Starting phenix.real_space_refine on Mon Aug 25 19:59:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xea_38284/08_2025/8xea_38284.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xea_38284/08_2025/8xea_38284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xea_38284/08_2025/8xea_38284.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xea_38284/08_2025/8xea_38284.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xea_38284/08_2025/8xea_38284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xea_38284/08_2025/8xea_38284.map" } resolution = 3.42 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= 0.041 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 138 5.16 5 C 19265 2.51 5 N 5065 2.21 5 O 5745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 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: 30213 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 888 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "B" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 8360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8360 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 57, 'TRANS': 1008} Chain breaks: 6 Chain: "E" Number of atoms: 8359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8359 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 57, 'TRANS': 1008} Chain breaks: 6 Chain: "F" Number of atoms: 8367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8367 Classifications: {'peptide': 1067} Link IDs: {'PTRANS': 57, 'TRANS': 1009} Chain breaks: 6 Chain: "G" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 888 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "I" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 888 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "J" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Time building chain proxies: 5.51, per 1000 atoms: 0.18 Number of scatterers: 30213 At special positions: 0 Unit cell: (154.96, 164.32, 209.04, 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 138 16.00 O 5745 8.00 N 5065 7.00 C 19265 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.05 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.04 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 136 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 166 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.04 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.03 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 538 " - pdb=" SG CYS F 590 " distance=2.03 Simple disulfide: pdb=" SG CYS F 617 " - pdb=" SG CYS F 649 " distance=2.03 Simple disulfide: pdb=" SG CYS F 662 " - pdb=" SG CYS F 671 " distance=2.03 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 760 " distance=2.03 Simple disulfide: pdb=" SG CYS F 743 " - pdb=" SG CYS F 749 " distance=2.03 Simple disulfide: pdb=" SG CYS F1032 " - pdb=" SG CYS F1043 " distance=2.03 Simple disulfide: pdb=" SG CYS F1082 " - pdb=" SG CYS F1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " 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: 2.01 Conformation dependent library (CDL) restraints added in 985.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7208 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 60 sheets defined 18.4% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.980A pdb=" N ASN A 32 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 343 Processing helix chain 'D' and resid 406 through 410 removed outlier: 3.580A pdb=" N ILE D 410 " --> pdb=" O VAL D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 743 removed outlier: 4.227A pdb=" N ILE D 742 " --> pdb=" O CYS D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 754 removed outlier: 3.640A pdb=" N SER D 750 " --> pdb=" O SER D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 759 through 783 removed outlier: 3.603A pdb=" N LEU D 763 " --> pdb=" O PHE D 759 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN D 779 " --> pdb=" O ASP D 775 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL D 781 " --> pdb=" O ASN D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 825 Processing helix chain 'D' and resid 850 through 855 Processing helix chain 'D' and resid 866 through 884 Processing helix chain 'D' and resid 886 through 890 Processing helix chain 'D' and resid 897 through 907 Processing helix chain 'D' and resid 908 through 910 No H-bonds generated for 'chain 'D' and resid 908 through 910' Processing helix chain 'D' and resid 913 through 919 removed outlier: 3.716A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 removed outlier: 3.960A pdb=" N GLN D 935 " --> pdb=" O ILE D 931 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASP D 936 " --> pdb=" O GLY D 932 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR D 941 " --> pdb=" O SER D 937 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 964 removed outlier: 4.639A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N HIS D 954 " --> pdb=" O ASP D 950 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN D 955 " --> pdb=" O VAL D 951 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 959 " --> pdb=" O ASN D 955 " (cutoff:3.500A) Processing helix chain 'D' and resid 977 through 984 removed outlier: 3.619A pdb=" N LEU D 981 " --> pdb=" O LEU D 977 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 993 removed outlier: 3.870A pdb=" N GLU D 990 " --> pdb=" O PRO D 986 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1032 removed outlier: 3.658A pdb=" N GLU D1017 " --> pdb=" O ILE D1013 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 383 through 387 Processing helix chain 'E' and resid 406 through 410 removed outlier: 3.628A pdb=" N ILE E 410 " --> pdb=" O VAL E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 746 through 754 removed outlier: 3.740A pdb=" N SER E 750 " --> pdb=" O SER E 746 " (cutoff:3.500A) Processing helix chain 'E' and resid 759 through 783 removed outlier: 4.140A pdb=" N THR E 778 " --> pdb=" O GLN E 774 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLN E 779 " --> pdb=" O ASP E 775 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU E 780 " --> pdb=" O LYS E 776 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL E 781 " --> pdb=" O ASN E 777 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 851 through 855 Processing helix chain 'E' and resid 866 through 884 Processing helix chain 'E' and resid 886 through 890 removed outlier: 3.544A pdb=" N GLY E 889 " --> pdb=" O TRP E 886 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 907 Processing helix chain 'E' and resid 908 through 910 No H-bonds generated for 'chain 'E' and resid 908 through 910' Processing helix chain 'E' and resid 913 through 941 removed outlier: 3.657A pdb=" N TYR E 917 " --> pdb=" O GLN E 913 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS E 921 " --> pdb=" O TYR E 917 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU E 922 " --> pdb=" O GLU E 918 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE E 934 " --> pdb=" O ALA E 930 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLN E 935 " --> pdb=" O ILE E 931 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP E 936 " --> pdb=" O GLY E 932 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR E 941 " --> pdb=" O SER E 937 " (cutoff:3.500A) Processing helix chain 'E' and resid 945 through 964 removed outlier: 4.837A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS E 954 " --> pdb=" O ASP E 950 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN E 955 " --> pdb=" O VAL E 951 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU E 959 " --> pdb=" O ASN E 955 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN E 960 " --> pdb=" O ALA E 956 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU E 962 " --> pdb=" O ALA E 958 " (cutoff:3.500A) Processing helix chain 'E' and resid 977 through 984 removed outlier: 3.562A pdb=" N LEU E 981 " --> pdb=" O LEU E 977 " (cutoff:3.500A) Processing helix chain 'E' and resid 985 through 988 Processing helix chain 'E' and resid 989 through 1032 removed outlier: 4.396A pdb=" N ARG E 995 " --> pdb=" O VAL E 991 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU E1017 " --> pdb=" O ILE E1013 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 304 Processing helix chain 'F' and resid 338 through 343 Processing helix chain 'F' and resid 364 through 370 removed outlier: 3.653A pdb=" N ILE F 368 " --> pdb=" O ASP F 364 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR F 369 " --> pdb=" O TYR F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 389 removed outlier: 4.147A pdb=" N ASN F 388 " --> pdb=" O THR F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 410 removed outlier: 3.597A pdb=" N ILE F 410 " --> pdb=" O VAL F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 422 removed outlier: 4.438A pdb=" N TYR F 421 " --> pdb=" O ASN F 417 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN F 422 " --> pdb=" O ILE F 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 417 through 422' Processing helix chain 'F' and resid 737 through 743 Processing helix chain 'F' and resid 746 through 757 removed outlier: 3.714A pdb=" N SER F 750 " --> pdb=" O SER F 746 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN F 755 " --> pdb=" O ASN F 751 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR F 756 " --> pdb=" O LEU F 752 " (cutoff:3.500A) Processing helix chain 'F' and resid 759 through 783 removed outlier: 3.687A pdb=" N LEU F 763 " --> pdb=" O PHE F 759 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR F 778 " --> pdb=" O GLN F 774 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN F 779 " --> pdb=" O ASP F 775 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU F 780 " --> pdb=" O LYS F 776 " (cutoff:3.500A) Processing helix chain 'F' and resid 816 through 826 removed outlier: 3.523A pdb=" N VAL F 826 " --> pdb=" O LEU F 822 " (cutoff:3.500A) Processing helix chain 'F' and resid 850 through 855 Processing helix chain 'F' and resid 866 through 884 removed outlier: 3.530A pdb=" N ILE F 870 " --> pdb=" O THR F 866 " (cutoff:3.500A) Processing helix chain 'F' and resid 886 through 890 removed outlier: 3.513A pdb=" N GLY F 889 " --> pdb=" O TRP F 886 " (cutoff:3.500A) Processing helix chain 'F' and resid 897 through 908 Processing helix chain 'F' and resid 913 through 941 removed outlier: 3.606A pdb=" N TYR F 917 " --> pdb=" O GLN F 913 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LYS F 921 " --> pdb=" O TYR F 917 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU F 922 " --> pdb=" O GLU F 918 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE F 934 " --> pdb=" O ALA F 930 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN F 935 " --> pdb=" O ILE F 931 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASP F 936 " --> pdb=" O GLY F 932 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR F 941 " --> pdb=" O SER F 937 " (cutoff:3.500A) Processing helix chain 'F' and resid 945 through 965 removed outlier: 4.825A pdb=" N VAL F 951 " --> pdb=" O LYS F 947 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS F 954 " --> pdb=" O ASP F 950 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN F 955 " --> pdb=" O VAL F 951 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU F 959 " --> pdb=" O ASN F 955 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN F 960 " --> pdb=" O ALA F 956 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU F 962 " --> pdb=" O ALA F 958 " (cutoff:3.500A) Processing helix chain 'F' and resid 977 through 984 removed outlier: 3.715A pdb=" N LEU F 981 " --> pdb=" O LEU F 977 " (cutoff:3.500A) Processing helix chain 'F' and resid 985 through 1033 removed outlier: 4.064A pdb=" N GLU F 990 " --> pdb=" O PRO F 986 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL F 991 " --> pdb=" O PRO F 987 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN F 992 " --> pdb=" O GLU F 988 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ARG F 995 " --> pdb=" O VAL F 991 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU F 996 " --> pdb=" O GLN F 992 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL F1033 " --> pdb=" O MET F1029 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 90 Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'J' and resid 92 through 94 No H-bonds generated for 'chain 'J' and resid 92 through 94' Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 4.052A pdb=" N SER A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 7 removed outlier: 3.722A pdb=" N SER B 22 " --> pdb=" O SER B 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 53 through 54 removed outlier: 6.454A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 28 through 31 removed outlier: 8.271A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR D 63 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL D 267 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER D 94 " --> pdb=" O ARG D 190 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG D 190 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 52 through 55 Processing sheet with id=AA8, first strand: chain 'D' and resid 127 through 131 Processing sheet with id=AA9, first strand: chain 'D' and resid 277 through 279 removed outlier: 7.439A pdb=" N LYS D 278 " --> pdb=" O THR D 286 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR D 286 " --> pdb=" O LYS D 278 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 311 through 314 removed outlier: 3.618A pdb=" N GLY D 311 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR D 599 " --> pdb=" O GLY D 311 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR D 313 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL D 597 " --> pdb=" O TYR D 313 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 325 through 328 Processing sheet with id=AB3, first strand: chain 'D' and resid 394 through 402 Processing sheet with id=AB4, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AB5, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AB6, first strand: chain 'D' and resid 654 through 660 removed outlier: 6.255A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N VAL D 656 " --> pdb=" O THR D 696 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE D 664 " --> pdb=" O ALA D 672 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 701 through 702 removed outlier: 6.320A pdb=" N ALA D 701 " --> pdb=" O ILE E 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.971A pdb=" N SER D 711 " --> pdb=" O THR D1076 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR D1076 " --> pdb=" O SER D 711 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN D 717 " --> pdb=" O ALA D1070 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY D1059 " --> pdb=" O SER D1055 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N SER D1055 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL D1061 " --> pdb=" O PRO D1053 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU D1063 " --> pdb=" O SER D1051 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER D1051 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR D1047 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 733 through 735 removed outlier: 4.611A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU D 861 " --> pdb=" O LYS D 733 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 787 through 788 removed outlier: 3.504A pdb=" N ILE D 788 " --> pdb=" O ALA F 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 3.685A pdb=" N SER D1123 " --> pdb=" O ALA D1087 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 1094 through 1097 Processing sheet with id=AC4, first strand: chain 'E' and resid 28 through 31 removed outlier: 8.556A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR E 63 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL E 267 " --> pdb=" O THR E 63 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER E 94 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG E 190 " --> pdb=" O SER E 94 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 52 through 55 Processing sheet with id=AC6, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.778A pdb=" N LEU E 84 " --> pdb=" O PHE E 238 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL E 126 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER E 172 " --> pdb=" O VAL E 126 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 277 through 279 removed outlier: 7.096A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 313 through 314 removed outlier: 3.544A pdb=" N TYR E 313 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL E 597 " --> pdb=" O TYR E 313 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 325 through 328 Processing sheet with id=AD1, first strand: chain 'E' and resid 391 through 392 Processing sheet with id=AD2, first strand: chain 'E' and resid 394 through 402 removed outlier: 3.582A pdb=" N ILE E 434 " --> pdb=" O VAL E 511 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU E 513 " --> pdb=" O CYS E 432 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AD5, first strand: chain 'E' and resid 654 through 660 removed outlier: 6.239A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N VAL E 656 " --> pdb=" O THR E 696 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE E 664 " --> pdb=" O ALA E 672 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 711 through 715 removed outlier: 3.731A pdb=" N THR E1076 " --> pdb=" O SER E1097 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 718 through 728 removed outlier: 6.890A pdb=" N GLY E1059 " --> pdb=" O SER E1055 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N SER E1055 " --> pdb=" O GLY E1059 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL E1061 " --> pdb=" O PRO E1053 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU E1063 " --> pdb=" O SER E1051 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER E1051 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL E1065 " --> pdb=" O LEU E1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 3.771A pdb=" N SER E1123 " --> pdb=" O ALA E1087 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 28 through 31 removed outlier: 8.275A pdb=" N ASN F 61 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR F 269 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR F 63 " --> pdb=" O VAL F 267 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL F 267 " --> pdb=" O THR F 63 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER F 94 " --> pdb=" O ARG F 190 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG F 190 " --> pdb=" O SER F 94 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N PHE F 201 " --> pdb=" O ASP F 228 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASP F 228 " --> pdb=" O PHE F 201 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE F 203 " --> pdb=" O LEU F 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 52 through 55 Processing sheet with id=AE3, first strand: chain 'F' and resid 84 through 85 removed outlier: 3.964A pdb=" N LEU F 84 " --> pdb=" O PHE F 238 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL F 126 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER F 172 " --> pdb=" O VAL F 126 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 277 through 279 removed outlier: 7.059A pdb=" N LYS F 278 " --> pdb=" O THR F 286 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 313 through 314 removed outlier: 3.542A pdb=" N TYR F 313 " --> pdb=" O VAL F 597 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL F 597 " --> pdb=" O TYR F 313 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 325 through 328 Processing sheet with id=AE7, first strand: chain 'F' and resid 394 through 403 removed outlier: 4.602A pdb=" N THR F 430 " --> pdb=" O PHE F 515 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'F' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'F' and resid 654 through 660 removed outlier: 6.273A pdb=" N GLU F 654 " --> pdb=" O ALA F 694 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N THR F 696 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N VAL F 656 " --> pdb=" O THR F 696 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE F 664 " --> pdb=" O ALA F 672 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.148A pdb=" N GLN F1071 " --> pdb=" O THR F 716 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N PHE F 718 " --> pdb=" O PRO F1069 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE F 720 " --> pdb=" O TYR F1067 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TYR F1067 " --> pdb=" O ILE F 720 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL F 722 " --> pdb=" O VAL F1065 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL F1065 " --> pdb=" O VAL F 722 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR F 724 " --> pdb=" O LEU F1063 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU F1063 " --> pdb=" O THR F 724 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE F 726 " --> pdb=" O VAL F1061 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL F1061 " --> pdb=" O ILE F 726 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLY F1059 " --> pdb=" O PRO F 728 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLY F1059 " --> pdb=" O SER F1055 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N SER F1055 " --> pdb=" O GLY F1059 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL F1061 " --> pdb=" O PRO F1053 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU F1063 " --> pdb=" O SER F1051 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER F1051 " --> pdb=" O LEU F1063 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL F1065 " --> pdb=" O LEU F1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 1120 through 1122 Processing sheet with id=AF4, first strand: chain 'F' and resid 1094 through 1097 Processing sheet with id=AF5, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AF6, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.878A pdb=" N SER G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 45 through 46 removed outlier: 3.538A pdb=" N SER G 106 " --> pdb=" O ARG G 97 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 5 through 7 removed outlier: 3.700A pdb=" N SER I 22 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 45 through 49 removed outlier: 6.362A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.712A pdb=" N ARG H 38 " --> pdb=" O GLU H 46 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AG4, first strand: chain 'H' and resid 49 through 51 Processing sheet with id=AG5, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AG6, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.853A pdb=" N THR J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) 958 hydrogen bonds defined for protein. 2568 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.62 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9726 1.35 - 1.47: 7959 1.47 - 1.60: 13071 1.60 - 1.72: 0 1.72 - 1.84: 177 Bond restraints: 30933 Sorted by residual: bond pdb=" C PRO F 986 " pdb=" N PRO F 987 " ideal model delta sigma weight residual 1.334 1.373 -0.039 8.40e-03 1.42e+04 2.17e+01 bond pdb=" C THR F 250 " pdb=" N PRO F 251 " ideal model delta sigma weight residual 1.334 1.422 -0.088 2.34e-02 1.83e+03 1.43e+01 bond pdb=" C THR E 250 " pdb=" N PRO E 251 " ideal model delta sigma weight residual 1.335 1.380 -0.045 1.36e-02 5.41e+03 1.08e+01 bond pdb=" C THR D 250 " pdb=" N PRO D 251 " ideal model delta sigma weight residual 1.334 1.390 -0.057 2.34e-02 1.83e+03 5.84e+00 bond pdb=" C LEU F 560 " pdb=" N PRO F 561 " ideal model delta sigma weight residual 1.333 1.363 -0.030 1.44e-02 4.82e+03 4.24e+00 ... (remaining 30928 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 41344 2.56 - 5.12: 602 5.12 - 7.68: 88 7.68 - 10.24: 27 10.24 - 12.80: 20 Bond angle restraints: 42081 Sorted by residual: angle pdb=" CB LYS E 786 " pdb=" CG LYS E 786 " pdb=" CD LYS E 786 " ideal model delta sigma weight residual 111.30 124.09 -12.79 2.30e+00 1.89e-01 3.09e+01 angle pdb=" C TYR E 489 " pdb=" N SER E 490 " pdb=" CA SER E 490 " ideal model delta sigma weight residual 120.68 128.29 -7.61 1.52e+00 4.33e-01 2.51e+01 angle pdb=" C LEU F 249 " pdb=" N THR F 250 " pdb=" CA THR F 250 " ideal model delta sigma weight residual 121.80 133.92 -12.12 2.44e+00 1.68e-01 2.47e+01 angle pdb=" N PRO D 986 " pdb=" CA PRO D 986 " pdb=" C PRO D 986 " ideal model delta sigma weight residual 110.70 116.45 -5.75 1.22e+00 6.72e-01 2.22e+01 angle pdb=" CA LYS E 786 " pdb=" CB LYS E 786 " pdb=" CG LYS E 786 " ideal model delta sigma weight residual 114.10 122.73 -8.63 2.00e+00 2.50e-01 1.86e+01 ... (remaining 42076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 15889 17.69 - 35.39: 1881 35.39 - 53.08: 480 53.08 - 70.78: 133 70.78 - 88.47: 37 Dihedral angle restraints: 18420 sinusoidal: 7188 harmonic: 11232 Sorted by residual: dihedral pdb=" CB CYS F 15 " pdb=" SG CYS F 15 " pdb=" SG CYS F 136 " pdb=" CB CYS F 136 " ideal model delta sinusoidal sigma weight residual -86.00 -174.47 88.47 1 1.00e+01 1.00e-02 9.34e+01 dihedral pdb=" CB CYS D 15 " pdb=" SG CYS D 15 " pdb=" SG CYS D 136 " pdb=" CB CYS D 136 " ideal model delta sinusoidal sigma weight residual -86.00 -171.83 85.83 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CB CYS E 738 " pdb=" SG CYS E 738 " pdb=" SG CYS E 760 " pdb=" CB CYS E 760 " ideal model delta sinusoidal sigma weight residual 93.00 8.04 84.96 1 1.00e+01 1.00e-02 8.76e+01 ... (remaining 18417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4075 0.074 - 0.147: 614 0.147 - 0.221: 19 0.221 - 0.295: 4 0.295 - 0.368: 3 Chirality restraints: 4715 Sorted by residual: chirality pdb=" CG LEU G 80 " pdb=" CB LEU G 80 " pdb=" CD1 LEU G 80 " pdb=" CD2 LEU G 80 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CB ILE E 101 " pdb=" CA ILE E 101 " pdb=" CG1 ILE E 101 " pdb=" CG2 ILE E 101 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CB ILE D 101 " pdb=" CA ILE D 101 " pdb=" CG1 ILE D 101 " pdb=" CG2 ILE D 101 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 4712 not shown) Planarity restraints: 5443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 985 " 0.052 5.00e-02 4.00e+02 7.73e-02 9.56e+00 pdb=" N PRO D 986 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO D 986 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 986 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 986 " -0.051 5.00e-02 4.00e+02 7.60e-02 9.23e+00 pdb=" N PRO D 987 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO D 987 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 987 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 152 " -0.025 2.00e-02 2.50e+03 1.92e-02 9.18e+00 pdb=" CG TRP D 152 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP D 152 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP D 152 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 152 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 152 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 152 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 152 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 152 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 152 " -0.009 2.00e-02 2.50e+03 ... (remaining 5440 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2625 2.74 - 3.28: 28846 3.28 - 3.82: 51578 3.82 - 4.36: 57037 4.36 - 4.90: 98576 Nonbonded interactions: 238662 Sorted by model distance: nonbonded pdb=" OG SER F 27 " pdb=" O TRP F 64 " model vdw 2.204 3.040 nonbonded pdb=" OG SER D 27 " pdb=" O TRP D 64 " model vdw 2.219 3.040 nonbonded pdb=" O ASN F 417 " pdb=" OH TYR F 453 " model vdw 2.224 3.040 nonbonded pdb=" OG SER E 27 " pdb=" O TRP E 64 " model vdw 2.238 3.040 nonbonded pdb=" O LEU D 966 " pdb=" OG SER D 975 " model vdw 2.265 3.040 ... (remaining 238657 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'D' and (resid 14 through 826 or resid 850 through 1140)) selection = (chain 'E' and (resid 14 through 826 or resid 850 through 1140)) selection = (chain 'F' and (resid 14 through 826 or resid 850 through 1140)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 24.050 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 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 0.088 30981 Z= 0.170 Angle : 0.816 12.798 42177 Z= 0.429 Chirality : 0.049 0.368 4715 Planarity : 0.006 0.077 5443 Dihedral : 16.745 87.382 11068 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.41 % Favored : 92.48 % Rotamer: Outliers : 0.45 % Allowed : 25.63 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.84 (0.13), residues: 3817 helix: -0.02 (0.21), residues: 613 sheet: -0.49 (0.17), residues: 886 loop : -1.94 (0.12), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 454 TYR 0.036 0.001 TYR D 351 PHE 0.024 0.001 PHE E 79 TRP 0.051 0.001 TRP D 152 HIS 0.004 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00334 (30933) covalent geometry : angle 0.81542 (42081) SS BOND : bond 0.00335 ( 48) SS BOND : angle 1.19440 ( 96) hydrogen bonds : bond 0.15409 ( 941) hydrogen bonds : angle 6.71112 ( 2568) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 251 time to evaluate : 0.757 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 34 MET cc_start: 0.2754 (mmt) cc_final: 0.2205 (mmm) REVERT: A 82 MET cc_start: -0.0826 (ptt) cc_final: -0.1212 (mtm) REVERT: D 77 LYS cc_start: 0.6334 (OUTLIER) cc_final: 0.5987 (ptpp) REVERT: D 177 MET cc_start: 0.4228 (ptt) cc_final: 0.4016 (ptm) REVERT: D 201 PHE cc_start: 0.8668 (t80) cc_final: 0.8174 (t80) REVERT: D 421 TYR cc_start: 0.5763 (m-80) cc_final: 0.5359 (m-10) REVERT: D 907 ASN cc_start: 0.8286 (t0) cc_final: 0.8028 (m110) REVERT: D 1031 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8273 (mt-10) REVERT: D 1088 HIS cc_start: 0.7309 (m90) cc_final: 0.7031 (m90) REVERT: D 1125 ASN cc_start: 0.6597 (p0) cc_final: 0.6299 (p0) REVERT: E 51 THR cc_start: 0.7656 (p) cc_final: 0.7404 (p) REVERT: E 420 ASP cc_start: 0.5116 (t0) cc_final: 0.4608 (t0) REVERT: E 716 THR cc_start: 0.7881 (p) cc_final: 0.7278 (p) REVERT: F 134 GLN cc_start: 0.9239 (mm110) cc_final: 0.8746 (pm20) REVERT: F 201 PHE cc_start: 0.8885 (t80) cc_final: 0.8397 (t80) REVERT: F 907 ASN cc_start: 0.8324 (t0) cc_final: 0.8049 (m110) REVERT: G 34 MET cc_start: 0.4082 (mmt) cc_final: 0.3830 (mmm) REVERT: I 103 THR cc_start: 0.3297 (p) cc_final: 0.3026 (p) outliers start: 15 outliers final: 2 residues processed: 266 average time/residue: 0.1694 time to fit residues: 72.9290 Evaluate side-chains 155 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 152 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain F residue 137 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 0.6980 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN D 360 ASN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 GLN D1011 GLN ** D1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 GLN ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN ** E 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 856 ASN E 920 GLN F 207 HIS F 282 ASN ** F 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 563 GLN F 690 GLN F 920 GLN F 992 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 GLN J 37 GLN J 79 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.085748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.057924 restraints weight = 226077.206| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 10.61 r_work: 0.3215 rms_B_bonded: 9.38 restraints_weight: 2.0000 r_work: 0.3280 rms_B_bonded: 7.09 restraints_weight: 4.0000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 30981 Z= 0.342 Angle : 0.855 14.364 42177 Z= 0.455 Chirality : 0.050 0.285 4715 Planarity : 0.007 0.084 5443 Dihedral : 5.694 55.458 4179 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.02 % Favored : 91.83 % Rotamer: Outliers : 5.39 % Allowed : 22.65 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -1.94 (0.13), residues: 3817 helix: -0.01 (0.20), residues: 655 sheet: -0.73 (0.18), residues: 808 loop : -1.96 (0.12), residues: 2354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 815 TYR 0.038 0.003 TYR E 265 PHE 0.029 0.003 PHE D1089 TRP 0.048 0.004 TRP A 36 HIS 0.008 0.002 HIS D 69 Details of bonding type rmsd covalent geometry : bond 0.00724 (30933) covalent geometry : angle 0.85397 (42081) SS BOND : bond 0.01491 ( 48) SS BOND : angle 1.31563 ( 96) hydrogen bonds : bond 0.04728 ( 941) hydrogen bonds : angle 5.91413 ( 2568) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 126 time to evaluate : 1.102 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 29 VAL cc_start: -0.1794 (m) cc_final: -0.2132 (t) REVERT: D 95 THR cc_start: 0.9303 (OUTLIER) cc_final: 0.9093 (m) REVERT: D 177 MET cc_start: 0.4994 (ptt) cc_final: 0.4534 (ptp) REVERT: D 192 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7900 (m-10) REVERT: D 796 TYR cc_start: 0.6787 (OUTLIER) cc_final: 0.6289 (m-80) REVERT: E 146 GLN cc_start: 0.5467 (OUTLIER) cc_final: 0.5206 (mm-40) REVERT: E 1018 ILE cc_start: 0.9702 (OUTLIER) cc_final: 0.9442 (tt) REVERT: F 644 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8782 (tp40) REVERT: F 822 LEU cc_start: 0.9762 (OUTLIER) cc_final: 0.9507 (mt) REVERT: F 995 ARG cc_start: 0.9456 (OUTLIER) cc_final: 0.9062 (ptp-110) REVERT: G 29 VAL cc_start: -0.0725 (m) cc_final: -0.1114 (t) REVERT: G 34 MET cc_start: 0.3290 (mmt) cc_final: 0.2862 (mmm) REVERT: G 82 MET cc_start: 0.2663 (mtm) cc_final: 0.1701 (mtm) REVERT: H 29 VAL cc_start: -0.0817 (m) cc_final: -0.1146 (t) REVERT: H 82 MET cc_start: 0.0761 (mtm) cc_final: -0.0010 (mtm) outliers start: 181 outliers final: 73 residues processed: 300 average time/residue: 0.1461 time to fit residues: 75.7352 Evaluate side-chains 175 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 94 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 186 PHE Chi-restraints excluded: chain D residue 192 PHE Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 796 TYR Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 887 THR Chi-restraints excluded: chain D residue 896 ILE Chi-restraints excluded: chain D residue 906 PHE Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 985 ASP Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 186 PHE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 587 ILE Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 887 THR Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 1018 ILE Chi-restraints excluded: chain E residue 1109 PHE Chi-restraints excluded: chain E residue 1120 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 66 HIS Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 186 PHE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 644 GLN Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 822 LEU Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 887 THR Chi-restraints excluded: chain F residue 896 ILE Chi-restraints excluded: chain F residue 976 VAL Chi-restraints excluded: chain F residue 995 ARG Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1077 THR Chi-restraints excluded: chain F residue 1096 VAL Chi-restraints excluded: chain F residue 1109 PHE Chi-restraints excluded: chain F residue 1120 THR Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain J residue 79 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 247 optimal weight: 0.9990 chunk 288 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 166 optimal weight: 30.0000 chunk 322 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 320 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 280 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN D 245 HIS ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 690 GLN D 804 GLN D 856 ASN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 751 ASN ** E 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 779 GLN ** E1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 690 GLN F 784 GLN F 856 ASN F 992 GLN I 6 GLN I 79 GLN H 39 GLN J 79 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.084782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.060677 restraints weight = 232381.451| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 8.21 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 30981 Z= 0.186 Angle : 0.634 13.246 42177 Z= 0.331 Chirality : 0.045 0.219 4715 Planarity : 0.005 0.065 5443 Dihedral : 5.258 58.105 4179 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.62 % Favored : 92.25 % Rotamer: Outliers : 3.85 % Allowed : 24.02 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.50 % 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: -1.71 (0.13), residues: 3817 helix: 0.36 (0.21), residues: 655 sheet: -0.52 (0.18), residues: 819 loop : -1.89 (0.12), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 24 TYR 0.021 0.002 TYR F 453 PHE 0.021 0.002 PHE E 79 TRP 0.020 0.002 TRP I 35 HIS 0.006 0.001 HIS E1083 Details of bonding type rmsd covalent geometry : bond 0.00401 (30933) covalent geometry : angle 0.63003 (42081) SS BOND : bond 0.00950 ( 48) SS BOND : angle 1.68855 ( 96) hydrogen bonds : bond 0.03553 ( 941) hydrogen bonds : angle 5.41028 ( 2568) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 90 time to evaluate : 1.177 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: D 192 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.8103 (m-10) REVERT: D 690 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.6941 (pm20) REVERT: D 902 MET cc_start: 0.9408 (OUTLIER) cc_final: 0.9185 (tpp) REVERT: D 1029 MET cc_start: 0.9514 (tpp) cc_final: 0.9249 (tpp) REVERT: D 1050 MET cc_start: 0.8362 (mtp) cc_final: 0.8057 (mtp) REVERT: E 421 TYR cc_start: 0.7164 (m-80) cc_final: 0.6820 (m-80) REVERT: E 697 MET cc_start: 0.8857 (mmm) cc_final: 0.8609 (tmm) REVERT: E 796 TYR cc_start: 0.6684 (OUTLIER) cc_final: 0.6187 (m-80) REVERT: F 105 ILE cc_start: 0.8119 (mt) cc_final: 0.7823 (mm) REVERT: F 153 MET cc_start: 0.8247 (mpp) cc_final: 0.7827 (mpp) REVERT: F 779 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8740 (mp10) REVERT: G 35 THR cc_start: 0.0334 (OUTLIER) cc_final: 0.0019 (m) outliers start: 129 outliers final: 63 residues processed: 211 average time/residue: 0.1588 time to fit residues: 56.9403 Evaluate side-chains 148 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 79 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 186 PHE Chi-restraints excluded: chain D residue 192 PHE Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 690 GLN Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 902 MET Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 1048 HIS Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 587 ILE Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 796 TYR Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain E residue 1109 PHE Chi-restraints excluded: chain E residue 1120 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 194 PHE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 246 ARG Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 386 LYS Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 644 GLN Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 734 THR Chi-restraints excluded: chain F residue 779 GLN Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 941 THR Chi-restraints excluded: chain F residue 976 VAL Chi-restraints excluded: chain F residue 995 ARG Chi-restraints excluded: chain F residue 1076 THR Chi-restraints excluded: chain F residue 1101 HIS Chi-restraints excluded: chain F residue 1113 GLN Chi-restraints excluded: chain F residue 1120 THR Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 79 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 219 optimal weight: 10.0000 chunk 203 optimal weight: 0.7980 chunk 353 optimal weight: 7.9990 chunk 172 optimal weight: 20.0000 chunk 98 optimal weight: 2.9990 chunk 285 optimal weight: 10.0000 chunk 8 optimal weight: 30.0000 chunk 176 optimal weight: 6.9990 chunk 185 optimal weight: 7.9990 chunk 335 optimal weight: 6.9990 chunk 355 optimal weight: 40.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 66 HIS ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 755 GLN E 804 GLN E 935 GLN F 17 ASN F 66 HIS F 149 ASN F 314 GLN ** F 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN F 690 GLN F 755 GLN F 856 ASN F 992 GLN F1011 GLN I 6 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.081548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.056615 restraints weight = 223208.592| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 8.38 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.6805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 30981 Z= 0.277 Angle : 0.720 15.558 42177 Z= 0.379 Chirality : 0.045 0.211 4715 Planarity : 0.005 0.059 5443 Dihedral : 5.438 58.922 4179 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.99 % Favored : 90.83 % Rotamer: Outliers : 5.19 % Allowed : 23.34 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.50 % 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: -1.77 (0.13), residues: 3817 helix: 0.50 (0.21), residues: 648 sheet: -0.82 (0.18), residues: 835 loop : -1.89 (0.12), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 246 TYR 0.026 0.002 TYR F 453 PHE 0.027 0.002 PHE D 464 TRP 0.025 0.002 TRP G 36 HIS 0.007 0.001 HIS D 69 Details of bonding type rmsd covalent geometry : bond 0.00589 (30933) covalent geometry : angle 0.71800 (42081) SS BOND : bond 0.00549 ( 48) SS BOND : angle 1.41447 ( 96) hydrogen bonds : bond 0.03747 ( 941) hydrogen bonds : angle 5.53396 ( 2568) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 100 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.1873 (mmm) cc_final: 0.1498 (mmm) REVERT: D 153 MET cc_start: 0.7656 (mpp) cc_final: 0.7315 (mpp) REVERT: D 192 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8323 (m-10) REVERT: D 796 TYR cc_start: 0.7132 (OUTLIER) cc_final: 0.6844 (m-80) REVERT: D 902 MET cc_start: 0.9468 (OUTLIER) cc_final: 0.9058 (tpt) REVERT: D 1029 MET cc_start: 0.9560 (tpp) cc_final: 0.9293 (tpp) REVERT: F 105 ILE cc_start: 0.8653 (mt) cc_final: 0.8409 (mm) REVERT: F 153 MET cc_start: 0.8449 (mpp) cc_final: 0.7994 (mpp) REVERT: F 169 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6979 (pm20) REVERT: F 201 PHE cc_start: 0.9443 (OUTLIER) cc_final: 0.9131 (t80) REVERT: F 725 GLU cc_start: 0.8504 (tt0) cc_final: 0.8248 (tt0) REVERT: F 752 LEU cc_start: 0.9746 (OUTLIER) cc_final: 0.9445 (tt) REVERT: F 796 TYR cc_start: 0.7366 (OUTLIER) cc_final: 0.7045 (m-80) REVERT: F 856 ASN cc_start: 0.8856 (OUTLIER) cc_final: 0.8634 (t0) REVERT: H 34 MET cc_start: 0.1523 (mmm) cc_final: 0.0617 (mmm) REVERT: H 82 MET cc_start: -0.5596 (mtm) cc_final: -0.5800 (mtm) outliers start: 174 outliers final: 102 residues processed: 262 average time/residue: 0.1475 time to fit residues: 66.9800 Evaluate side-chains 192 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 82 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 192 PHE Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 796 TYR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 887 THR Chi-restraints excluded: chain D residue 902 MET Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 981 LEU Chi-restraints excluded: chain D residue 985 ASP Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 186 PHE Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 317 ASN Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 587 ILE Chi-restraints excluded: chain E residue 591 SER Chi-restraints excluded: chain E residue 656 VAL Chi-restraints excluded: chain E residue 714 ILE Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 732 THR Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 887 THR Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 991 VAL Chi-restraints excluded: chain E residue 1061 VAL Chi-restraints excluded: chain E residue 1101 HIS Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain E residue 1120 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 17 ASN Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 201 PHE Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 546 LEU Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 656 VAL Chi-restraints excluded: chain F residue 716 THR Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 734 THR Chi-restraints excluded: chain F residue 752 LEU Chi-restraints excluded: chain F residue 788 ILE Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 796 TYR Chi-restraints excluded: chain F residue 856 ASN Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 887 THR Chi-restraints excluded: chain F residue 976 VAL Chi-restraints excluded: chain F residue 985 ASP Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1077 THR Chi-restraints excluded: chain F residue 1101 HIS Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1120 THR Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain F residue 1133 VAL Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain J residue 47 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 304 optimal weight: 2.9990 chunk 261 optimal weight: 7.9990 chunk 13 optimal weight: 40.0000 chunk 86 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 167 optimal weight: 7.9990 chunk 321 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 41 optimal weight: 0.0970 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 GLN E 66 HIS E 134 GLN E 207 HIS ** E 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 ASN ** F 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 690 GLN I 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.082000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.060602 restraints weight = 247392.961| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 5.86 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.7130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30981 Z= 0.168 Angle : 0.614 13.203 42177 Z= 0.318 Chirality : 0.044 0.201 4715 Planarity : 0.005 0.060 5443 Dihedral : 5.234 58.020 4177 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.12 % Favored : 91.70 % Rotamer: Outliers : 3.85 % Allowed : 24.44 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.50 % 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: -1.70 (0.13), residues: 3817 helix: 0.67 (0.21), residues: 641 sheet: -0.74 (0.18), residues: 821 loop : -1.88 (0.12), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 905 TYR 0.024 0.001 TYR F 453 PHE 0.024 0.002 PHE F 55 TRP 0.024 0.002 TRP G 36 HIS 0.015 0.001 HIS E 505 Details of bonding type rmsd covalent geometry : bond 0.00369 (30933) covalent geometry : angle 0.61229 (42081) SS BOND : bond 0.00392 ( 48) SS BOND : angle 1.11572 ( 96) hydrogen bonds : bond 0.03235 ( 941) hydrogen bonds : angle 5.33451 ( 2568) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 89 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 111 ASP cc_start: 0.8909 (t70) cc_final: 0.8517 (p0) REVERT: D 153 MET cc_start: 0.7760 (mpp) cc_final: 0.7304 (mpp) REVERT: D 192 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.8213 (m-10) REVERT: D 983 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8470 (mtm110) REVERT: D 1029 MET cc_start: 0.9612 (tpp) cc_final: 0.9334 (tpp) REVERT: E 111 ASP cc_start: 0.8807 (t70) cc_final: 0.8541 (p0) REVERT: E 113 LYS cc_start: 0.8746 (tptp) cc_final: 0.8533 (tptp) REVERT: E 559 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7804 (t80) REVERT: E 745 ASP cc_start: 0.8822 (m-30) cc_final: 0.7940 (p0) REVERT: F 105 ILE cc_start: 0.8656 (mt) cc_final: 0.8389 (mm) REVERT: F 153 MET cc_start: 0.8592 (mpp) cc_final: 0.8072 (mpp) REVERT: F 201 PHE cc_start: 0.9471 (OUTLIER) cc_final: 0.9075 (t80) REVERT: F 468 ILE cc_start: 0.7576 (OUTLIER) cc_final: 0.6916 (tp) REVERT: F 725 GLU cc_start: 0.8717 (tt0) cc_final: 0.8443 (tt0) REVERT: F 752 LEU cc_start: 0.9769 (OUTLIER) cc_final: 0.9491 (tt) REVERT: F 775 ASP cc_start: 0.9077 (OUTLIER) cc_final: 0.8832 (m-30) REVERT: F 796 TYR cc_start: 0.7159 (OUTLIER) cc_final: 0.6945 (m-80) REVERT: F 995 ARG cc_start: 0.9335 (OUTLIER) cc_final: 0.8891 (ptp-110) REVERT: F 1018 ILE cc_start: 0.9734 (OUTLIER) cc_final: 0.9493 (tt) outliers start: 129 outliers final: 83 residues processed: 212 average time/residue: 0.1454 time to fit residues: 52.8322 Evaluate side-chains 176 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 83 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 192 PHE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 906 PHE Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 983 ARG Chi-restraints excluded: chain D residue 985 ASP Chi-restraints excluded: chain D residue 1101 HIS Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 77 LYS Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 317 ASN Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 587 ILE Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 732 THR Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 991 VAL Chi-restraints excluded: chain E residue 1061 VAL Chi-restraints excluded: chain E residue 1101 HIS Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 66 HIS Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 194 PHE Chi-restraints excluded: chain F residue 201 PHE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 336 CYS Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 421 TYR Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 656 VAL Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 734 THR Chi-restraints excluded: chain F residue 752 LEU Chi-restraints excluded: chain F residue 775 ASP Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 796 TYR Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 941 THR Chi-restraints excluded: chain F residue 976 VAL Chi-restraints excluded: chain F residue 995 ARG Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1018 ILE Chi-restraints excluded: chain F residue 1076 THR Chi-restraints excluded: chain F residue 1101 HIS Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1120 THR Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain F residue 1133 VAL Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain J residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 2 optimal weight: 20.0000 chunk 362 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 302 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 158 optimal weight: 20.0000 chunk 124 optimal weight: 1.9990 chunk 323 optimal weight: 8.9990 chunk 237 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 GLN ** E 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 317 ASN ** E1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 690 GLN F 804 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.081715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.061335 restraints weight = 244853.680| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 5.91 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.7596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 30981 Z= 0.159 Angle : 0.609 18.870 42177 Z= 0.312 Chirality : 0.044 0.181 4715 Planarity : 0.005 0.063 5443 Dihedral : 5.046 57.016 4177 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.17 % Favored : 91.64 % Rotamer: Outliers : 4.08 % Allowed : 24.32 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.50 % 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: -1.59 (0.13), residues: 3817 helix: 0.82 (0.21), residues: 646 sheet: -0.75 (0.18), residues: 839 loop : -1.81 (0.12), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 158 TYR 0.023 0.001 TYR F 453 PHE 0.019 0.001 PHE E 79 TRP 0.039 0.001 TRP H 36 HIS 0.011 0.001 HIS E 505 Details of bonding type rmsd covalent geometry : bond 0.00352 (30933) covalent geometry : angle 0.60807 (42081) SS BOND : bond 0.00405 ( 48) SS BOND : angle 1.03459 ( 96) hydrogen bonds : bond 0.03123 ( 941) hydrogen bonds : angle 5.19129 ( 2568) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 94 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 111 ASP cc_start: 0.8837 (t70) cc_final: 0.8503 (p0) REVERT: D 153 MET cc_start: 0.7871 (mpp) cc_final: 0.7390 (mpp) REVERT: D 177 MET cc_start: 0.4329 (ptm) cc_final: 0.4020 (ppp) REVERT: D 178 ASP cc_start: 0.7731 (p0) cc_final: 0.7322 (t0) REVERT: D 179 LEU cc_start: 0.5538 (OUTLIER) cc_final: 0.4977 (pp) REVERT: D 697 MET cc_start: 0.8868 (mmm) cc_final: 0.8508 (tmm) REVERT: D 796 TYR cc_start: 0.6949 (OUTLIER) cc_final: 0.6675 (m-10) REVERT: D 937 SER cc_start: 0.9473 (OUTLIER) cc_final: 0.9160 (p) REVERT: D 983 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8244 (mtm180) REVERT: D 1002 GLN cc_start: 0.9382 (mm-40) cc_final: 0.9181 (tm-30) REVERT: D 1018 ILE cc_start: 0.9791 (OUTLIER) cc_final: 0.9468 (tt) REVERT: D 1029 MET cc_start: 0.9644 (tpp) cc_final: 0.9358 (tpp) REVERT: D 1041 ASP cc_start: 0.8726 (t70) cc_final: 0.8520 (t0) REVERT: D 1113 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8570 (mp10) REVERT: E 14 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8217 (pm20) REVERT: E 26 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8365 (tp40) REVERT: E 111 ASP cc_start: 0.8828 (t70) cc_final: 0.8566 (p0) REVERT: E 113 LYS cc_start: 0.8851 (tptp) cc_final: 0.8628 (tptp) REVERT: E 140 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.8012 (t80) REVERT: E 559 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.7886 (t80) REVERT: E 644 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8724 (tp40) REVERT: E 725 GLU cc_start: 0.8670 (tt0) cc_final: 0.8418 (tt0) REVERT: E 745 ASP cc_start: 0.8974 (m-30) cc_final: 0.8143 (p0) REVERT: F 153 MET cc_start: 0.8592 (mpp) cc_final: 0.8076 (mpp) REVERT: F 201 PHE cc_start: 0.9458 (OUTLIER) cc_final: 0.9250 (t80) REVERT: F 468 ILE cc_start: 0.7357 (OUTLIER) cc_final: 0.6580 (tp) REVERT: F 697 MET cc_start: 0.8794 (mmm) cc_final: 0.8492 (tpt) REVERT: F 725 GLU cc_start: 0.8773 (tt0) cc_final: 0.8465 (tt0) REVERT: F 752 LEU cc_start: 0.9774 (OUTLIER) cc_final: 0.9519 (tt) REVERT: F 775 ASP cc_start: 0.9135 (OUTLIER) cc_final: 0.8920 (m-30) REVERT: F 1002 GLN cc_start: 0.9392 (mm-40) cc_final: 0.9136 (mm-40) REVERT: F 1018 ILE cc_start: 0.9762 (OUTLIER) cc_final: 0.9438 (tt) REVERT: F 1029 MET cc_start: 0.9643 (tpp) cc_final: 0.9187 (tpp) REVERT: F 1113 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8529 (mp-120) REVERT: I 29 PHE cc_start: 0.4601 (OUTLIER) cc_final: 0.4215 (p90) outliers start: 137 outliers final: 95 residues processed: 225 average time/residue: 0.1463 time to fit residues: 57.0943 Evaluate side-chains 195 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 82 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 796 TYR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 906 PHE Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 983 ARG Chi-restraints excluded: chain D residue 985 ASP Chi-restraints excluded: chain D residue 1018 ILE Chi-restraints excluded: chain D residue 1048 HIS Chi-restraints excluded: chain D residue 1055 SER Chi-restraints excluded: chain D residue 1101 HIS Chi-restraints excluded: chain D residue 1113 GLN Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 77 LYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 140 PHE Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 317 ASN Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 587 ILE Chi-restraints excluded: chain E residue 591 SER Chi-restraints excluded: chain E residue 644 GLN Chi-restraints excluded: chain E residue 656 VAL Chi-restraints excluded: chain E residue 714 ILE Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 796 TYR Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 887 THR Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 991 VAL Chi-restraints excluded: chain E residue 1061 VAL Chi-restraints excluded: chain E residue 1084 ASP Chi-restraints excluded: chain E residue 1101 HIS Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain E residue 1120 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 66 HIS Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 201 PHE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 336 CYS Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 421 TYR Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 656 VAL Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 734 THR Chi-restraints excluded: chain F residue 752 LEU Chi-restraints excluded: chain F residue 775 ASP Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 941 THR Chi-restraints excluded: chain F residue 976 VAL Chi-restraints excluded: chain F residue 985 ASP Chi-restraints excluded: chain F residue 995 ARG Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1018 ILE Chi-restraints excluded: chain F residue 1077 THR Chi-restraints excluded: chain F residue 1101 HIS Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1113 GLN Chi-restraints excluded: chain F residue 1120 THR Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain F residue 1133 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain I residue 29 PHE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain J residue 47 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 291 optimal weight: 10.0000 chunk 376 optimal weight: 30.0000 chunk 175 optimal weight: 50.0000 chunk 312 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 357 optimal weight: 7.9990 chunk 203 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 309 optimal weight: 7.9990 chunk 5 optimal weight: 40.0000 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 17 ASN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 920 GLN E 14 GLN ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 935 GLN ** E1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 690 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.080426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.056499 restraints weight = 215154.560| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 7.47 r_work: 0.3013 rms_B_bonded: 6.90 restraints_weight: 2.0000 r_work: 0.3077 rms_B_bonded: 5.70 restraints_weight: 4.0000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.8272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 30981 Z= 0.229 Angle : 0.647 13.425 42177 Z= 0.335 Chirality : 0.044 0.184 4715 Planarity : 0.005 0.067 5443 Dihedral : 5.174 57.648 4177 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.75 % Favored : 91.07 % Rotamer: Outliers : 4.59 % Allowed : 24.20 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -1.66 (0.13), residues: 3817 helix: 0.92 (0.21), residues: 636 sheet: -0.92 (0.18), residues: 862 loop : -1.84 (0.13), residues: 2319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 905 TYR 0.025 0.002 TYR F 453 PHE 0.024 0.002 PHE D 192 TRP 0.036 0.002 TRP G 36 HIS 0.010 0.001 HIS E 505 Details of bonding type rmsd covalent geometry : bond 0.00494 (30933) covalent geometry : angle 0.64382 (42081) SS BOND : bond 0.00689 ( 48) SS BOND : angle 1.46009 ( 96) hydrogen bonds : bond 0.03358 ( 941) hydrogen bonds : angle 5.32626 ( 2568) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 79 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 111 ASP cc_start: 0.8917 (t70) cc_final: 0.8624 (p0) REVERT: D 113 LYS cc_start: 0.9060 (tptp) cc_final: 0.8779 (tptp) REVERT: D 529 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8477 (ptpp) REVERT: D 697 MET cc_start: 0.8952 (mmm) cc_final: 0.8660 (tmm) REVERT: D 796 TYR cc_start: 0.6697 (OUTLIER) cc_final: 0.6273 (m-10) REVERT: D 975 SER cc_start: 0.9482 (OUTLIER) cc_final: 0.9147 (m) REVERT: D 983 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8568 (mtm110) REVERT: D 1002 GLN cc_start: 0.9528 (mm-40) cc_final: 0.9306 (mm-40) REVERT: E 17 ASN cc_start: 0.6341 (OUTLIER) cc_final: 0.6093 (m-40) REVERT: E 111 ASP cc_start: 0.8908 (t70) cc_final: 0.8578 (p0) REVERT: E 113 LYS cc_start: 0.9049 (tptp) cc_final: 0.8824 (tptp) REVERT: E 559 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.7901 (t80) REVERT: E 725 GLU cc_start: 0.8843 (tt0) cc_final: 0.8625 (tt0) REVERT: E 745 ASP cc_start: 0.8975 (m-30) cc_final: 0.7969 (p0) REVERT: F 111 ASP cc_start: 0.9036 (t70) cc_final: 0.8670 (p0) REVERT: F 242 LEU cc_start: 0.8208 (tp) cc_final: 0.7890 (tp) REVERT: F 468 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7730 (mm) REVERT: F 587 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8572 (mp) REVERT: F 725 GLU cc_start: 0.8932 (tt0) cc_final: 0.8721 (tt0) REVERT: F 775 ASP cc_start: 0.9064 (OUTLIER) cc_final: 0.8842 (m-30) REVERT: F 1002 GLN cc_start: 0.9561 (mm-40) cc_final: 0.9338 (mm-40) REVERT: F 1029 MET cc_start: 0.9650 (tpp) cc_final: 0.9429 (tpp) outliers start: 154 outliers final: 105 residues processed: 224 average time/residue: 0.1438 time to fit residues: 56.4504 Evaluate side-chains 192 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 78 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 796 TYR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 975 SER Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 983 ARG Chi-restraints excluded: chain D residue 985 ASP Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain D residue 1048 HIS Chi-restraints excluded: chain D residue 1050 MET Chi-restraints excluded: chain D residue 1055 SER Chi-restraints excluded: chain D residue 1101 HIS Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 77 LYS Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 587 ILE Chi-restraints excluded: chain E residue 591 SER Chi-restraints excluded: chain E residue 656 VAL Chi-restraints excluded: chain E residue 714 ILE Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain E residue 732 THR Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 796 TYR Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 887 THR Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 991 VAL Chi-restraints excluded: chain E residue 1061 VAL Chi-restraints excluded: chain E residue 1084 ASP Chi-restraints excluded: chain E residue 1101 HIS Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain E residue 1120 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 66 HIS Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 201 PHE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 317 ASN Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 336 CYS Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 421 TYR Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 546 LEU Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 591 SER Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 656 VAL Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 734 THR Chi-restraints excluded: chain F residue 775 ASP Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 912 THR Chi-restraints excluded: chain F residue 941 THR Chi-restraints excluded: chain F residue 976 VAL Chi-restraints excluded: chain F residue 985 ASP Chi-restraints excluded: chain F residue 995 ARG Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1077 THR Chi-restraints excluded: chain F residue 1101 HIS Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1120 THR Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain F residue 1133 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain J residue 47 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 178 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 184 optimal weight: 0.9990 chunk 273 optimal weight: 0.2980 chunk 196 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 chunk 333 optimal weight: 0.9990 chunk 181 optimal weight: 8.9990 chunk 356 optimal weight: 50.0000 chunk 81 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 207 HIS ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 GLN E 17 ASN ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 690 GLN F1106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.080406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.059180 restraints weight = 241386.258| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 5.72 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.8609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 30981 Z= 0.174 Angle : 0.618 13.812 42177 Z= 0.317 Chirality : 0.044 0.198 4715 Planarity : 0.005 0.065 5443 Dihedral : 5.114 57.372 4177 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.12 % Favored : 91.70 % Rotamer: Outliers : 3.79 % Allowed : 24.98 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -1.62 (0.14), residues: 3817 helix: 0.93 (0.21), residues: 641 sheet: -0.92 (0.18), residues: 849 loop : -1.79 (0.13), residues: 2327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 905 TYR 0.023 0.001 TYR F 453 PHE 0.018 0.001 PHE E 79 TRP 0.038 0.002 TRP G 36 HIS 0.009 0.001 HIS E 505 Details of bonding type rmsd covalent geometry : bond 0.00382 (30933) covalent geometry : angle 0.61667 (42081) SS BOND : bond 0.00343 ( 48) SS BOND : angle 1.07850 ( 96) hydrogen bonds : bond 0.03138 ( 941) hydrogen bonds : angle 5.22234 ( 2568) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 84 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 111 ASP cc_start: 0.8926 (t70) cc_final: 0.8637 (p0) REVERT: D 153 MET cc_start: 0.7763 (mpp) cc_final: 0.7241 (mpp) REVERT: D 697 MET cc_start: 0.8872 (mmm) cc_final: 0.8576 (tmm) REVERT: D 796 TYR cc_start: 0.6967 (OUTLIER) cc_final: 0.6617 (m-10) REVERT: D 937 SER cc_start: 0.9598 (OUTLIER) cc_final: 0.9280 (p) REVERT: D 983 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8489 (mtm110) REVERT: D 1002 GLN cc_start: 0.9425 (mm-40) cc_final: 0.9201 (tm-30) REVERT: D 1018 ILE cc_start: 0.9785 (OUTLIER) cc_final: 0.9470 (tt) REVERT: D 1029 MET cc_start: 0.9649 (tpp) cc_final: 0.9340 (tpp) REVERT: D 1113 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8468 (mp10) REVERT: E 111 ASP cc_start: 0.8809 (t70) cc_final: 0.8447 (p0) REVERT: E 113 LYS cc_start: 0.8988 (tptp) cc_final: 0.8769 (tptp) REVERT: E 362 VAL cc_start: 0.7484 (OUTLIER) cc_final: 0.7259 (m) REVERT: E 559 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.7950 (t80) REVERT: E 725 GLU cc_start: 0.8669 (tt0) cc_final: 0.8372 (tt0) REVERT: E 745 ASP cc_start: 0.9025 (m-30) cc_final: 0.8096 (p0) REVERT: F 111 ASP cc_start: 0.9077 (t70) cc_final: 0.8712 (p0) REVERT: F 180 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7581 (tp30) REVERT: F 242 LEU cc_start: 0.8216 (tp) cc_final: 0.7919 (tp) REVERT: F 468 ILE cc_start: 0.7467 (OUTLIER) cc_final: 0.6951 (mm) REVERT: F 587 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8632 (mp) REVERT: F 725 GLU cc_start: 0.8782 (tt0) cc_final: 0.8462 (tt0) REVERT: F 775 ASP cc_start: 0.9133 (OUTLIER) cc_final: 0.8921 (m-30) REVERT: F 1002 GLN cc_start: 0.9410 (mm-40) cc_final: 0.9147 (mm-40) REVERT: F 1029 MET cc_start: 0.9651 (tpp) cc_final: 0.9366 (tpp) REVERT: F 1113 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8527 (mp-120) REVERT: G 36 TRP cc_start: 0.5523 (m100) cc_final: 0.4759 (m100) outliers start: 127 outliers final: 97 residues processed: 204 average time/residue: 0.1575 time to fit residues: 55.3514 Evaluate side-chains 184 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 75 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 796 TYR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 983 ARG Chi-restraints excluded: chain D residue 985 ASP Chi-restraints excluded: chain D residue 1018 ILE Chi-restraints excluded: chain D residue 1048 HIS Chi-restraints excluded: chain D residue 1055 SER Chi-restraints excluded: chain D residue 1101 HIS Chi-restraints excluded: chain D residue 1113 GLN Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 77 LYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 587 ILE Chi-restraints excluded: chain E residue 591 SER Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain E residue 732 THR Chi-restraints excluded: chain E residue 740 MET Chi-restraints excluded: chain E residue 796 TYR Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 991 VAL Chi-restraints excluded: chain E residue 1061 VAL Chi-restraints excluded: chain E residue 1084 ASP Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain E residue 1120 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 66 HIS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 194 PHE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 317 ASN Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 336 CYS Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 421 TYR Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 546 LEU Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 690 GLN Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 734 THR Chi-restraints excluded: chain F residue 775 ASP Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 796 TYR Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 912 THR Chi-restraints excluded: chain F residue 941 THR Chi-restraints excluded: chain F residue 976 VAL Chi-restraints excluded: chain F residue 985 ASP Chi-restraints excluded: chain F residue 995 ARG Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1077 THR Chi-restraints excluded: chain F residue 1101 HIS Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1106 GLN Chi-restraints excluded: chain F residue 1113 GLN Chi-restraints excluded: chain F residue 1120 THR Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain F residue 1133 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain J residue 47 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 144 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 351 optimal weight: 30.0000 chunk 213 optimal weight: 4.9990 chunk 158 optimal weight: 0.9980 chunk 356 optimal weight: 50.0000 chunk 148 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 246 optimal weight: 0.9990 chunk 240 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 GLN ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 856 ASN ** E1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 690 GLN F1106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.079759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.058654 restraints weight = 241851.208| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 5.65 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.8838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30981 Z= 0.176 Angle : 0.631 13.983 42177 Z= 0.319 Chirality : 0.044 0.211 4715 Planarity : 0.005 0.065 5443 Dihedral : 5.096 56.914 4175 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.44 % Favored : 91.38 % Rotamer: Outliers : 3.79 % Allowed : 25.22 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -1.61 (0.14), residues: 3817 helix: 0.91 (0.21), residues: 640 sheet: -0.90 (0.18), residues: 819 loop : -1.78 (0.13), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 158 TYR 0.023 0.001 TYR F 453 PHE 0.019 0.001 PHE E 79 TRP 0.031 0.002 TRP G 36 HIS 0.009 0.001 HIS E 505 Details of bonding type rmsd covalent geometry : bond 0.00386 (30933) covalent geometry : angle 0.62937 (42081) SS BOND : bond 0.00346 ( 48) SS BOND : angle 1.06344 ( 96) hydrogen bonds : bond 0.03155 ( 941) hydrogen bonds : angle 5.22430 ( 2568) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 76 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 111 ASP cc_start: 0.8944 (t70) cc_final: 0.8660 (p0) REVERT: D 113 LYS cc_start: 0.9091 (tptp) cc_final: 0.8868 (tppt) REVERT: D 153 MET cc_start: 0.7844 (mpp) cc_final: 0.7303 (mpp) REVERT: D 697 MET cc_start: 0.8841 (mmm) cc_final: 0.8562 (tmm) REVERT: D 796 TYR cc_start: 0.6950 (OUTLIER) cc_final: 0.6611 (m-10) REVERT: D 937 SER cc_start: 0.9608 (OUTLIER) cc_final: 0.9291 (p) REVERT: D 983 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8313 (mtm180) REVERT: D 1002 GLN cc_start: 0.9419 (mm-40) cc_final: 0.9196 (tm-30) REVERT: D 1018 ILE cc_start: 0.9783 (OUTLIER) cc_final: 0.9450 (tt) REVERT: D 1029 MET cc_start: 0.9641 (tpp) cc_final: 0.9322 (tpp) REVERT: D 1113 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8457 (mp10) REVERT: E 111 ASP cc_start: 0.8850 (t70) cc_final: 0.8466 (p0) REVERT: E 113 LYS cc_start: 0.8983 (tptp) cc_final: 0.8766 (tptp) REVERT: E 362 VAL cc_start: 0.7666 (OUTLIER) cc_final: 0.7445 (m) REVERT: E 559 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.8036 (t80) REVERT: E 587 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8780 (mp) REVERT: E 725 GLU cc_start: 0.8675 (tt0) cc_final: 0.8369 (tt0) REVERT: E 745 ASP cc_start: 0.9002 (m-30) cc_final: 0.8060 (p0) REVERT: E 983 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8370 (mtm110) REVERT: F 111 ASP cc_start: 0.9084 (t70) cc_final: 0.8747 (p0) REVERT: F 180 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7602 (tp30) REVERT: F 242 LEU cc_start: 0.8069 (tp) cc_final: 0.7795 (tp) REVERT: F 468 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.6903 (mm) REVERT: F 587 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8649 (mp) REVERT: F 690 GLN cc_start: 0.6653 (OUTLIER) cc_final: 0.6324 (pm20) REVERT: F 725 GLU cc_start: 0.8798 (tt0) cc_final: 0.8472 (tt0) REVERT: F 775 ASP cc_start: 0.9123 (OUTLIER) cc_final: 0.8910 (m-30) REVERT: F 1002 GLN cc_start: 0.9400 (mm-40) cc_final: 0.9140 (mm-40) REVERT: F 1018 ILE cc_start: 0.9736 (OUTLIER) cc_final: 0.9514 (tt) REVERT: F 1029 MET cc_start: 0.9648 (tpp) cc_final: 0.9362 (tpp) REVERT: F 1113 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8483 (mp-120) REVERT: G 36 TRP cc_start: 0.5647 (m100) cc_final: 0.5031 (m100) REVERT: H 51 ILE cc_start: 0.7681 (tt) cc_final: 0.7457 (tt) outliers start: 127 outliers final: 100 residues processed: 198 average time/residue: 0.1581 time to fit residues: 54.6622 Evaluate side-chains 189 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 73 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 796 TYR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 983 ARG Chi-restraints excluded: chain D residue 985 ASP Chi-restraints excluded: chain D residue 1018 ILE Chi-restraints excluded: chain D residue 1048 HIS Chi-restraints excluded: chain D residue 1055 SER Chi-restraints excluded: chain D residue 1101 HIS Chi-restraints excluded: chain D residue 1113 GLN Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 77 LYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 587 ILE Chi-restraints excluded: chain E residue 591 SER Chi-restraints excluded: chain E residue 714 ILE Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain E residue 732 THR Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 796 TYR Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 983 ARG Chi-restraints excluded: chain E residue 991 VAL Chi-restraints excluded: chain E residue 1061 VAL Chi-restraints excluded: chain E residue 1084 ASP Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain E residue 1120 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 66 HIS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 201 PHE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 317 ASN Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 336 CYS Chi-restraints excluded: chain F residue 421 TYR Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 546 LEU Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 591 SER Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 656 VAL Chi-restraints excluded: chain F residue 690 GLN Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 734 THR Chi-restraints excluded: chain F residue 775 ASP Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 912 THR Chi-restraints excluded: chain F residue 941 THR Chi-restraints excluded: chain F residue 985 ASP Chi-restraints excluded: chain F residue 995 ARG Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1018 ILE Chi-restraints excluded: chain F residue 1077 THR Chi-restraints excluded: chain F residue 1101 HIS Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1106 GLN Chi-restraints excluded: chain F residue 1113 GLN Chi-restraints excluded: chain F residue 1120 THR Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain F residue 1133 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain J residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 190 optimal weight: 8.9990 chunk 280 optimal weight: 9.9990 chunk 160 optimal weight: 0.2980 chunk 193 optimal weight: 0.2980 chunk 376 optimal weight: 30.0000 chunk 123 optimal weight: 6.9990 chunk 364 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 246 optimal weight: 3.9990 chunk 337 optimal weight: 3.9990 chunk 173 optimal weight: 20.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 GLN E 17 ASN ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 ASN E 856 ASN ** E1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 690 GLN H 32 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.080046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.058672 restraints weight = 238412.377| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 5.64 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.9041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 30981 Z= 0.164 Angle : 0.623 14.049 42177 Z= 0.315 Chirality : 0.044 0.188 4715 Planarity : 0.005 0.064 5443 Dihedral : 5.044 56.640 4175 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.28 % Favored : 91.54 % Rotamer: Outliers : 3.67 % Allowed : 25.45 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -1.58 (0.14), residues: 3817 helix: 1.05 (0.22), residues: 623 sheet: -0.98 (0.18), residues: 859 loop : -1.74 (0.13), residues: 2335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 158 TYR 0.023 0.001 TYR F 453 PHE 0.019 0.001 PHE E 79 TRP 0.033 0.001 TRP G 36 HIS 0.009 0.001 HIS E 505 Details of bonding type rmsd covalent geometry : bond 0.00365 (30933) covalent geometry : angle 0.62123 (42081) SS BOND : bond 0.00302 ( 48) SS BOND : angle 1.04392 ( 96) hydrogen bonds : bond 0.03101 ( 941) hydrogen bonds : angle 5.18497 ( 2568) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 78 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 111 ASP cc_start: 0.8943 (t70) cc_final: 0.8661 (p0) REVERT: D 153 MET cc_start: 0.7794 (mpp) cc_final: 0.7264 (mpp) REVERT: D 177 MET cc_start: 0.6046 (ppp) cc_final: 0.5809 (ppp) REVERT: D 178 ASP cc_start: 0.8412 (p0) cc_final: 0.7578 (t0) REVERT: D 529 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8510 (ptpp) REVERT: D 697 MET cc_start: 0.8835 (mmm) cc_final: 0.8563 (tmm) REVERT: D 796 TYR cc_start: 0.6980 (OUTLIER) cc_final: 0.6596 (m-10) REVERT: D 937 SER cc_start: 0.9580 (OUTLIER) cc_final: 0.9262 (p) REVERT: D 983 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8315 (mtm180) REVERT: D 1002 GLN cc_start: 0.9408 (mm-40) cc_final: 0.9191 (tm-30) REVERT: D 1018 ILE cc_start: 0.9765 (OUTLIER) cc_final: 0.9419 (tt) REVERT: D 1029 MET cc_start: 0.9649 (tpp) cc_final: 0.9336 (tpp) REVERT: D 1113 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8502 (mp10) REVERT: E 111 ASP cc_start: 0.8797 (t70) cc_final: 0.8404 (p0) REVERT: E 113 LYS cc_start: 0.9000 (tptp) cc_final: 0.8789 (tptp) REVERT: E 362 VAL cc_start: 0.7689 (OUTLIER) cc_final: 0.7473 (m) REVERT: E 559 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8130 (t80) REVERT: E 587 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8785 (mp) REVERT: E 725 GLU cc_start: 0.8611 (tt0) cc_final: 0.8211 (tt0) REVERT: E 745 ASP cc_start: 0.9041 (m-30) cc_final: 0.8094 (p0) REVERT: E 983 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8474 (mtm110) REVERT: F 111 ASP cc_start: 0.9072 (t70) cc_final: 0.8749 (p0) REVERT: F 180 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7644 (tp30) REVERT: F 242 LEU cc_start: 0.8022 (tp) cc_final: 0.7741 (tp) REVERT: F 468 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.6850 (mm) REVERT: F 587 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8665 (mp) REVERT: F 725 GLU cc_start: 0.8754 (tt0) cc_final: 0.8419 (tt0) REVERT: F 775 ASP cc_start: 0.9113 (OUTLIER) cc_final: 0.8899 (m-30) REVERT: F 995 ARG cc_start: 0.9377 (OUTLIER) cc_final: 0.8914 (ptp-110) REVERT: F 1002 GLN cc_start: 0.9415 (mm-40) cc_final: 0.9153 (mm-40) REVERT: F 1018 ILE cc_start: 0.9728 (OUTLIER) cc_final: 0.9508 (tt) REVERT: F 1029 MET cc_start: 0.9657 (tpp) cc_final: 0.9367 (tpp) REVERT: F 1113 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8557 (mp-120) REVERT: G 36 TRP cc_start: 0.5555 (m100) cc_final: 0.5158 (m100) REVERT: H 51 ILE cc_start: 0.7697 (tt) cc_final: 0.7443 (tt) outliers start: 123 outliers final: 98 residues processed: 194 average time/residue: 0.1577 time to fit residues: 53.1500 Evaluate side-chains 190 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 75 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 796 TYR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 983 ARG Chi-restraints excluded: chain D residue 985 ASP Chi-restraints excluded: chain D residue 1018 ILE Chi-restraints excluded: chain D residue 1048 HIS Chi-restraints excluded: chain D residue 1050 MET Chi-restraints excluded: chain D residue 1055 SER Chi-restraints excluded: chain D residue 1101 HIS Chi-restraints excluded: chain D residue 1113 GLN Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 587 ILE Chi-restraints excluded: chain E residue 591 SER Chi-restraints excluded: chain E residue 732 THR Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 796 TYR Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 983 ARG Chi-restraints excluded: chain E residue 991 VAL Chi-restraints excluded: chain E residue 1061 VAL Chi-restraints excluded: chain E residue 1084 ASP Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain E residue 1120 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 66 HIS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 194 PHE Chi-restraints excluded: chain F residue 201 PHE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 317 ASN Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 336 CYS Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 421 TYR Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 546 LEU Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 591 SER Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 656 VAL Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 734 THR Chi-restraints excluded: chain F residue 775 ASP Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 796 TYR Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 900 MET Chi-restraints excluded: chain F residue 941 THR Chi-restraints excluded: chain F residue 985 ASP Chi-restraints excluded: chain F residue 995 ARG Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1018 ILE Chi-restraints excluded: chain F residue 1077 THR Chi-restraints excluded: chain F residue 1101 HIS Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1113 GLN Chi-restraints excluded: chain F residue 1120 THR Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain F residue 1133 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain J residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 320 optimal weight: 4.9990 chunk 160 optimal weight: 10.0000 chunk 317 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 168 optimal weight: 30.0000 chunk 162 optimal weight: 8.9990 chunk 152 optimal weight: 9.9990 chunk 326 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 361 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 GLN E 17 ASN ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 ASN E 856 ASN ** E1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 690 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.079960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.058779 restraints weight = 240878.009| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 5.63 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.9050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.167 30981 Z= 0.212 Angle : 0.742 59.140 42177 Z= 0.400 Chirality : 0.049 1.477 4715 Planarity : 0.005 0.124 5443 Dihedral : 5.057 56.619 4175 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.49 % Favored : 91.30 % Rotamer: Outliers : 3.85 % Allowed : 25.31 % Favored : 70.85 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.99 % 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: -1.58 (0.14), residues: 3817 helix: 1.05 (0.22), residues: 623 sheet: -0.99 (0.18), residues: 859 loop : -1.74 (0.13), residues: 2335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 158 TYR 0.054 0.001 TYR D 351 PHE 0.019 0.001 PHE E 79 TRP 0.028 0.001 TRP G 36 HIS 0.008 0.001 HIS E 505 Details of bonding type rmsd covalent geometry : bond 0.00447 (30933) covalent geometry : angle 0.74159 (42081) SS BOND : bond 0.00276 ( 48) SS BOND : angle 0.99772 ( 96) hydrogen bonds : bond 0.03101 ( 941) hydrogen bonds : angle 5.18736 ( 2568) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9560.12 seconds wall clock time: 163 minutes 47.52 seconds (9827.52 seconds total)