 0.9990 chunk 309 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 393 optimal weight: 0.9980 chunk 238 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 200 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 362 optimal weight: 0.5980 chunk 109 optimal weight: 30.0000 chunk 47 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN A1036 GLN ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.075489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.052010 restraints weight = 235974.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.053211 restraints weight = 132955.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.053502 restraints weight = 85516.931| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 35868 Z= 0.178 Angle : 0.596 13.912 48891 Z= 0.301 Chirality : 0.044 0.250 5484 Planarity : 0.004 0.053 6288 Dihedral : 4.664 59.220 4867 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.47 % Favored : 93.51 % Rotamer: Outliers : 2.00 % Allowed : 11.28 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.96 (0.13), residues: 4470 helix: 1.17 (0.21), residues: 682 sheet: -0.25 (0.15), residues: 1144 loop : -1.35 (0.12), residues: 2644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 633 HIS 0.006 0.001 HIS C 339 PHE 0.027 0.001 PHE B 371 TYR 0.020 0.001 TYR L 55 ARG 0.004 0.001 ARG B 847 Details of bonding type rmsd hydrogen bonds : bond 0.03415 ( 1194) hydrogen bonds : angle 5.57835 ( 3216) SS BOND : bond 0.00234 ( 54) SS BOND : angle 0.74206 ( 108) covalent geometry : bond 0.00387 (35814) covalent geometry : angle 0.59581 (48783) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 137 time to evaluate : 3.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 THR cc_start: 0.7908 (OUTLIER) cc_final: 0.7610 (p) REVERT: A 513 LEU cc_start: 0.9468 (tp) cc_final: 0.9121 (pp) REVERT: H 53 MET cc_start: 0.5846 (mpp) cc_final: 0.4711 (mpp) REVERT: H 132 LYS cc_start: 0.7953 (tmmt) cc_final: 0.7531 (ptpt) REVERT: H 215 HIS cc_start: 0.6974 (t70) cc_final: 0.6477 (t70) REVERT: B 326 ILE cc_start: 0.9443 (OUTLIER) cc_final: 0.9232 (pt) REVERT: B 741 TYR cc_start: 0.7379 (t80) cc_final: 0.7013 (t80) REVERT: B 844 ILE cc_start: 0.7178 (OUTLIER) cc_final: 0.6323 (tt) REVERT: G 45 MET cc_start: 0.8609 (mmm) cc_final: 0.8388 (mmm) REVERT: G 53 MET cc_start: 0.8544 (mmm) cc_final: 0.8238 (tpp) REVERT: L 116 VAL cc_start: 0.7299 (OUTLIER) cc_final: 0.7072 (m) REVERT: L 145 GLU cc_start: 0.1310 (pt0) cc_final: 0.0531 (tt0) outliers start: 78 outliers final: 56 residues processed: 201 average time/residue: 0.4322 time to fit residues: 148.5623 Evaluate side-chains 187 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 127 time to evaluate : 3.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain K residue 53 MET Chi-restraints excluded: chain K residue 67 ARG Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain J residue 69 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 91 TRP Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 241 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 353 optimal weight: 0.9980 chunk 188 optimal weight: 0.9980 chunk 220 optimal weight: 0.6980 chunk 375 optimal weight: 0.0970 chunk 289 optimal weight: 0.0000 chunk 202 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 286 optimal weight: 9.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 GLN H 75 GLN G 186 GLN ** G 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.076621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.053248 restraints weight = 233032.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.054612 restraints weight = 131912.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.054982 restraints weight = 81007.063| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 35868 Z= 0.102 Angle : 0.568 20.555 48891 Z= 0.283 Chirality : 0.043 0.240 5484 Planarity : 0.004 0.047 6288 Dihedral : 4.408 57.582 4863 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.56 % Allowed : 12.08 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 4470 helix: 1.33 (0.21), residues: 684 sheet: -0.12 (0.15), residues: 1154 loop : -1.25 (0.12), residues: 2632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 633 HIS 0.002 0.000 HIS B1048 PHE 0.026 0.001 PHE B 371 TYR 0.029 0.001 TYR J 55 ARG 0.005 0.000 ARG H 43 Details of bonding type rmsd hydrogen bonds : bond 0.03185 ( 1194) hydrogen bonds : angle 5.32887 ( 3216) SS BOND : bond 0.00166 ( 54) SS BOND : angle 0.67072 ( 108) covalent geometry : bond 0.00223 (35814) covalent geometry : angle 0.56816 (48783) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 139 time to evaluate : 6.380 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: A 318 PHE cc_start: 0.6910 (m-80) cc_final: 0.6385 (m-80) REVERT: A 333 THR cc_start: 0.7750 (OUTLIER) cc_final: 0.7447 (p) REVERT: A 513 LEU cc_start: 0.9462 (tp) cc_final: 0.9121 (pp) REVERT: A 670 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7848 (mt) REVERT: H 132 LYS cc_start: 0.7927 (tmmt) cc_final: 0.7531 (ptpt) REVERT: H 215 HIS cc_start: 0.6915 (t70) cc_final: 0.6368 (t70) REVERT: B 317 ASN cc_start: 0.8122 (p0) cc_final: 0.7335 (p0) REVERT: B 326 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9208 (pt) REVERT: B 844 ILE cc_start: 0.7148 (OUTLIER) cc_final: 0.6263 (tt) REVERT: B 1002 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8480 (pm20) REVERT: J 101 ASP cc_start: 0.8952 (t0) cc_final: 0.8472 (t0) REVERT: G 53 MET cc_start: 0.8433 (mmm) cc_final: 0.8159 (tpp) REVERT: L 116 VAL cc_start: 0.7267 (OUTLIER) cc_final: 0.6997 (m) REVERT: C 869 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.8027 (mtm) outliers start: 61 outliers final: 41 residues processed: 188 average time/residue: 0.5753 time to fit residues: 186.1632 Evaluate side-chains 176 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 128 time to evaluate : 3.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain K residue 67 ARG Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain J residue 69 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 91 TRP Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 869 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 136 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 350 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 115 optimal weight: 20.0000 chunk 232 optimal weight: 0.9990 chunk 230 optimal weight: 1.9990 chunk 245 optimal weight: 2.9990 chunk 128 optimal weight: 30.0000 chunk 166 optimal weight: 0.0870 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.075918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.052447 restraints weight = 232622.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.053809 restraints weight = 130984.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.054153 restraints weight = 85383.592| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 35868 Z= 0.131 Angle : 0.585 20.546 48891 Z= 0.291 Chirality : 0.043 0.187 5484 Planarity : 0.004 0.045 6288 Dihedral : 4.365 57.535 4859 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 1.46 % Allowed : 12.28 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.80 (0.13), residues: 4470 helix: 1.23 (0.21), residues: 694 sheet: -0.16 (0.15), residues: 1168 loop : -1.23 (0.12), residues: 2608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 633 HIS 0.004 0.001 HIS C 339 PHE 0.026 0.001 PHE B 371 TYR 0.026 0.001 TYR J 55 ARG 0.008 0.000 ARG G 43 Details of bonding type rmsd hydrogen bonds : bond 0.03211 ( 1194) hydrogen bonds : angle 5.33843 ( 3216) SS BOND : bond 0.00157 ( 54) SS BOND : angle 0.65109 ( 108) covalent geometry : bond 0.00290 (35814) covalent geometry : angle 0.58487 (48783) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 131 time to evaluate : 3.904 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: A 333 THR cc_start: 0.7785 (OUTLIER) cc_final: 0.7487 (p) REVERT: A 513 LEU cc_start: 0.9462 (tp) cc_final: 0.9121 (pp) REVERT: A 670 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7939 (mt) REVERT: H 53 MET cc_start: 0.6489 (mpp) cc_final: 0.5641 (mpp) REVERT: H 132 LYS cc_start: 0.7935 (tmmt) cc_final: 0.7603 (ptpt) REVERT: H 215 HIS cc_start: 0.6960 (t70) cc_final: 0.6486 (t70) REVERT: B 1002 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8515 (pm20) REVERT: J 101 ASP cc_start: 0.8913 (t0) cc_final: 0.8453 (t0) REVERT: G 53 MET cc_start: 0.8475 (mmm) cc_final: 0.8007 (mmm) REVERT: G 159 ASP cc_start: 0.8145 (t0) cc_final: 0.7703 (p0) REVERT: L 116 VAL cc_start: 0.7258 (OUTLIER) cc_final: 0.7023 (m) REVERT: C 869 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.8094 (mtm) outliers start: 57 outliers final: 39 residues processed: 177 average time/residue: 0.4462 time to fit residues: 137.2924 Evaluate side-chains 168 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 124 time to evaluate : 3.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain K residue 67 ARG Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain J residue 69 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 869 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 76 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 198 optimal weight: 0.7980 chunk 159 optimal weight: 7.9990 chunk 390 optimal weight: 0.4980 chunk 379 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 442 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 256 optimal weight: 0.2980 chunk 184 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** G 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.075907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.052434 restraints weight = 231208.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.053602 restraints weight = 131419.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.054087 restraints weight = 80907.897| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35868 Z= 0.126 Angle : 0.585 20.339 48891 Z= 0.290 Chirality : 0.043 0.230 5484 Planarity : 0.004 0.046 6288 Dihedral : 4.353 57.280 4859 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.26 % Allowed : 12.54 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.76 (0.13), residues: 4470 helix: 1.24 (0.21), residues: 694 sheet: -0.12 (0.15), residues: 1145 loop : -1.19 (0.12), residues: 2631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP I 91 HIS 0.003 0.001 HIS C 339 PHE 0.025 0.001 PHE B 371 TYR 0.024 0.001 TYR J 55 ARG 0.004 0.000 ARG C 905 Details of bonding type rmsd hydrogen bonds : bond 0.03180 ( 1194) hydrogen bonds : angle 5.29044 ( 3216) SS BOND : bond 0.00159 ( 54) SS BOND : angle 0.64189 ( 108) covalent geometry : bond 0.00278 (35814) covalent geometry : angle 0.58512 (48783) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 130 time to evaluate : 8.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 THR cc_start: 0.7815 (OUTLIER) cc_final: 0.7520 (p) REVERT: A 513 LEU cc_start: 0.9472 (tp) cc_final: 0.9132 (pp) REVERT: A 670 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7907 (mt) REVERT: H 53 MET cc_start: 0.6283 (mpp) cc_final: 0.5445 (mpp) REVERT: H 132 LYS cc_start: 0.7769 (tmmt) cc_final: 0.7407 (ptpt) REVERT: H 215 HIS cc_start: 0.7063 (t70) cc_final: 0.6613 (t70) REVERT: J 101 ASP cc_start: 0.8944 (t0) cc_final: 0.8481 (t0) REVERT: G 53 MET cc_start: 0.8513 (mmm) cc_final: 0.8007 (mmm) REVERT: G 159 ASP cc_start: 0.8133 (t0) cc_final: 0.7703 (p0) REVERT: L 116 VAL cc_start: 0.7278 (OUTLIER) cc_final: 0.7049 (m) REVERT: C 869 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.8081 (mtm) outliers start: 49 outliers final: 37 residues processed: 170 average time/residue: 0.5356 time to fit residues: 157.4150 Evaluate side-chains 169 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 128 time to evaluate : 6.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain J residue 69 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 869 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 329 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 229 optimal weight: 0.0670 chunk 23 optimal weight: 0.7980 chunk 119 optimal weight: 0.3980 chunk 83 optimal weight: 0.8980 chunk 302 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 37 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 chunk 228 optimal weight: 0.5980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 334 ASN ** K 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 ASN J 95 GLN ** G 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.076506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.052925 restraints weight = 231183.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.054506 restraints weight = 126513.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.054745 restraints weight = 79139.248| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 35868 Z= 0.099 Angle : 0.573 20.292 48891 Z= 0.282 Chirality : 0.043 0.191 5484 Planarity : 0.004 0.047 6288 Dihedral : 4.248 55.788 4859 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.10 % Allowed : 12.64 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.64 (0.13), residues: 4470 helix: 1.36 (0.21), residues: 691 sheet: -0.03 (0.15), residues: 1152 loop : -1.13 (0.12), residues: 2627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP I 91 HIS 0.006 0.001 HIS I 179 PHE 0.024 0.001 PHE B 371 TYR 0.022 0.001 TYR J 55 ARG 0.004 0.000 ARG K 67 Details of bonding type rmsd hydrogen bonds : bond 0.03073 ( 1194) hydrogen bonds : angle 5.15349 ( 3216) SS BOND : bond 0.00159 ( 54) SS BOND : angle 0.64725 ( 108) covalent geometry : bond 0.00217 (35814) covalent geometry : angle 0.57331 (48783) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14339.94 seconds wall clock time: 253 minutes 24.33 seconds (15204.33 seconds total)