Starting phenix.real_space_refine on Tue Aug 26 08:23:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kt3_62556/08_2025/9kt3_62556.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kt3_62556/08_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_62556/08_2025/9kt3_62556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kt3_62556/08_2025/9kt3_62556.map" model { file = "/net/cci-nas-00/data/ceres_data/9kt3_62556/08_2025/9kt3_62556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kt3_62556/08_2025/9kt3_62556.cif" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.037 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 6.55, per 1000 atoms: 0.19 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: 2.05 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.17 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: 7.69 Time building geometry restraints manager: 3.01 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: 0.03 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: 18.880 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: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 27.280 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.700 ------------------------------------------------------------------------------- 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 : 5.71 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 158 TYR 0.016 0.001 TYR B 756 PHE 0.020 0.001 PHE A1121 TRP 0.007 0.001 TRP G 52 HIS 0.003 0.000 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00262 (35814) covalent geometry : angle 0.55784 (48783) SS BOND : bond 0.00343 ( 54) SS BOND : angle 0.66614 ( 108) hydrogen bonds : bond 0.24552 ( 1194) hydrogen bonds : angle 9.25526 ( 3216) *********************** 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 : 1.016 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: 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: 0.5487 (m-80) REVERT: A 441 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7210 (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: 0.6121 (ptpt) REVERT: H 215 HIS cc_start: 0.4219 (t70) cc_final: 0.3395 (t70) REVERT: B 152 TRP cc_start: 0.7143 (m100) cc_final: 0.6638 (m100) REVERT: B 250 THR cc_start: -0.1656 (OUTLIER) cc_final: -0.2079 (m) REVERT: B 367 VAL cc_start: 0.8578 (m) cc_final: 0.8151 (t) REVERT: B 402 ILE cc_start: 0.0232 (OUTLIER) cc_final: 0.0015 (pp) REVERT: B 739 THR cc_start: 0.6541 (OUTLIER) cc_final: 0.5895 (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: 0.6423 (p) REVERT: L 53 MET cc_start: 0.4542 (OUTLIER) cc_final: 0.4249 (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: 0.7346 (p) REVERT: C 776 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8231 (tmmt) outliers start: 130 outliers final: 26 residues processed: 577 average time/residue: 0.1978 time to fit residues: 179.5954 Evaluate side-chains 227 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 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 109 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 258 TRP 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 432 optimal weight: 0.9980 chunk 197 optimal weight: 0.0470 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 1.9990 chunk 424 optimal weight: 0.1980 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN A 239 GLN A 282 ASN A 314 GLN A 540 ASN A 542 ASN A 607 GLN A 836 GLN ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 95 GLN K 218 HIS H 120 GLN B 50 HIS B 122 ASN B 394 ASN B 405 ASN B 690 GLN J 43 GLN ** G 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 GLN I 120 GLN C 31 ASN C 211 ASN C 239 GLN C 414 GLN C 607 GLN C 690 GLN C 955 ASN C 957 GLN C1011 GLN C1113 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.080127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.056303 restraints weight = 233617.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.057864 restraints weight = 128461.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.057917 restraints weight = 96060.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.058593 restraints weight = 67710.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.058810 restraints weight = 54538.475| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35868 Z= 0.146 Angle : 0.652 11.539 48891 Z= 0.331 Chirality : 0.046 0.204 5484 Planarity : 0.005 0.090 6288 Dihedral : 5.185 57.686 4907 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.91 % Favored : 94.05 % Rotamer: Outliers : 2.08 % Allowed : 8.77 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.05 (0.12), residues: 4470 helix: 0.64 (0.20), residues: 664 sheet: -1.08 (0.14), residues: 1155 loop : -2.11 (0.11), residues: 2651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 509 TYR 0.023 0.001 TYR I 117 PHE 0.032 0.002 PHE B 56 TRP 0.020 0.001 TRP C 633 HIS 0.013 0.001 HIS G 90 Details of bonding type rmsd covalent geometry : bond 0.00318 (35814) covalent geometry : angle 0.65161 (48783) SS BOND : bond 0.00259 ( 54) SS BOND : angle 0.94130 ( 108) hydrogen bonds : bond 0.04301 ( 1194) hydrogen bonds : angle 6.58628 ( 3216) *********************** 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 294 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 213 time to evaluate : 1.130 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: 0.6822 (m-80) cc_final: 0.6425 (m-80) REVERT: A 326 ILE cc_start: 0.6697 (OUTLIER) cc_final: 0.6345 (mm) REVERT: A 441 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7703 (mt) REVERT: A 869 MET cc_start: 0.8377 (mtt) cc_final: 0.8161 (ptp) REVERT: H 2 MET cc_start: 0.4197 (mtm) cc_final: 0.2925 (tmm) REVERT: H 132 LYS cc_start: 0.8201 (tmmt) cc_final: 0.7626 (ptpt) REVERT: H 215 HIS cc_start: 0.6200 (t70) cc_final: 0.5497 (t70) REVERT: B 170 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7792 (m-80) REVERT: B 740 MET cc_start: 0.7155 (mmm) cc_final: 0.6867 (mmp) REVERT: B 741 TYR cc_start: 0.6602 (t80) cc_final: 0.6342 (t80) REVERT: B 844 ILE cc_start: 0.6937 (OUTLIER) cc_final: 0.6392 (tt) REVERT: G 101 MET cc_start: 0.9325 (tpp) cc_final: 0.9016 (tpp) REVERT: I 112 TRP cc_start: 0.7174 (p-90) cc_final: 0.6571 (p-90) REVERT: I 117 TYR cc_start: 0.6601 (t80) cc_final: 0.6270 (t80) REVERT: C 988 GLU cc_start: 0.8291 (mp0) cc_final: 0.8085 (mp0) outliers start: 81 outliers final: 37 residues processed: 277 average time/residue: 0.1927 time to fit residues: 86.7074 Evaluate side-chains 198 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 1.321 ------------------------------------------------------------------------------- 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 249 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 858 LEU 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 170 TYR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 1032 CYS 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 G residue 19 LEU Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 90 HIS 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 328 ARG Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 503 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 133 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 41 optimal weight: 0.0970 chunk 202 optimal weight: 1.9990 chunk 137 optimal weight: 30.0000 chunk 339 optimal weight: 6.9990 chunk 88 optimal weight: 0.1980 chunk 373 optimal weight: 0.7980 chunk 220 optimal weight: 0.8980 chunk 136 optimal weight: 6.9990 chunk 221 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 188 ASN A 354 ASN A 625 HIS ** K 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 ASN B 405 ASN B 836 GLN B1101 HIS ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 HIS J 218 HIS ** G 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 HIS ** C 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.079170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.055767 restraints weight = 233890.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.057161 restraints weight = 129082.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.057675 restraints weight = 78863.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.057808 restraints weight = 59070.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.057981 restraints weight = 50156.167| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2891 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= 0.129 Angle : 0.593 13.489 48891 Z= 0.299 Chirality : 0.044 0.162 5484 Planarity : 0.005 0.072 6288 Dihedral : 4.469 55.135 4874 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.85 % Allowed : 9.44 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.12), residues: 4470 helix: 1.26 (0.21), residues: 658 sheet: -0.68 (0.14), residues: 1157 loop : -1.84 (0.11), residues: 2655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 67 TYR 0.020 0.001 TYR L 55 PHE 0.023 0.001 PHE B 318 TRP 0.023 0.001 TRP C 633 HIS 0.008 0.001 HIS G 90 Details of bonding type rmsd covalent geometry : bond 0.00286 (35814) covalent geometry : angle 0.59136 (48783) SS BOND : bond 0.00310 ( 54) SS BOND : angle 1.04203 ( 108) hydrogen bonds : bond 0.03750 ( 1194) hydrogen bonds : angle 6.09275 ( 3216) *********************** 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 243 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 171 time to evaluate : 1.079 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: A 154 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7298 (pm20) REVERT: A 318 PHE cc_start: 0.6720 (m-80) cc_final: 0.6152 (m-80) REVERT: A 326 ILE cc_start: 0.6651 (OUTLIER) cc_final: 0.6312 (mm) REVERT: H 2 MET cc_start: 0.3794 (mtm) cc_final: 0.2445 (tmm) REVERT: H 132 LYS cc_start: 0.7902 (tmmt) cc_final: 0.7398 (ptmt) REVERT: H 215 HIS cc_start: 0.6641 (t70) cc_final: 0.6027 (t70) REVERT: B 78 LYS cc_start: 0.3839 (OUTLIER) cc_final: 0.2388 (ttpt) REVERT: B 740 MET cc_start: 0.7523 (mmm) cc_final: 0.6892 (mmp) REVERT: B 741 TYR cc_start: 0.7109 (t80) cc_final: 0.6654 (t80) REVERT: B 844 ILE cc_start: 0.6961 (OUTLIER) cc_final: 0.6377 (tt) REVERT: G 45 MET cc_start: 0.8419 (mmm) cc_final: 0.8204 (mmm) REVERT: G 101 MET cc_start: 0.9301 (tpp) cc_final: 0.9083 (tpp) REVERT: C 869 MET cc_start: 0.7905 (mtm) cc_final: 0.7567 (mtm) outliers start: 72 outliers final: 41 residues processed: 229 average time/residue: 0.1794 time to fit residues: 69.3893 Evaluate side-chains 195 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 150 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 154 GLU 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 334 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 572 THR 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 1116 THR Chi-restraints excluded: chain K residue 67 ARG 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 64 THR Chi-restraints excluded: chain B residue 78 LYS 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 481 ASN Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 844 ILE 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 132 LYS Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain I residue 81 ASP 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 477 ASN Chi-restraints excluded: chain C residue 481 ASN 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 7 optimal weight: 5.9990 chunk 393 optimal weight: 5.9990 chunk 279 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 chunk 125 optimal weight: 30.0000 chunk 195 optimal weight: 4.9990 chunk 371 optimal weight: 0.8980 chunk 357 optimal weight: 1.9990 chunk 331 optimal weight: 30.0000 chunk 162 optimal weight: 0.4980 chunk 283 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN A1002 GLN A1011 GLN ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 HIS B 207 HIS B 540 ASN B 564 GLN J 43 GLN G 72 GLN ** G 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C1058 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.077383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.053904 restraints weight = 233184.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.055124 restraints weight = 132164.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.055654 restraints weight = 81431.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.055730 restraints weight = 62137.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.055961 restraints weight = 52625.350| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 35868 Z= 0.160 Angle : 0.595 11.713 48891 Z= 0.300 Chirality : 0.044 0.177 5484 Planarity : 0.005 0.058 6288 Dihedral : 4.540 56.302 4871 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.18 % Allowed : 10.21 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.12), residues: 4470 helix: 1.24 (0.21), residues: 673 sheet: -0.39 (0.15), residues: 1136 loop : -1.61 (0.12), residues: 2661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 67 TYR 0.020 0.001 TYR K 55 PHE 0.019 0.001 PHE A 927 TRP 0.034 0.001 TRP B 258 HIS 0.006 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00353 (35814) covalent geometry : angle 0.59328 (48783) SS BOND : bond 0.00219 ( 54) SS BOND : angle 1.03577 ( 108) hydrogen bonds : bond 0.03518 ( 1194) hydrogen bonds : angle 5.80942 ( 3216) *********************** 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 232 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 147 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 ILE cc_start: 0.6892 (OUTLIER) cc_final: 0.6513 (mm) REVERT: A 513 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8971 (tp) REVERT: H 2 MET cc_start: 0.3924 (mtm) cc_final: 0.2415 (tmm) REVERT: H 45 MET cc_start: 0.8194 (mpp) cc_final: 0.7713 (mmt) REVERT: H 132 LYS cc_start: 0.7817 (tmmt) cc_final: 0.7392 (ptmt) REVERT: H 215 HIS cc_start: 0.6831 (t70) cc_final: 0.6264 (t70) REVERT: B 741 TYR cc_start: 0.7205 (t80) cc_final: 0.6933 (t80) REVERT: B 844 ILE cc_start: 0.7128 (OUTLIER) cc_final: 0.6494 (tt) REVERT: G 76 VAL cc_start: 0.9043 (OUTLIER) cc_final: 0.8831 (t) REVERT: I 112 TRP cc_start: 0.7208 (p-90) cc_final: 0.6573 (p-90) REVERT: C 869 MET cc_start: 0.8134 (mtm) cc_final: 0.7871 (mtm) outliers start: 85 outliers final: 45 residues processed: 217 average time/residue: 0.1689 time to fit residues: 63.1778 Evaluate side-chains 183 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 134 time to evaluate : 1.186 ------------------------------------------------------------------------------- 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 236 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 572 THR 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 977 LEU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain K residue 67 ARG 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 64 THR 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 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 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 121 VAL Chi-restraints excluded: chain C residue 328 ARG 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 738 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 70 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 218 optimal weight: 0.7980 chunk 216 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 433 optimal weight: 0.5980 chunk 118 optimal weight: 20.0000 chunk 443 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 213 optimal weight: 5.9990 chunk 175 optimal weight: 0.0670 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 GLN ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN ** 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 = 0.4079 r_free = 0.4079 target = 0.077865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.054431 restraints weight = 232589.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.055698 restraints weight = 128628.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.056136 restraints weight = 82542.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.056260 restraints weight = 59365.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.056522 restraints weight = 53356.680| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 35868 Z= 0.111 Angle : 0.562 13.961 48891 Z= 0.283 Chirality : 0.043 0.214 5484 Planarity : 0.004 0.055 6288 Dihedral : 4.392 55.316 4865 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.77 % Allowed : 10.62 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.13), residues: 4470 helix: 1.43 (0.21), residues: 675 sheet: -0.30 (0.15), residues: 1154 loop : -1.46 (0.12), residues: 2641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 43 TYR 0.017 0.001 TYR I 117 PHE 0.024 0.001 PHE A 80 TRP 0.028 0.001 TRP B 258 HIS 0.003 0.001 HIS G 90 Details of bonding type rmsd covalent geometry : bond 0.00242 (35814) covalent geometry : angle 0.56126 (48783) SS BOND : bond 0.00177 ( 54) SS BOND : angle 0.93833 ( 108) hydrogen bonds : bond 0.03307 ( 1194) hydrogen bonds : angle 5.56286 ( 3216) *********************** 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 226 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 157 time to evaluate : 0.977 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: A 318 PHE cc_start: 0.6648 (m-80) cc_final: 0.6182 (m-80) REVERT: A 326 ILE cc_start: 0.6893 (OUTLIER) cc_final: 0.6578 (mm) REVERT: A 513 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.8992 (tp) REVERT: H 2 MET cc_start: 0.3947 (mtm) cc_final: 0.2444 (tmm) REVERT: H 53 MET cc_start: 0.5943 (mpp) cc_final: 0.4853 (mpp) REVERT: H 132 LYS cc_start: 0.7837 (tmmt) cc_final: 0.7433 (ptmt) REVERT: H 215 HIS cc_start: 0.6929 (t70) cc_final: 0.6491 (t70) REVERT: B 326 ILE cc_start: 0.9277 (OUTLIER) cc_final: 0.9067 (pt) REVERT: B 844 ILE cc_start: 0.6998 (OUTLIER) cc_final: 0.6325 (tt) REVERT: G 101 MET cc_start: 0.9151 (tpp) cc_final: 0.8817 (tpp) REVERT: L 41 TRP cc_start: 0.7939 (m100) cc_final: 0.7725 (m100) REVERT: I 113 ILE cc_start: 0.3092 (OUTLIER) cc_final: 0.2885 (tt) REVERT: C 869 MET cc_start: 0.8031 (mtm) cc_final: 0.7808 (mtm) outliers start: 69 outliers final: 45 residues processed: 213 average time/residue: 0.1666 time to fit residues: 59.8046 Evaluate side-chains 187 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 137 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 326 ILE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 572 THR 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 864 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain K residue 67 ARG 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 64 THR Chi-restraints excluded: chain B residue 318 PHE 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 529 LYS 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 L residue 201 LEU Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 113 ILE 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 738 CYS Chi-restraints excluded: chain C residue 747 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 129 optimal weight: 0.9980 chunk 445 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 chunk 333 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 356 optimal weight: 5.9990 chunk 427 optimal weight: 3.9990 chunk 400 optimal weight: 0.6980 chunk 206 optimal weight: 6.9990 chunk 382 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 B1005 GLN ** 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 = 0.4068 r_free = 0.4068 target = 0.077280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.054128 restraints weight = 233173.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.055148 restraints weight = 130397.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.055524 restraints weight = 85324.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.055676 restraints weight = 65143.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.056009 restraints weight = 53491.838| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 35868 Z= 0.121 Angle : 0.566 17.232 48891 Z= 0.283 Chirality : 0.043 0.160 5484 Planarity : 0.004 0.051 6288 Dihedral : 4.325 56.070 4861 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.10 % Allowed : 10.44 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.13), residues: 4470 helix: 1.45 (0.21), residues: 670 sheet: -0.19 (0.15), residues: 1165 loop : -1.36 (0.12), residues: 2635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 328 TYR 0.017 0.001 TYR B 741 PHE 0.014 0.001 PHE B 318 TRP 0.018 0.001 TRP B 258 HIS 0.004 0.001 HIS I 90 Details of bonding type rmsd covalent geometry : bond 0.00267 (35814) covalent geometry : angle 0.56509 (48783) SS BOND : bond 0.00169 ( 54) SS BOND : angle 0.94190 ( 108) hydrogen bonds : bond 0.03243 ( 1194) hydrogen bonds : angle 5.47399 ( 3216) *********************** 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 223 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 141 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 THR cc_start: 0.8452 (OUTLIER) cc_final: 0.8132 (t) REVERT: A 318 PHE cc_start: 0.6788 (m-80) cc_final: 0.6404 (m-80) REVERT: A 326 ILE cc_start: 0.6521 (OUTLIER) cc_final: 0.6168 (mm) REVERT: A 513 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.8969 (tp) REVERT: H 2 MET cc_start: 0.3531 (mtm) cc_final: 0.1879 (tmm) REVERT: H 53 MET cc_start: 0.5734 (mpp) cc_final: 0.4784 (mpp) REVERT: H 132 LYS cc_start: 0.7852 (tmmt) cc_final: 0.7437 (ptmt) REVERT: H 215 HIS cc_start: 0.6897 (t70) cc_final: 0.6352 (t70) REVERT: B 326 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9138 (pt) REVERT: B 844 ILE cc_start: 0.6886 (OUTLIER) cc_final: 0.6264 (tt) REVERT: G 101 MET cc_start: 0.9226 (tpp) cc_final: 0.8928 (tpp) REVERT: I 112 TRP cc_start: 0.7370 (p-90) cc_final: 0.6984 (p-90) REVERT: I 113 ILE cc_start: 0.3359 (OUTLIER) cc_final: 0.3121 (tt) REVERT: C 869 MET cc_start: 0.8074 (mtm) cc_final: 0.7873 (mtm) outliers start: 82 outliers final: 58 residues processed: 206 average time/residue: 0.1639 time to fit residues: 58.1433 Evaluate side-chains 195 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 131 time to evaluate : 1.162 ------------------------------------------------------------------------------- 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 299 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 572 THR 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 864 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 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 64 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 318 PHE 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 529 LYS 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 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 76 VAL Chi-restraints excluded: chain G residue 89 LEU 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 113 ILE 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 592 PHE 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 83 optimal weight: 2.9990 chunk 370 optimal weight: 1.9990 chunk 261 optimal weight: 5.9990 chunk 419 optimal weight: 0.8980 chunk 330 optimal weight: 7.9990 chunk 425 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 362 optimal weight: 0.0970 chunk 252 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 239 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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** J 85 ASN ** 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 = 0.4058 r_free = 0.4058 target = 0.076778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.053477 restraints weight = 233641.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.055352 restraints weight = 133013.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.054882 restraints weight = 85838.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.055419 restraints weight = 65368.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.055602 restraints weight = 57043.097| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 35868 Z= 0.128 Angle : 0.571 17.981 48891 Z= 0.287 Chirality : 0.043 0.194 5484 Planarity : 0.004 0.048 6288 Dihedral : 4.330 56.649 4861 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.95 % Allowed : 11.05 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.13), residues: 4470 helix: 1.40 (0.21), residues: 671 sheet: -0.15 (0.15), residues: 1179 loop : -1.27 (0.12), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 328 TYR 0.018 0.001 TYR L 42 PHE 0.017 0.001 PHE A 329 TRP 0.022 0.001 TRP C 633 HIS 0.004 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00283 (35814) covalent geometry : angle 0.56989 (48783) SS BOND : bond 0.00156 ( 54) SS BOND : angle 0.90976 ( 108) hydrogen bonds : bond 0.03251 ( 1194) hydrogen bonds : angle 5.42333 ( 3216) *********************** 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 218 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 142 time to evaluate : 0.877 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: A 299 THR cc_start: 0.8510 (OUTLIER) cc_final: 0.8245 (t) REVERT: A 326 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6846 (mm) REVERT: A 513 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.8949 (tp) REVERT: H 132 LYS cc_start: 0.7829 (tmmt) cc_final: 0.7434 (ptmt) REVERT: H 215 HIS cc_start: 0.7017 (t70) cc_final: 0.6438 (t70) REVERT: B 844 ILE cc_start: 0.7042 (OUTLIER) cc_final: 0.6378 (tt) REVERT: B 1050 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7756 (ptm) REVERT: J 101 ASP cc_start: 0.8949 (t0) cc_final: 0.8497 (t0) REVERT: G 98 ASP cc_start: 0.8158 (m-30) cc_final: 0.7878 (m-30) REVERT: G 101 MET cc_start: 0.9261 (tpp) cc_final: 0.8961 (tpp) REVERT: I 112 TRP cc_start: 0.7576 (p-90) cc_final: 0.6682 (p-90) REVERT: C 869 MET cc_start: 0.8135 (mtm) cc_final: 0.7915 (mtm) outliers start: 76 outliers final: 53 residues processed: 204 average time/residue: 0.1536 time to fit residues: 53.6797 Evaluate side-chains 187 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 129 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 572 THR 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 864 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 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 109 THR Chi-restraints excluded: chain B residue 341 VAL 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 1032 CYS Chi-restraints excluded: chain B residue 1050 MET 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 76 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 201 LEU 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 1032 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 92 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 278 optimal weight: 7.9990 chunk 355 optimal weight: 6.9990 chunk 295 optimal weight: 7.9990 chunk 364 optimal weight: 2.9990 chunk 385 optimal weight: 4.9990 chunk 280 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN ** A 616 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** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 GLN ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 GLN C 188 ASN ** C 422 ASN ** 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 = 0.3982 r_free = 0.3982 target = 0.073443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.048952 restraints weight = 217326.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.050242 restraints weight = 115533.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.051130 restraints weight = 76717.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.051657 restraints weight = 58273.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.052014 restraints weight = 48952.247| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 35868 Z= 0.241 Angle : 0.668 15.949 48891 Z= 0.341 Chirality : 0.045 0.224 5484 Planarity : 0.005 0.052 6288 Dihedral : 4.839 59.886 4861 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.00 % Allowed : 11.44 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.13), residues: 4470 helix: 0.82 (0.20), residues: 689 sheet: -0.36 (0.15), residues: 1128 loop : -1.33 (0.12), residues: 2653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 995 TYR 0.026 0.002 TYR A 904 PHE 0.019 0.002 PHE A 329 TRP 0.035 0.002 TRP I 118 HIS 0.008 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00525 (35814) covalent geometry : angle 0.66712 (48783) SS BOND : bond 0.00411 ( 54) SS BOND : angle 1.06641 ( 108) hydrogen bonds : bond 0.03790 ( 1194) hydrogen bonds : angle 5.80633 ( 3216) *********************** 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 215 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 137 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8183 (t) REVERT: A 513 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8795 (tp) REVERT: A 670 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.8022 (mt) REVERT: H 53 MET cc_start: 0.6278 (mpp) cc_final: 0.5424 (mpp) REVERT: H 132 LYS cc_start: 0.7996 (tmmt) cc_final: 0.7663 (ptpt) REVERT: H 215 HIS cc_start: 0.7018 (t70) cc_final: 0.6812 (t70) REVERT: B 844 ILE cc_start: 0.6763 (OUTLIER) cc_final: 0.6115 (tt) REVERT: G 45 MET cc_start: 0.8493 (mmm) cc_final: 0.8036 (mmm) REVERT: G 98 ASP cc_start: 0.8314 (m-30) cc_final: 0.8004 (m-30) REVERT: G 101 MET cc_start: 0.9341 (tpp) cc_final: 0.9018 (tpp) REVERT: L 53 MET cc_start: 0.4323 (mmt) cc_final: 0.4070 (mmt) REVERT: L 145 GLU cc_start: 0.1763 (pt0) cc_final: 0.0776 (tt0) outliers start: 78 outliers final: 53 residues processed: 201 average time/residue: 0.1719 time to fit residues: 58.2833 Evaluate side-chains 179 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 122 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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 299 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 572 THR 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 738 CYS Chi-restraints excluded: chain A residue 762 GLN 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 67 ARG Chi-restraints excluded: chain H residue 109 ASP 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 529 LYS 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 869 MET 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 56 GLU 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 89 LEU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 201 LEU 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 109 THR 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 632 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 223 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 365 optimal weight: 0.0870 chunk 142 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 54 optimal weight: 0.0870 chunk 416 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 366 optimal weight: 0.9980 overall best weight: 0.8338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A1036 GLN ** 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 751 ASN ** B1002 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.075543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.051695 restraints weight = 231305.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.053284 restraints weight = 129268.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.053375 restraints weight = 89652.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.053492 restraints weight = 65837.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.053740 restraints weight = 56160.900| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 35868 Z= 0.127 Angle : 0.613 18.422 48891 Z= 0.307 Chirality : 0.045 0.666 5484 Planarity : 0.004 0.057 6288 Dihedral : 4.531 56.763 4856 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.38 % Allowed : 12.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.13), residues: 4470 helix: 1.03 (0.21), residues: 693 sheet: -0.26 (0.15), residues: 1132 loop : -1.26 (0.12), residues: 2645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 35 TYR 0.021 0.001 TYR B 92 PHE 0.042 0.001 PHE I 30 TRP 0.031 0.001 TRP I 118 HIS 0.004 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00284 (35814) covalent geometry : angle 0.61162 (48783) SS BOND : bond 0.00168 ( 54) SS BOND : angle 0.98572 ( 108) hydrogen bonds : bond 0.03378 ( 1194) hydrogen bonds : angle 5.53237 ( 3216) *********************** 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 190 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 136 time to evaluate : 1.004 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: A 299 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8260 (t) REVERT: A 513 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.8958 (tp) REVERT: A 670 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7939 (mt) REVERT: H 53 MET cc_start: 0.6489 (mpp) cc_final: 0.5597 (mpp) REVERT: H 132 LYS cc_start: 0.7940 (tmmt) cc_final: 0.7578 (ptpt) REVERT: H 215 HIS cc_start: 0.7200 (t70) cc_final: 0.6901 (t70) REVERT: B 844 ILE cc_start: 0.6901 (OUTLIER) cc_final: 0.6132 (tt) REVERT: J 101 ASP cc_start: 0.9010 (t0) cc_final: 0.8552 (t0) REVERT: G 45 MET cc_start: 0.8458 (mmm) cc_final: 0.8022 (mmm) REVERT: G 98 ASP cc_start: 0.8236 (m-30) cc_final: 0.7943 (m-30) REVERT: G 101 MET cc_start: 0.9328 (tpp) cc_final: 0.9010 (tpp) REVERT: L 145 GLU cc_start: 0.1232 (pt0) cc_final: 0.0373 (tt0) outliers start: 54 outliers final: 39 residues processed: 181 average time/residue: 0.1871 time to fit residues: 57.0079 Evaluate side-chains 173 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 1.305 ------------------------------------------------------------------------------- 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 299 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 572 THR 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 738 CYS 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 67 ARG Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain B residue 48 VAL 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 869 MET 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 89 LEU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 201 LEU 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 503 VAL Chi-restraints excluded: chain C residue 632 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 171 optimal weight: 3.9990 chunk 362 optimal weight: 0.0970 chunk 124 optimal weight: 6.9990 chunk 411 optimal weight: 0.0670 chunk 275 optimal weight: 6.9990 chunk 109 optimal weight: 30.0000 chunk 443 optimal weight: 0.9980 chunk 114 optimal weight: 9.9990 chunk 233 optimal weight: 0.5980 chunk 37 optimal weight: 6.9990 chunk 347 optimal weight: 6.9990 overall best weight: 1.1518 ------------------------------------------------------------------------------- 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** ** B1002 GLN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.075150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.051513 restraints weight = 232903.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.052561 restraints weight = 130018.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.053103 restraints weight = 87045.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.053327 restraints weight = 63172.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.053496 restraints weight = 52512.809| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 35868 Z= 0.150 Angle : 0.615 18.055 48891 Z= 0.308 Chirality : 0.044 0.424 5484 Planarity : 0.004 0.054 6288 Dihedral : 4.496 56.000 4856 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 1.31 % Allowed : 12.41 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.13), residues: 4470 helix: 1.12 (0.21), residues: 685 sheet: -0.22 (0.15), residues: 1117 loop : -1.24 (0.12), residues: 2668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 35 TYR 0.017 0.001 TYR B 741 PHE 0.029 0.001 PHE A 318 TRP 0.027 0.001 TRP C 633 HIS 0.004 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00332 (35814) covalent geometry : angle 0.61418 (48783) SS BOND : bond 0.00167 ( 54) SS BOND : angle 0.92570 ( 108) hydrogen bonds : bond 0.03370 ( 1194) hydrogen bonds : angle 5.50542 ( 3216) ********************** 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 181 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 130 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8336 (t) REVERT: A 513 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.8969 (tp) REVERT: A 670 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7922 (mt) REVERT: H 53 MET cc_start: 0.6554 (mpp) cc_final: 0.5840 (mpp) REVERT: H 132 LYS cc_start: 0.7953 (tmmt) cc_final: 0.7582 (ptpt) REVERT: H 215 HIS cc_start: 0.7261 (t70) cc_final: 0.6974 (t70) REVERT: J 101 ASP cc_start: 0.8991 (t0) cc_final: 0.8543 (t0) REVERT: G 45 MET cc_start: 0.8463 (mmm) cc_final: 0.8053 (mmm) REVERT: G 98 ASP cc_start: 0.8266 (m-30) cc_final: 0.7889 (m-30) REVERT: G 101 MET cc_start: 0.9317 (tpp) cc_final: 0.8999 (tpp) REVERT: L 145 GLU cc_start: 0.1235 (pt0) cc_final: 0.0367 (tt0) outliers start: 51 outliers final: 40 residues processed: 175 average time/residue: 0.1875 time to fit residues: 56.1215 Evaluate side-chains 166 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 123 time to evaluate : 1.179 ------------------------------------------------------------------------------- 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 299 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 572 THR 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 738 CYS 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 67 ARG Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 869 MET 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 76 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 201 LEU 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 503 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 747 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 75 optimal weight: 1.9990 chunk 275 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 401 optimal weight: 5.9990 chunk 298 optimal weight: 0.9990 chunk 430 optimal weight: 1.9990 chunk 230 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 310 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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** ** B1002 GLN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.074967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.051697 restraints weight = 231672.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.052692 restraints weight = 135429.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.053077 restraints weight = 92383.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.053407 restraints weight = 65530.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.053501 restraints weight = 52389.960| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4907 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= 0.150 Angle : 0.615 18.036 48891 Z= 0.307 Chirality : 0.044 0.360 5484 Planarity : 0.004 0.055 6288 Dihedral : 4.505 54.511 4856 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.23 % Allowed : 12.54 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.13), residues: 4470 helix: 1.12 (0.21), residues: 686 sheet: -0.20 (0.15), residues: 1099 loop : -1.21 (0.12), residues: 2685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 35 TYR 0.016 0.001 TYR I 117 PHE 0.018 0.001 PHE A 329 TRP 0.027 0.001 TRP C 633 HIS 0.007 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00332 (35814) covalent geometry : angle 0.61423 (48783) SS BOND : bond 0.00167 ( 54) SS BOND : angle 0.95440 ( 108) hydrogen bonds : bond 0.03372 ( 1194) hydrogen bonds : angle 5.50711 ( 3216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7039.20 seconds wall clock time: 122 minutes 0.80 seconds (7320.80 seconds total)