Starting phenix.real_space_refine on Sat Feb 7 16:38:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ker_37165/02_2026/8ker_37165.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ker_37165/02_2026/8ker_37165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ker_37165/02_2026/8ker_37165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ker_37165/02_2026/8ker_37165.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ker_37165/02_2026/8ker_37165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ker_37165/02_2026/8ker_37165.map" } resolution = 2.95 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= 0.002 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 144 5.16 5 C 22128 2.51 5 N 5829 2.21 5 O 6702 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 147 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34803 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 8331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8331 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 57, 'TRANS': 1007} Chain breaks: 3 Chain: "H" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1631 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain: "I" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1639 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 10, 'TRANS': 207} Chain: "A" Number of atoms: 8331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8331 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 57, 'TRANS': 1007} Chain breaks: 3 Chain: "D" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1631 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain: "E" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1639 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 10, 'TRANS': 207} Chain: "B" Number of atoms: 8331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8331 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 57, 'TRANS': 1007} Chain breaks: 3 Chain: "F" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1631 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain: "G" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1639 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 10, 'TRANS': 207} Time building chain proxies: 7.85, per 1000 atoms: 0.23 Number of scatterers: 34803 At special positions: 0 Unit cell: (177.31, 195.16, 204.68, 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 144 16.00 O 6702 8.00 N 5829 7.00 C 22128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 135 " - pdb=" SG CYS H 195 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.03 Simple disulfide: pdb=" SG CYS I 147 " - pdb=" SG CYS I 203 " distance=2.03 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 195 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 203 " distance=2.03 Simple disulfide: pdb=" SG CYS B 132 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 135 " - pdb=" SG CYS F 195 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.03 Simple disulfide: pdb=" SG CYS G 147 " - pdb=" SG CYS G 203 " 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: 3.01 Conformation dependent library (CDL) restraints added in 1.5 seconds 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8346 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 74 sheets defined 16.2% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'C' and resid 258 through 262 removed outlier: 4.430A pdb=" N GLY C 261 " --> pdb=" O TRP C 258 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA C 262 " --> pdb=" O THR C 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 258 through 262' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.859A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.107A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 546 removed outlier: 3.743A pdb=" N GLY C 545 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 754 removed outlier: 3.569A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.643A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 887 through 891 removed outlier: 4.010A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 removed outlier: 3.598A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 941 removed outlier: 6.867A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.739A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.591A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.942A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 129 removed outlier: 3.672A pdb=" N LEU H 126 " --> pdb=" O SER H 122 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS H 127 " --> pdb=" O ASP H 123 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER H 128 " --> pdb=" O GLU H 124 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY H 129 " --> pdb=" O GLN H 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 122 through 129' Processing helix chain 'I' and resid 192 through 196 removed outlier: 3.616A pdb=" N LEU I 196 " --> pdb=" O SER I 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 removed outlier: 4.424A pdb=" N GLY A 261 " --> pdb=" O TRP A 258 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A 262 " --> pdb=" O THR A 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 258 through 262' Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.512A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.920A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.070A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.617A pdb=" N GLY A 545 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.773A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.562A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.632A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 941 removed outlier: 4.327A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.938A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.604A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.579A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.837A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 removed outlier: 3.644A pdb=" N LEU D 126 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS D 127 " --> pdb=" O ASP D 123 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER D 128 " --> pdb=" O GLU D 124 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY D 129 " --> pdb=" O GLN D 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 122 through 129' Processing helix chain 'E' and resid 192 through 196 removed outlier: 3.645A pdb=" N LEU E 196 " --> pdb=" O SER E 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 removed outlier: 4.424A pdb=" N GLY B 261 " --> pdb=" O TRP B 258 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 262 " --> pdb=" O THR B 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 258 through 262' Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.529A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.856A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.041A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 748 through 754 removed outlier: 3.644A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.535A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.514A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.521A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.650A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 6.899A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.750A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.194A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.909A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 129 removed outlier: 3.645A pdb=" N LEU F 126 " --> pdb=" O SER F 122 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS F 127 " --> pdb=" O ASP F 123 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER F 128 " --> pdb=" O GLU F 124 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY F 129 " --> pdb=" O GLN F 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 122 through 129' Processing helix chain 'G' and resid 192 through 196 removed outlier: 3.698A pdb=" N LEU G 196 " --> pdb=" O SER G 193 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 30 through 32 removed outlier: 3.857A pdb=" N SER C 61 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 37 through 38 removed outlier: 7.318A pdb=" N VAL C 37 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AA4, first strand: chain 'C' and resid 49 through 56 removed outlier: 3.888A pdb=" N ASP C 54 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AA6, first strand: chain 'C' and resid 94 through 97 removed outlier: 4.101A pdb=" N SER C 95 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU C 97 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.353A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.907A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 453 removed outlier: 3.648A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 538 through 541 Processing sheet with id=AB2, first strand: chain 'C' and resid 565 through 566 removed outlier: 7.168A pdb=" N PHE C 565 " --> pdb=" O PHE A 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.965A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 701 through 703 removed outlier: 6.053A pdb=" N ALA C 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.159A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.159A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.209A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 1120 through 1121 Processing sheet with id=AB9, first strand: chain 'H' and resid 4 through 5 removed outlier: 3.645A pdb=" N ARG H 24 " --> pdb=" O THR H 5 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE H 71 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR H 72 " --> pdb=" O ARG H 65 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG H 65 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER H 63 " --> pdb=" O THR H 74 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 11 through 13 removed outlier: 3.825A pdb=" N LEU H 11 " --> pdb=" O LYS H 104 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU H 106 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR H 87 " --> pdb=" O TYR H 36 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 115 through 119 removed outlier: 3.543A pdb=" N SER H 115 " --> pdb=" O ASN H 138 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN H 138 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE H 117 " --> pdb=" O LEU H 136 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS H 135 " --> pdb=" O SER H 178 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER H 178 " --> pdb=" O CYS H 135 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TYR H 174 " --> pdb=" O ASN H 139 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER H 177 " --> pdb=" O SER H 163 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER H 163 " --> pdb=" O SER H 177 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN H 161 " --> pdb=" O THR H 179 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 146 through 151 removed outlier: 4.091A pdb=" N LYS H 146 " --> pdb=" O THR H 198 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR H 198 " --> pdb=" O LYS H 146 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS H 208 " --> pdb=" O CYS H 195 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 3 through 5 removed outlier: 3.809A pdb=" N ARG I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER I 77 " --> pdb=" O GLU I 72 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU I 72 " --> pdb=" O SER I 77 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR I 79 " --> pdb=" O SER I 70 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER I 70 " --> pdb=" O TYR I 79 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN I 81 " --> pdb=" O THR I 68 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 33 through 34 removed outlier: 4.182A pdb=" N ASP I 33 " --> pdb=" O GLY I 98 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 38 through 39 Processing sheet with id=AC7, first strand: chain 'I' and resid 127 through 131 removed outlier: 4.350A pdb=" N GLY I 146 " --> pdb=" O LEU I 131 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LYS I 150 " --> pdb=" O LEU I 185 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU I 185 " --> pdb=" O LYS I 150 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR I 152 " --> pdb=" O TYR I 183 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 159 through 161 Processing sheet with id=AC9, first strand: chain 'I' and resid 171 through 172 removed outlier: 3.850A pdb=" N VAL I 188 " --> pdb=" O HIS I 171 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 30 through 32 removed outlier: 3.556A pdb=" N SER A 32 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 61 " --> pdb=" O SER A 32 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 37 through 38 removed outlier: 7.335A pdb=" N VAL A 37 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 229 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 49 through 56 removed outlier: 3.582A pdb=" N ASP A 54 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 94 through 97 removed outlier: 3.590A pdb=" N SER A 95 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU A 97 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASN A 188 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.132A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.847A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.660A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'A' and resid 538 through 541 removed outlier: 3.874A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N PHE A 565 " --> pdb=" O PHE B 44 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.031A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.550A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.550A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.325A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AE5, first strand: chain 'D' and resid 4 through 5 removed outlier: 3.658A pdb=" N ARG D 24 " --> pdb=" O THR D 5 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR D 72 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG D 65 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER D 63 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 11 through 13 removed outlier: 7.086A pdb=" N LEU D 11 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR D 87 " --> pdb=" O TYR D 36 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU D 33 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N SER D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 115 through 119 removed outlier: 3.851A pdb=" N ASN D 138 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS D 135 " --> pdb=" O SER D 178 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER D 178 " --> pdb=" O CYS D 135 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TYR D 174 " --> pdb=" O ASN D 139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER D 177 " --> pdb=" O SER D 163 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER D 163 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN D 161 " --> pdb=" O THR D 179 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 146 through 151 removed outlier: 4.049A pdb=" N LYS D 146 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR D 198 " --> pdb=" O LYS D 146 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS D 208 " --> pdb=" O CYS D 195 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 3 through 5 removed outlier: 3.774A pdb=" N ARG E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU E 80 " --> pdb=" O LEU E 20 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER E 77 " --> pdb=" O GLU E 72 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU E 72 " --> pdb=" O SER E 77 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR E 79 " --> pdb=" O SER E 70 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER E 70 " --> pdb=" O TYR E 79 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN E 81 " --> pdb=" O THR E 68 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 33 through 34 removed outlier: 4.175A pdb=" N ASP E 33 " --> pdb=" O GLY E 98 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 38 through 39 Processing sheet with id=AF3, first strand: chain 'E' and resid 127 through 131 removed outlier: 4.314A pdb=" N GLY E 146 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LYS E 150 " --> pdb=" O LEU E 185 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU E 185 " --> pdb=" O LYS E 150 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR E 152 " --> pdb=" O TYR E 183 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 159 through 161 Processing sheet with id=AF5, first strand: chain 'E' and resid 171 through 172 removed outlier: 3.877A pdb=" N VAL E 188 " --> pdb=" O HIS E 171 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.513A pdb=" N SER B 32 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER B 61 " --> pdb=" O SER B 32 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 37 through 38 removed outlier: 7.319A pdb=" N VAL B 37 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 49 through 56 removed outlier: 3.829A pdb=" N ASP B 54 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE B 56 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AG1, first strand: chain 'B' and resid 94 through 97 removed outlier: 4.072A pdb=" N SER B 95 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU B 97 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN B 188 " --> pdb=" O GLU B 97 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 310 through 317 removed outlier: 6.786A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.541A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.992A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.641A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.010A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.105A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.105A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.157A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AH2, first strand: chain 'F' and resid 4 through 5 removed outlier: 3.710A pdb=" N ARG F 24 " --> pdb=" O THR F 5 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE F 71 " --> pdb=" O CYS F 23 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR F 72 " --> pdb=" O ARG F 65 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG F 65 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER F 63 " --> pdb=" O THR F 74 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 11 through 13 removed outlier: 7.034A pdb=" N LEU F 11 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR F 87 " --> pdb=" O TYR F 36 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU F 33 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N SER F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 115 through 119 removed outlier: 3.614A pdb=" N ASN F 138 " --> pdb=" O SER F 115 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE F 117 " --> pdb=" O LEU F 136 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER F 178 " --> pdb=" O CYS F 135 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR F 174 " --> pdb=" O ASN F 139 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER F 177 " --> pdb=" O SER F 163 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER F 163 " --> pdb=" O SER F 177 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN F 161 " --> pdb=" O THR F 179 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 146 through 151 removed outlier: 4.065A pdb=" N LYS F 146 " --> pdb=" O THR F 198 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR F 198 " --> pdb=" O LYS F 146 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS F 208 " --> pdb=" O CYS F 195 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 3 through 5 removed outlier: 3.807A pdb=" N ARG G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER G 77 " --> pdb=" O GLU G 72 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU G 72 " --> pdb=" O SER G 77 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR G 79 " --> pdb=" O SER G 70 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER G 70 " --> pdb=" O TYR G 79 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN G 81 " --> pdb=" O THR G 68 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 33 through 34 removed outlier: 4.121A pdb=" N ASP G 33 " --> pdb=" O GLY G 98 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AH9, first strand: chain 'G' and resid 127 through 131 removed outlier: 4.342A pdb=" N GLY G 146 " --> pdb=" O LEU G 131 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LYS G 150 " --> pdb=" O LEU G 185 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU G 185 " --> pdb=" O LYS G 150 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR G 152 " --> pdb=" O TYR G 183 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 159 through 161 Processing sheet with id=AI2, first strand: chain 'G' and resid 171 through 172 removed outlier: 3.832A pdb=" N VAL G 188 " --> pdb=" O HIS G 171 " (cutoff:3.500A) 927 hydrogen bonds defined for protein. 2529 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: 8.13 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11189 1.34 - 1.46: 8438 1.46 - 1.58: 15827 1.58 - 1.70: 0 1.70 - 1.82: 183 Bond restraints: 35637 Sorted by residual: bond pdb=" C GLN C 173 " pdb=" N PRO C 174 " ideal model delta sigma weight residual 1.333 1.352 -0.019 1.01e-02 9.80e+03 3.53e+00 bond pdb=" C GLN B 173 " pdb=" N PRO B 174 " ideal model delta sigma weight residual 1.333 1.352 -0.018 1.01e-02 9.80e+03 3.33e+00 bond pdb=" C GLN B1142 " pdb=" N PRO B1143 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.23e-02 6.61e+03 2.42e+00 bond pdb=" C GLN C1142 " pdb=" N PRO C1143 " ideal model delta sigma weight residual 1.336 1.351 -0.015 1.23e-02 6.61e+03 1.54e+00 bond pdb=" C GLN E 13 " pdb=" N PRO E 14 " ideal model delta sigma weight residual 1.332 1.345 -0.013 1.12e-02 7.97e+03 1.38e+00 ... (remaining 35632 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 47918 1.79 - 3.57: 528 3.57 - 5.36: 42 5.36 - 7.15: 6 7.15 - 8.93: 4 Bond angle restraints: 48498 Sorted by residual: angle pdb=" N VAL G 63 " pdb=" CA VAL G 63 " pdb=" C VAL G 63 " ideal model delta sigma weight residual 113.20 109.38 3.82 9.60e-01 1.09e+00 1.58e+01 angle pdb=" N PHE B 562 " pdb=" CA PHE B 562 " pdb=" C PHE B 562 " ideal model delta sigma weight residual 114.64 109.59 5.05 1.52e+00 4.33e-01 1.10e+01 angle pdb=" N ASP D 171 " pdb=" CA ASP D 171 " pdb=" C ASP D 171 " ideal model delta sigma weight residual 114.04 110.18 3.86 1.24e+00 6.50e-01 9.70e+00 angle pdb=" N ILE H 29 " pdb=" CA ILE H 29 " pdb=" C ILE H 29 " ideal model delta sigma weight residual 112.29 109.48 2.81 9.40e-01 1.13e+00 8.95e+00 angle pdb=" N ASP F 171 " pdb=" CA ASP F 171 " pdb=" C ASP F 171 " ideal model delta sigma weight residual 114.04 110.38 3.66 1.24e+00 6.50e-01 8.72e+00 ... (remaining 48493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 20290 16.05 - 32.11: 820 32.11 - 48.16: 135 48.16 - 64.21: 27 64.21 - 80.26: 4 Dihedral angle restraints: 21276 sinusoidal: 8256 harmonic: 13020 Sorted by residual: dihedral pdb=" CA ASP A 290 " pdb=" C ASP A 290 " pdb=" N CYS A 291 " pdb=" CA CYS A 291 " ideal model delta harmonic sigma weight residual 180.00 158.06 21.94 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ASP C 745 " pdb=" C ASP C 745 " pdb=" N SER C 746 " pdb=" CA SER C 746 " ideal model delta harmonic sigma weight residual 180.00 158.35 21.65 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA ASP B 745 " pdb=" C ASP B 745 " pdb=" N SER B 746 " pdb=" CA SER B 746 " ideal model delta harmonic sigma weight residual 180.00 162.64 17.36 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 21273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3300 0.027 - 0.054: 1371 0.054 - 0.081: 347 0.081 - 0.109: 388 0.109 - 0.136: 57 Chirality restraints: 5463 Sorted by residual: chirality pdb=" CB ILE B 210 " pdb=" CA ILE B 210 " pdb=" CG1 ILE B 210 " pdb=" CG2 ILE B 210 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CB ILE C 210 " pdb=" CA ILE C 210 " pdb=" CG1 ILE C 210 " pdb=" CG2 ILE C 210 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA VAL A 289 " pdb=" N VAL A 289 " pdb=" C VAL A 289 " pdb=" CB VAL A 289 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 5460 not shown) Planarity restraints: 6267 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " -0.031 5.00e-02 4.00e+02 4.79e-02 3.66e+00 pdb=" N PRO C 521 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 462 " -0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO C 463 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 463 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 463 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 462 " -0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO B 463 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 463 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 463 " -0.026 5.00e-02 4.00e+02 ... (remaining 6264 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3091 2.75 - 3.29: 33936 3.29 - 3.82: 56340 3.82 - 4.36: 64498 4.36 - 4.90: 112278 Nonbonded interactions: 270143 Sorted by model distance: nonbonded pdb=" OD1 ASN B 123 " pdb=" OG1 THR B 125 " model vdw 2.210 3.040 nonbonded pdb=" OE1 GLN C 314 " pdb=" OG SER C 596 " model vdw 2.217 3.040 nonbonded pdb=" OG SER B 884 " pdb=" OG1 THR B 887 " model vdw 2.246 3.040 nonbonded pdb=" OD2 ASP B 808 " pdb=" OG SER B 810 " model vdw 2.251 3.040 nonbonded pdb=" OG SER C 884 " pdb=" OG1 THR C 887 " model vdw 2.251 3.040 ... (remaining 270138 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } 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: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 33.360 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.090 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:7.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 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 : 0.002 0.044 35688 Z= 0.098 Angle : 0.472 8.933 48600 Z= 0.269 Chirality : 0.040 0.136 5463 Planarity : 0.004 0.048 6267 Dihedral : 8.484 80.263 12777 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.01 % Favored : 94.97 % Rotamer: Outliers : 4.69 % Allowed : 6.22 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.65 (0.11), residues: 4449 helix: 0.34 (0.20), residues: 616 sheet: -2.46 (0.16), residues: 835 loop : -3.26 (0.09), residues: 2998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1014 TYR 0.004 0.000 TYR A 39 PHE 0.008 0.001 PHE C 157 TRP 0.002 0.000 TRP D 97 HIS 0.002 0.000 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00173 (35637) covalent geometry : angle 0.47205 (48498) SS BOND : bond 0.00121 ( 51) SS BOND : angle 0.42538 ( 102) hydrogen bonds : bond 0.23247 ( 906) hydrogen bonds : angle 8.48818 ( 2529) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 398 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 PHE cc_start: 0.8471 (m-80) cc_final: 0.8099 (m-80) REVERT: C 190 ARG cc_start: 0.5790 (OUTLIER) cc_final: 0.4937 (mmm160) REVERT: C 291 CYS cc_start: 0.5832 (t) cc_final: 0.4775 (t) REVERT: C 758 SER cc_start: 0.8727 (m) cc_final: 0.8413 (p) REVERT: C 950 ASP cc_start: 0.8363 (t70) cc_final: 0.8103 (t0) REVERT: C 957 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8305 (tm-30) REVERT: C 1010 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8140 (mp10) REVERT: H 37 HIS cc_start: 0.5528 (t-170) cc_final: 0.5204 (t-90) REVERT: I 82 MET cc_start: 0.2219 (pmm) cc_final: 0.0811 (pmm) REVERT: A 54 ASP cc_start: 0.7939 (t70) cc_final: 0.7575 (t0) REVERT: A 105 TRP cc_start: 0.7415 (m-90) cc_final: 0.7030 (m-90) REVERT: A 136 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.7166 (m-80) REVERT: A 175 PHE cc_start: 0.5889 (p90) cc_final: 0.5381 (p90) REVERT: A 200 TYR cc_start: 0.9067 (m-80) cc_final: 0.8806 (m-80) REVERT: A 424 LYS cc_start: 0.3366 (OUTLIER) cc_final: 0.1917 (ttpp) REVERT: A 752 LEU cc_start: 0.9388 (pp) cc_final: 0.9163 (pp) REVERT: A 756 TYR cc_start: 0.7567 (m-80) cc_final: 0.7141 (m-10) REVERT: A 759 PHE cc_start: 0.8548 (m-80) cc_final: 0.7984 (m-80) REVERT: A 779 GLN cc_start: 0.8478 (tt0) cc_final: 0.8253 (tm-30) REVERT: A 854 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7560 (mppt) REVERT: E 56 ASP cc_start: 0.2657 (m-30) cc_final: 0.0790 (m-30) REVERT: E 104 ASN cc_start: 0.7158 (m110) cc_final: 0.6903 (m110) REVERT: E 106 TYR cc_start: 0.8631 (m-80) cc_final: 0.8345 (m-80) REVERT: E 120 VAL cc_start: 0.3121 (OUTLIER) cc_final: 0.2821 (t) REVERT: E 196 LEU cc_start: -0.3168 (OUTLIER) cc_final: -0.3735 (tm) REVERT: B 175 PHE cc_start: 0.6606 (p90) cc_final: 0.6326 (p90) REVERT: B 192 PHE cc_start: 0.8284 (m-80) cc_final: 0.7705 (m-10) REVERT: B 200 TYR cc_start: 0.8298 (m-80) cc_final: 0.8032 (m-80) REVERT: B 207 HIS cc_start: 0.6375 (t-170) cc_final: 0.5962 (m-70) REVERT: B 537 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8113 (tttt) REVERT: B 950 ASP cc_start: 0.8555 (t70) cc_final: 0.8335 (t0) REVERT: B 1010 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8742 (mp10) REVERT: F 35 TRP cc_start: 0.6679 (OUTLIER) cc_final: 0.5976 (t-100) REVERT: F 170 LYS cc_start: 0.7594 (tptt) cc_final: 0.7159 (pptt) REVERT: F 174 TYR cc_start: 0.5498 (m-80) cc_final: 0.4737 (m-10) REVERT: F 182 LEU cc_start: 0.3445 (OUTLIER) cc_final: 0.3236 (pt) REVERT: G 38 ARG cc_start: 0.8404 (ttm170) cc_final: 0.8091 (tmm-80) REVERT: G 90 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8269 (m) outliers start: 183 outliers final: 26 residues processed: 561 average time/residue: 0.6655 time to fit residues: 449.4122 Evaluate side-chains 249 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 210 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 148 GLN Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 124 LYS Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 148 GLN Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain F residue 35 TRP Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain G residue 1 GLU Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 105 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 40.0000 chunk 197 optimal weight: 40.0000 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 0.6980 chunk 424 optimal weight: 8.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 ASN C 100 ASN C 123 ASN C 164 ASN C 188 ASN C 207 HIS C 218 GLN C 271 GLN C 314 GLN C 360 ASN C 370 ASN C 409 GLN C 414 GLN C 487 ASN C 540 ASN C 563 GLN C 690 GLN C 762 GLN C 784 GLN C 853 GLN C 901 GLN C 914 ASN C 949 GLN C 957 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1011 GLN C1048 HIS C1119 ASN H 3 GLN H 89 GLN H 101 GLN H 148 GLN I 81 GLN A 70 HIS A 82 ASN A 88 ASN A 100 ASN A 123 ASN A 164 ASN A 207 HIS A 218 GLN A 271 GLN A 334 ASN A 339 HIS A 370 ASN A 409 GLN A 414 GLN A 448 ASN A 487 ASN A 532 ASN A 563 GLN A 710 ASN A 784 GLN A 853 GLN A 901 GLN A 913 GLN A 914 ASN A 949 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN A1011 GLN A1048 HIS A1119 ASN A1125 ASN D 3 GLN D 38 GLN D 89 GLN D 101 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN D 167 GLN D 200 GLN E 81 GLN E 204 ASN ** B 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 271 GLN B 334 ASN B 360 ASN B 370 ASN B 388 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN B 540 ASN B 563 GLN B 564 GLN B 613 GLN B 677 GLN B 690 GLN B 710 ASN B 784 GLN B 853 GLN B 901 GLN B 913 GLN B 914 ASN B 949 GLN B 965 GLN B 992 GLN B1010 GLN B1011 GLN B1048 HIS ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN B1125 ASN F 3 GLN F 38 GLN F 101 GLN F 148 GLN F 167 GLN Total number of N/Q/H flips: 105 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.145932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.092356 restraints weight = 127614.774| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 7.54 r_work: 0.2895 rms_B_bonded: 5.55 restraints_weight: 2.0000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 35688 Z= 0.273 Angle : 0.681 13.762 48600 Z= 0.345 Chirality : 0.047 0.292 5463 Planarity : 0.005 0.057 6267 Dihedral : 5.389 86.298 4924 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.92 % Favored : 93.05 % Rotamer: Outliers : 3.46 % Allowed : 10.73 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.12), residues: 4449 helix: 1.23 (0.21), residues: 631 sheet: -2.12 (0.16), residues: 847 loop : -2.90 (0.10), residues: 2971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 237 TYR 0.021 0.002 TYR C 707 PHE 0.033 0.002 PHE B 906 TRP 0.018 0.001 TRP C 436 HIS 0.010 0.001 HIS A 70 Details of bonding type rmsd covalent geometry : bond 0.00623 (35637) covalent geometry : angle 0.68061 (48498) SS BOND : bond 0.00338 ( 51) SS BOND : angle 0.84468 ( 102) hydrogen bonds : bond 0.04463 ( 906) hydrogen bonds : angle 5.92805 ( 2529) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 204 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 153 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8384 (ptt) REVERT: C 207 HIS cc_start: 0.8219 (t70) cc_final: 0.7623 (m-70) REVERT: C 265 TYR cc_start: 0.5029 (t80) cc_final: 0.4613 (t80) REVERT: C 855 PHE cc_start: 0.7169 (OUTLIER) cc_final: 0.6963 (p90) REVERT: C 950 ASP cc_start: 0.8971 (t70) cc_final: 0.8740 (t0) REVERT: C 1010 GLN cc_start: 0.9395 (OUTLIER) cc_final: 0.9005 (mp10) REVERT: H 104 LYS cc_start: 0.2850 (tmtt) cc_final: 0.2632 (mptt) REVERT: I 82 MET cc_start: 0.2747 (pmm) cc_final: 0.1481 (pmm) REVERT: A 41 ASP cc_start: 0.8813 (t0) cc_final: 0.8455 (p0) REVERT: A 105 TRP cc_start: 0.7646 (m-90) cc_final: 0.7373 (m-90) REVERT: A 175 PHE cc_start: 0.7131 (p90) cc_final: 0.6195 (p90) REVERT: A 177 MET cc_start: 0.5867 (tmm) cc_final: 0.4361 (tmm) REVERT: A 200 TYR cc_start: 0.9573 (m-80) cc_final: 0.9005 (m-80) REVERT: A 207 HIS cc_start: 0.8775 (t70) cc_final: 0.8569 (t-90) REVERT: A 759 PHE cc_start: 0.9066 (m-80) cc_final: 0.8729 (m-80) REVERT: A 854 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7555 (mppt) REVERT: E 104 ASN cc_start: 0.7370 (m110) cc_final: 0.7096 (m110) REVERT: E 106 TYR cc_start: 0.8495 (m-80) cc_final: 0.8222 (m-80) REVERT: E 120 VAL cc_start: 0.2561 (OUTLIER) cc_final: 0.2183 (t) REVERT: E 213 LYS cc_start: 0.2854 (tptt) cc_final: 0.1182 (mmtt) REVERT: B 175 PHE cc_start: 0.8160 (p90) cc_final: 0.7298 (p90) REVERT: B 178 ASP cc_start: 0.8573 (p0) cc_final: 0.8165 (p0) REVERT: B 200 TYR cc_start: 0.9381 (m-80) cc_final: 0.8870 (m-80) REVERT: B 599 THR cc_start: 0.9645 (OUTLIER) cc_final: 0.9250 (p) REVERT: B 740 MET cc_start: 0.9290 (tpp) cc_final: 0.9014 (ttp) REVERT: B 904 TYR cc_start: 0.9114 (m-10) cc_final: 0.8425 (m-10) REVERT: B 950 ASP cc_start: 0.9197 (t70) cc_final: 0.8922 (t0) REVERT: B 1010 GLN cc_start: 0.9413 (OUTLIER) cc_final: 0.9002 (mp10) REVERT: F 140 PHE cc_start: 0.3923 (p90) cc_final: 0.3710 (p90) REVERT: F 141 TYR cc_start: 0.5458 (t80) cc_final: 0.5132 (t80) REVERT: F 170 LYS cc_start: 0.7543 (tptt) cc_final: 0.7194 (pptt) REVERT: F 174 TYR cc_start: 0.5309 (m-80) cc_final: 0.4870 (m-10) REVERT: F 182 LEU cc_start: 0.4263 (OUTLIER) cc_final: 0.4002 (pt) outliers start: 135 outliers final: 52 residues processed: 315 average time/residue: 0.5792 time to fit residues: 222.8041 Evaluate side-chains 216 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 156 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain I residue 32 TYR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 124 LYS Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 108 TYR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain G residue 1 GLU Chi-restraints excluded: chain G residue 92 MET Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 120 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 74 optimal weight: 0.9990 chunk 251 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 378 optimal weight: 0.6980 chunk 255 optimal weight: 10.0000 chunk 379 optimal weight: 0.9980 chunk 361 optimal weight: 0.9980 chunk 288 optimal weight: 0.9980 chunk 315 optimal weight: 2.9990 chunk 44 optimal weight: 20.0000 chunk 301 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 913 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 GLN A 613 GLN A 690 GLN A 762 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 992 GLN B1088 HIS F 90 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.147098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.090471 restraints weight = 127684.949| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 8.12 r_work: 0.2973 rms_B_bonded: 5.51 restraints_weight: 2.0000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35688 Z= 0.117 Angle : 0.557 12.812 48600 Z= 0.274 Chirality : 0.043 0.214 5463 Planarity : 0.004 0.074 6267 Dihedral : 4.766 83.541 4883 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.00 % Favored : 93.98 % Rotamer: Outliers : 3.00 % Allowed : 11.67 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.12), residues: 4449 helix: 1.72 (0.21), residues: 624 sheet: -2.05 (0.16), residues: 834 loop : -2.66 (0.10), residues: 2991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 24 TYR 0.017 0.001 TYR E 32 PHE 0.027 0.001 PHE A 136 TRP 0.034 0.001 TRP F 35 HIS 0.004 0.001 HIS H 37 Details of bonding type rmsd covalent geometry : bond 0.00265 (35637) covalent geometry : angle 0.55610 (48498) SS BOND : bond 0.00141 ( 51) SS BOND : angle 0.73377 ( 102) hydrogen bonds : bond 0.03672 ( 906) hydrogen bonds : angle 5.39961 ( 2529) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 166 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 153 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8477 (ptt) REVERT: C 197 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8750 (pt) REVERT: C 207 HIS cc_start: 0.7965 (t70) cc_final: 0.7448 (m90) REVERT: C 265 TYR cc_start: 0.4731 (t80) cc_final: 0.4483 (t80) REVERT: C 581 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8431 (p) REVERT: C 950 ASP cc_start: 0.8833 (t70) cc_final: 0.8605 (t0) REVERT: C 1010 GLN cc_start: 0.9320 (OUTLIER) cc_final: 0.8941 (mp10) REVERT: A 42 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8055 (mtpp) REVERT: A 200 TYR cc_start: 0.9532 (m-80) cc_final: 0.8919 (m-80) REVERT: A 759 PHE cc_start: 0.8869 (m-80) cc_final: 0.8519 (m-80) REVERT: A 854 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7499 (mppt) REVERT: D 71 PHE cc_start: 0.0684 (m-80) cc_final: 0.0350 (m-10) REVERT: E 104 ASN cc_start: 0.7951 (m110) cc_final: 0.7731 (m110) REVERT: E 106 TYR cc_start: 0.8569 (m-80) cc_final: 0.8310 (m-80) REVERT: E 120 VAL cc_start: 0.4703 (OUTLIER) cc_final: 0.4456 (t) REVERT: E 150 LYS cc_start: -0.0507 (mppt) cc_final: -0.1027 (mmtt) REVERT: E 213 LYS cc_start: 0.3220 (tptt) cc_final: 0.2291 (mmtt) REVERT: B 42 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8620 (mtpp) REVERT: B 175 PHE cc_start: 0.8277 (p90) cc_final: 0.7483 (p90) REVERT: B 178 ASP cc_start: 0.8714 (p0) cc_final: 0.8307 (p0) REVERT: B 192 PHE cc_start: 0.8355 (m-80) cc_final: 0.8152 (m-10) REVERT: B 200 TYR cc_start: 0.9302 (m-80) cc_final: 0.8715 (m-80) REVERT: B 229 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8700 (pp) REVERT: B 457 ARG cc_start: 0.4160 (OUTLIER) cc_final: 0.3109 (mtm110) REVERT: B 599 THR cc_start: 0.9646 (OUTLIER) cc_final: 0.9243 (p) REVERT: B 904 TYR cc_start: 0.8962 (m-10) cc_final: 0.8259 (m-10) REVERT: B 950 ASP cc_start: 0.9015 (t70) cc_final: 0.8746 (t0) REVERT: B 1010 GLN cc_start: 0.9306 (OUTLIER) cc_final: 0.8892 (mp10) REVERT: F 141 TYR cc_start: 0.5862 (t80) cc_final: 0.5569 (t80) REVERT: F 170 LYS cc_start: 0.7465 (tptt) cc_final: 0.7185 (pptt) REVERT: F 174 TYR cc_start: 0.5328 (m-80) cc_final: 0.5117 (m-10) REVERT: G 38 ARG cc_start: 0.8854 (ttm170) cc_final: 0.8391 (tmm-80) REVERT: G 203 CYS cc_start: 0.3067 (p) cc_final: 0.2773 (p) outliers start: 117 outliers final: 49 residues processed: 264 average time/residue: 0.5469 time to fit residues: 178.9799 Evaluate side-chains 211 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 150 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 124 LYS Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain G residue 1 GLU Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 120 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 242 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 392 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 276 optimal weight: 0.0270 chunk 282 optimal weight: 20.0000 chunk 75 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 60 optimal weight: 0.0040 chunk 307 optimal weight: 0.4980 chunk 235 optimal weight: 3.9990 overall best weight: 0.3850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 HIS A 762 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 GLN B 409 GLN B 448 ASN B 913 GLN B 992 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.147813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.095323 restraints weight = 128007.177| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 7.55 r_work: 0.2973 rms_B_bonded: 5.39 restraints_weight: 2.0000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 35688 Z= 0.097 Angle : 0.537 12.251 48600 Z= 0.265 Chirality : 0.043 0.226 5463 Planarity : 0.004 0.075 6267 Dihedral : 4.689 81.965 4878 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.18 % Favored : 93.80 % Rotamer: Outliers : 2.94 % Allowed : 11.83 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.12), residues: 4449 helix: 1.95 (0.22), residues: 624 sheet: -2.08 (0.16), residues: 946 loop : -2.42 (0.10), residues: 2879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 403 TYR 0.016 0.001 TYR E 79 PHE 0.021 0.001 PHE A 141 TRP 0.016 0.001 TRP F 35 HIS 0.009 0.001 HIS H 37 Details of bonding type rmsd covalent geometry : bond 0.00219 (35637) covalent geometry : angle 0.53693 (48498) SS BOND : bond 0.00128 ( 51) SS BOND : angle 0.61313 ( 102) hydrogen bonds : bond 0.03213 ( 906) hydrogen bonds : angle 5.04961 ( 2529) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 164 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 197 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8700 (pt) REVERT: C 207 HIS cc_start: 0.7665 (t70) cc_final: 0.7176 (m90) REVERT: C 581 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8577 (p) REVERT: C 745 ASP cc_start: 0.9032 (m-30) cc_final: 0.8600 (p0) REVERT: C 855 PHE cc_start: 0.7354 (OUTLIER) cc_final: 0.6397 (p90) REVERT: C 950 ASP cc_start: 0.8922 (t70) cc_final: 0.8713 (t0) REVERT: C 1010 GLN cc_start: 0.9342 (OUTLIER) cc_final: 0.8980 (mp10) REVERT: I 79 TYR cc_start: 0.6034 (OUTLIER) cc_final: 0.5832 (t80) REVERT: A 143 ASP cc_start: 0.0938 (OUTLIER) cc_final: -0.0140 (p0) REVERT: A 177 MET cc_start: 0.7492 (tmm) cc_final: 0.7286 (tmm) REVERT: A 200 TYR cc_start: 0.9561 (m-80) cc_final: 0.8997 (m-80) REVERT: A 759 PHE cc_start: 0.8914 (m-80) cc_final: 0.8593 (m-80) REVERT: A 779 GLN cc_start: 0.9506 (tt0) cc_final: 0.9159 (tm-30) REVERT: A 854 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7475 (mppt) REVERT: E 104 ASN cc_start: 0.7011 (m110) cc_final: 0.6700 (m110) REVERT: E 106 TYR cc_start: 0.8577 (m-80) cc_final: 0.8266 (m-80) REVERT: E 120 VAL cc_start: 0.3412 (OUTLIER) cc_final: 0.3063 (t) REVERT: E 213 LYS cc_start: 0.3161 (tptt) cc_final: 0.2081 (mmtt) REVERT: B 153 MET cc_start: 0.8472 (pmm) cc_final: 0.8135 (ppp) REVERT: B 175 PHE cc_start: 0.7703 (p90) cc_final: 0.6878 (p90) REVERT: B 177 MET cc_start: 0.7411 (mmm) cc_final: 0.7046 (mmm) REVERT: B 178 ASP cc_start: 0.8445 (p0) cc_final: 0.8011 (p0) REVERT: B 192 PHE cc_start: 0.8400 (m-80) cc_final: 0.8181 (m-10) REVERT: B 200 TYR cc_start: 0.9344 (m-80) cc_final: 0.8779 (m-80) REVERT: B 571 ASP cc_start: 0.8522 (t0) cc_final: 0.8077 (p0) REVERT: B 599 THR cc_start: 0.9655 (OUTLIER) cc_final: 0.9272 (p) REVERT: B 904 TYR cc_start: 0.9031 (m-10) cc_final: 0.8444 (m-10) REVERT: B 950 ASP cc_start: 0.9107 (t70) cc_final: 0.8858 (t0) REVERT: B 1010 GLN cc_start: 0.9363 (OUTLIER) cc_final: 0.8980 (mp10) REVERT: F 140 PHE cc_start: 0.3303 (p90) cc_final: 0.3057 (p90) REVERT: F 141 TYR cc_start: 0.5804 (t80) cc_final: 0.5407 (t80) REVERT: F 170 LYS cc_start: 0.7402 (tptt) cc_final: 0.7016 (pptt) REVERT: F 174 TYR cc_start: 0.5246 (m-80) cc_final: 0.5031 (m-10) REVERT: G 203 CYS cc_start: 0.2658 (p) cc_final: 0.2394 (p) outliers start: 115 outliers final: 51 residues processed: 262 average time/residue: 0.5520 time to fit residues: 180.1998 Evaluate side-chains 213 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 152 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 79 TYR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 124 LYS Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 108 TYR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain G residue 1 GLU Chi-restraints excluded: chain G residue 92 MET Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 120 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 441 optimal weight: 30.0000 chunk 344 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 313 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 440 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 327 optimal weight: 6.9990 chunk 271 optimal weight: 50.0000 chunk 203 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 ASN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C 965 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.142134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.073093 restraints weight = 94553.977| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 6.55 r_work: 0.2932 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 35688 Z= 0.230 Angle : 0.604 11.102 48600 Z= 0.302 Chirality : 0.044 0.192 5463 Planarity : 0.004 0.074 6267 Dihedral : 4.949 80.807 4878 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.74 % Favored : 93.23 % Rotamer: Outliers : 3.00 % Allowed : 12.47 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.12), residues: 4449 helix: 1.81 (0.22), residues: 632 sheet: -2.06 (0.16), residues: 969 loop : -2.39 (0.11), residues: 2848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 97 TYR 0.034 0.002 TYR B 92 PHE 0.022 0.002 PHE C 136 TRP 0.017 0.001 TRP A 105 HIS 0.006 0.001 HIS D 55 Details of bonding type rmsd covalent geometry : bond 0.00528 (35637) covalent geometry : angle 0.60357 (48498) SS BOND : bond 0.00254 ( 51) SS BOND : angle 0.82215 ( 102) hydrogen bonds : bond 0.03849 ( 906) hydrogen bonds : angle 5.21197 ( 2529) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 167 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 197 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8610 (pp) REVERT: C 238 PHE cc_start: 0.6929 (OUTLIER) cc_final: 0.6675 (t80) REVERT: C 309 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8791 (mp0) REVERT: C 745 ASP cc_start: 0.9009 (m-30) cc_final: 0.8718 (p0) REVERT: C 855 PHE cc_start: 0.7286 (OUTLIER) cc_final: 0.6404 (p90) REVERT: C 858 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9194 (pt) REVERT: C 950 ASP cc_start: 0.8776 (t70) cc_final: 0.8551 (t0) REVERT: C 985 ASP cc_start: 0.9112 (OUTLIER) cc_final: 0.8476 (p0) REVERT: C 1010 GLN cc_start: 0.9279 (OUTLIER) cc_final: 0.8895 (mp10) REVERT: A 200 TYR cc_start: 0.9338 (m-80) cc_final: 0.8739 (m-80) REVERT: A 242 LEU cc_start: 0.9296 (mm) cc_final: 0.8920 (tm) REVERT: A 759 PHE cc_start: 0.8903 (m-80) cc_final: 0.8686 (m-80) REVERT: A 854 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7517 (mppt) REVERT: E 104 ASN cc_start: 0.7249 (m110) cc_final: 0.7026 (m110) REVERT: B 175 PHE cc_start: 0.7856 (p90) cc_final: 0.7382 (p90) REVERT: B 192 PHE cc_start: 0.8575 (m-80) cc_final: 0.8276 (m-10) REVERT: B 457 ARG cc_start: 0.3129 (OUTLIER) cc_final: 0.2929 (ttm-80) REVERT: B 571 ASP cc_start: 0.8680 (t0) cc_final: 0.8299 (p0) REVERT: B 759 PHE cc_start: 0.8865 (m-80) cc_final: 0.8499 (m-80) REVERT: B 904 TYR cc_start: 0.8950 (m-10) cc_final: 0.8402 (m-10) REVERT: B 950 ASP cc_start: 0.9011 (t70) cc_final: 0.8761 (t0) REVERT: B 1010 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.8741 (mp10) REVERT: B 1017 GLU cc_start: 0.9284 (tt0) cc_final: 0.9073 (tp30) REVERT: F 140 PHE cc_start: 0.3349 (p90) cc_final: 0.3130 (p90) REVERT: F 141 TYR cc_start: 0.5772 (t80) cc_final: 0.5362 (t80) REVERT: F 170 LYS cc_start: 0.7343 (tptt) cc_final: 0.7033 (pptt) REVERT: G 38 ARG cc_start: 0.8446 (ttm170) cc_final: 0.7948 (ttt90) outliers start: 117 outliers final: 51 residues processed: 265 average time/residue: 0.6017 time to fit residues: 199.1801 Evaluate side-chains 204 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 144 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 124 LYS Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain G residue 1 GLU Chi-restraints excluded: chain G residue 92 MET Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 335 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 373 optimal weight: 0.7980 chunk 161 optimal weight: 9.9990 chunk 104 optimal weight: 0.7980 chunk 203 optimal weight: 3.9990 chunk 120 optimal weight: 0.0980 chunk 443 optimal weight: 10.0000 chunk 254 optimal weight: 2.9990 chunk 391 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 HIS ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 762 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 992 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.155742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.098433 restraints weight = 73563.156| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 5.10 r_work: 0.3058 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 35688 Z= 0.104 Angle : 0.556 12.238 48600 Z= 0.273 Chirality : 0.043 0.220 5463 Planarity : 0.004 0.084 6267 Dihedral : 4.789 80.933 4873 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.41 % Favored : 93.57 % Rotamer: Outliers : 2.48 % Allowed : 13.36 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.12), residues: 4449 helix: 1.97 (0.22), residues: 631 sheet: -1.87 (0.16), residues: 977 loop : -2.33 (0.11), residues: 2841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 97 TYR 0.035 0.001 TYR B 160 PHE 0.021 0.001 PHE A 141 TRP 0.025 0.001 TRP A 105 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00237 (35637) covalent geometry : angle 0.55575 (48498) SS BOND : bond 0.00136 ( 51) SS BOND : angle 0.78569 ( 102) hydrogen bonds : bond 0.03231 ( 906) hydrogen bonds : angle 4.97232 ( 2529) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 154 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 197 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8582 (pp) REVERT: C 309 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8763 (mp0) REVERT: C 581 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8599 (p) REVERT: C 745 ASP cc_start: 0.8858 (m-30) cc_final: 0.8579 (OUTLIER) REVERT: C 855 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.6193 (p90) REVERT: C 858 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9212 (pt) REVERT: C 950 ASP cc_start: 0.8737 (t70) cc_final: 0.8503 (t0) REVERT: C 1010 GLN cc_start: 0.9224 (OUTLIER) cc_final: 0.8834 (mp10) REVERT: I 79 TYR cc_start: 0.5967 (OUTLIER) cc_final: 0.5555 (t80) REVERT: A 54 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.8517 (t70) REVERT: A 170 TYR cc_start: 0.8304 (t80) cc_final: 0.8070 (t80) REVERT: A 200 TYR cc_start: 0.9307 (m-80) cc_final: 0.8709 (m-80) REVERT: A 242 LEU cc_start: 0.9257 (mm) cc_final: 0.8870 (tm) REVERT: A 759 PHE cc_start: 0.8905 (m-80) cc_final: 0.8615 (m-80) REVERT: A 854 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7535 (mppt) REVERT: E 105 ILE cc_start: 0.6969 (OUTLIER) cc_final: 0.6714 (mp) REVERT: E 150 LYS cc_start: -0.1609 (mmtt) cc_final: -0.1888 (mmtm) REVERT: B 175 PHE cc_start: 0.7699 (p90) cc_final: 0.7320 (p90) REVERT: B 457 ARG cc_start: 0.2228 (OUTLIER) cc_final: 0.1892 (mtm110) REVERT: B 571 ASP cc_start: 0.8381 (t0) cc_final: 0.8100 (p0) REVERT: B 599 THR cc_start: 0.9744 (OUTLIER) cc_final: 0.9377 (p) REVERT: B 759 PHE cc_start: 0.8923 (m-80) cc_final: 0.8557 (m-80) REVERT: B 904 TYR cc_start: 0.8911 (m-10) cc_final: 0.8407 (m-10) REVERT: B 950 ASP cc_start: 0.8968 (t70) cc_final: 0.8689 (t0) REVERT: B 992 GLN cc_start: 0.9434 (OUTLIER) cc_final: 0.9212 (tp-100) REVERT: B 1010 GLN cc_start: 0.9283 (OUTLIER) cc_final: 0.8863 (mp10) REVERT: B 1017 GLU cc_start: 0.9260 (tt0) cc_final: 0.9047 (tp30) REVERT: F 170 LYS cc_start: 0.7373 (tptt) cc_final: 0.7028 (pptt) REVERT: G 32 TYR cc_start: 0.7238 (OUTLIER) cc_final: 0.6817 (t80) REVERT: G 38 ARG cc_start: 0.8249 (ttm170) cc_final: 0.8037 (tmm-80) REVERT: G 203 CYS cc_start: 0.2734 (p) cc_final: 0.2353 (p) outliers start: 97 outliers final: 45 residues processed: 234 average time/residue: 0.6092 time to fit residues: 176.5313 Evaluate side-chains 198 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 140 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 79 TYR Chi-restraints excluded: chain I residue 93 TYR Chi-restraints excluded: chain I residue 124 LYS Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain G residue 1 GLU Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 310 optimal weight: 4.9990 chunk 359 optimal weight: 0.4980 chunk 404 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 276 optimal weight: 7.9990 chunk 330 optimal weight: 30.0000 chunk 415 optimal weight: 5.9990 chunk 401 optimal weight: 2.9990 chunk 208 optimal weight: 4.9990 chunk 431 optimal weight: 9.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 ASN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 GLN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.140988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.072700 restraints weight = 94612.463| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 6.53 r_work: 0.2911 rms_B_bonded: 5.03 restraints_weight: 2.0000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 35688 Z= 0.244 Angle : 0.629 15.105 48600 Z= 0.314 Chirality : 0.045 0.341 5463 Planarity : 0.004 0.076 6267 Dihedral : 4.824 76.916 4869 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.37 % Favored : 92.61 % Rotamer: Outliers : 2.61 % Allowed : 13.54 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.12), residues: 4449 helix: 1.86 (0.22), residues: 633 sheet: -1.83 (0.16), residues: 986 loop : -2.25 (0.11), residues: 2830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 995 TYR 0.037 0.002 TYR B 160 PHE 0.022 0.002 PHE F 140 TRP 0.029 0.002 TRP G 47 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00556 (35637) covalent geometry : angle 0.62771 (48498) SS BOND : bond 0.00231 ( 51) SS BOND : angle 0.95180 ( 102) hydrogen bonds : bond 0.03868 ( 906) hydrogen bonds : angle 5.19080 ( 2529) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 146 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 ASN cc_start: 0.5424 (OUTLIER) cc_final: 0.5133 (p0) REVERT: C 197 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8547 (pp) REVERT: C 238 PHE cc_start: 0.7036 (OUTLIER) cc_final: 0.6756 (t80) REVERT: C 336 CYS cc_start: 0.4933 (OUTLIER) cc_final: 0.4333 (m) REVERT: C 745 ASP cc_start: 0.9109 (m-30) cc_final: 0.8706 (p0) REVERT: C 855 PHE cc_start: 0.7402 (OUTLIER) cc_final: 0.6309 (p90) REVERT: C 858 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9178 (pt) REVERT: C 1010 GLN cc_start: 0.9291 (OUTLIER) cc_final: 0.8801 (mp10) REVERT: I 79 TYR cc_start: 0.6279 (OUTLIER) cc_final: 0.6077 (t80) REVERT: A 54 ASP cc_start: 0.8962 (OUTLIER) cc_final: 0.8610 (t70) REVERT: A 759 PHE cc_start: 0.9016 (m-80) cc_final: 0.8778 (m-80) REVERT: A 854 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7530 (mppt) REVERT: A 1029 MET cc_start: 0.9538 (tpp) cc_final: 0.9329 (tpp) REVERT: E 105 ILE cc_start: 0.7243 (OUTLIER) cc_final: 0.6919 (mp) REVERT: E 150 LYS cc_start: -0.1745 (mmtt) cc_final: -0.1993 (mmtm) REVERT: E 213 LYS cc_start: 0.3742 (tptt) cc_final: 0.3205 (tptt) REVERT: B 224 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8448 (pm20) REVERT: B 238 PHE cc_start: 0.7455 (OUTLIER) cc_final: 0.7085 (t80) REVERT: B 571 ASP cc_start: 0.8824 (t0) cc_final: 0.8568 (p0) REVERT: B 759 PHE cc_start: 0.8929 (m-80) cc_final: 0.8651 (m-80) REVERT: B 904 TYR cc_start: 0.8972 (m-10) cc_final: 0.8434 (m-10) REVERT: B 950 ASP cc_start: 0.9004 (t70) cc_final: 0.8754 (t0) REVERT: B 1010 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.8753 (mp10) REVERT: B 1017 GLU cc_start: 0.9331 (tt0) cc_final: 0.9129 (tm-30) REVERT: F 170 LYS cc_start: 0.7188 (tptt) cc_final: 0.6898 (pptt) REVERT: G 203 CYS cc_start: 0.2909 (p) cc_final: 0.2543 (p) outliers start: 102 outliers final: 51 residues processed: 232 average time/residue: 0.6034 time to fit residues: 173.2299 Evaluate side-chains 199 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 134 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 79 TYR Chi-restraints excluded: chain I residue 93 TYR Chi-restraints excluded: chain I residue 124 LYS Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 108 TYR Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain G residue 1 GLU Chi-restraints excluded: chain G residue 92 MET Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 120 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 74 optimal weight: 0.7980 chunk 246 optimal weight: 0.9990 chunk 201 optimal weight: 0.4980 chunk 402 optimal weight: 0.9980 chunk 331 optimal weight: 8.9990 chunk 161 optimal weight: 9.9990 chunk 123 optimal weight: 50.0000 chunk 313 optimal weight: 1.9990 chunk 86 optimal weight: 0.0870 chunk 349 optimal weight: 0.9990 chunk 134 optimal weight: 0.0050 overall best weight: 0.4772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN B 207 HIS ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.145574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.092424 restraints weight = 127455.754| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 6.81 r_work: 0.2911 rms_B_bonded: 5.66 restraints_weight: 2.0000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 35688 Z= 0.103 Angle : 0.575 14.087 48600 Z= 0.283 Chirality : 0.044 0.307 5463 Planarity : 0.004 0.075 6267 Dihedral : 4.615 77.065 4863 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.47 % Favored : 93.50 % Rotamer: Outliers : 2.15 % Allowed : 14.21 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.12), residues: 4449 helix: 1.98 (0.22), residues: 631 sheet: -1.77 (0.16), residues: 1011 loop : -2.16 (0.11), residues: 2807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 97 TYR 0.055 0.001 TYR E 108 PHE 0.021 0.001 PHE A 141 TRP 0.030 0.001 TRP A 105 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00237 (35637) covalent geometry : angle 0.57371 (48498) SS BOND : bond 0.00158 ( 51) SS BOND : angle 0.94303 ( 102) hydrogen bonds : bond 0.03257 ( 906) hydrogen bonds : angle 4.91234 ( 2529) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 152 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 153 MET cc_start: 0.7691 (pmm) cc_final: 0.7385 (pmm) REVERT: C 197 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8613 (pp) REVERT: C 336 CYS cc_start: 0.3474 (OUTLIER) cc_final: 0.2247 (m) REVERT: C 581 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8505 (p) REVERT: C 745 ASP cc_start: 0.9202 (m-30) cc_final: 0.8725 (p0) REVERT: C 855 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.6387 (p90) REVERT: C 858 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9250 (pt) REVERT: C 950 ASP cc_start: 0.8917 (t70) cc_final: 0.8674 (t0) REVERT: C 994 ASP cc_start: 0.9151 (m-30) cc_final: 0.8947 (t70) REVERT: C 1010 GLN cc_start: 0.9332 (OUTLIER) cc_final: 0.8947 (mp10) REVERT: I 38 ARG cc_start: 0.5852 (mmm-85) cc_final: 0.5652 (mmm160) REVERT: I 79 TYR cc_start: 0.6592 (OUTLIER) cc_final: 0.6312 (t80) REVERT: A 54 ASP cc_start: 0.8951 (OUTLIER) cc_final: 0.8606 (t70) REVERT: A 759 PHE cc_start: 0.9038 (m-80) cc_final: 0.8814 (m-80) REVERT: A 854 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7411 (mppt) REVERT: B 571 ASP cc_start: 0.8755 (t0) cc_final: 0.8367 (p0) REVERT: B 599 THR cc_start: 0.9740 (OUTLIER) cc_final: 0.9393 (p) REVERT: B 697 MET cc_start: 0.8923 (ptp) cc_final: 0.8636 (mtm) REVERT: B 759 PHE cc_start: 0.8995 (m-80) cc_final: 0.8710 (m-80) REVERT: B 904 TYR cc_start: 0.9033 (m-10) cc_final: 0.8675 (m-10) REVERT: B 950 ASP cc_start: 0.9070 (t70) cc_final: 0.8826 (t0) REVERT: B 1010 GLN cc_start: 0.9368 (OUTLIER) cc_final: 0.8974 (mp10) REVERT: B 1017 GLU cc_start: 0.9406 (tt0) cc_final: 0.9146 (tp30) REVERT: F 170 LYS cc_start: 0.7175 (tptt) cc_final: 0.6878 (pptt) REVERT: G 38 ARG cc_start: 0.8294 (ttm170) cc_final: 0.8078 (tmm-80) REVERT: G 203 CYS cc_start: 0.2912 (p) cc_final: 0.2555 (p) outliers start: 84 outliers final: 45 residues processed: 222 average time/residue: 0.5515 time to fit residues: 152.5640 Evaluate side-chains 193 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 137 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain I residue 32 TYR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 79 TYR Chi-restraints excluded: chain I residue 93 TYR Chi-restraints excluded: chain I residue 124 LYS Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain G residue 1 GLU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 120 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 65 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 219 optimal weight: 0.6980 chunk 135 optimal weight: 50.0000 chunk 412 optimal weight: 9.9990 chunk 322 optimal weight: 2.9990 chunk 236 optimal weight: 6.9990 chunk 198 optimal weight: 9.9990 chunk 267 optimal weight: 10.0000 chunk 301 optimal weight: 7.9990 chunk 369 optimal weight: 0.0060 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.141547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.078473 restraints weight = 97241.071| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 6.20 r_work: 0.2960 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35688 Z= 0.121 Angle : 0.579 13.876 48600 Z= 0.285 Chirality : 0.044 0.313 5463 Planarity : 0.004 0.075 6267 Dihedral : 4.566 76.458 4861 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.70 % Favored : 93.28 % Rotamer: Outliers : 1.69 % Allowed : 14.77 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.12), residues: 4449 helix: 2.03 (0.22), residues: 630 sheet: -1.70 (0.15), residues: 1010 loop : -2.09 (0.11), residues: 2809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 97 TYR 0.023 0.001 TYR C 160 PHE 0.024 0.001 PHE F 140 TRP 0.037 0.001 TRP A 105 HIS 0.005 0.001 HIS E 207 Details of bonding type rmsd covalent geometry : bond 0.00278 (35637) covalent geometry : angle 0.57873 (48498) SS BOND : bond 0.00211 ( 51) SS BOND : angle 0.69937 ( 102) hydrogen bonds : bond 0.03207 ( 906) hydrogen bonds : angle 4.85599 ( 2529) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 145 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 197 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8561 (pp) REVERT: C 336 CYS cc_start: 0.3600 (OUTLIER) cc_final: 0.2409 (m) REVERT: C 581 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8496 (p) REVERT: C 745 ASP cc_start: 0.9021 (m-30) cc_final: 0.8709 (p0) REVERT: C 855 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.6264 (p90) REVERT: C 858 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9219 (pt) REVERT: C 950 ASP cc_start: 0.8773 (t70) cc_final: 0.8541 (t0) REVERT: C 994 ASP cc_start: 0.9171 (m-30) cc_final: 0.8941 (t70) REVERT: C 1010 GLN cc_start: 0.9261 (OUTLIER) cc_final: 0.8872 (mp10) REVERT: I 59 TYR cc_start: 0.3393 (m-80) cc_final: 0.3182 (m-80) REVERT: I 79 TYR cc_start: 0.6802 (OUTLIER) cc_final: 0.6593 (t80) REVERT: A 54 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8551 (t70) REVERT: A 200 TYR cc_start: 0.9371 (m-80) cc_final: 0.8806 (m-80) REVERT: A 759 PHE cc_start: 0.8949 (m-80) cc_final: 0.8728 (m-80) REVERT: A 854 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7467 (mppt) REVERT: B 571 ASP cc_start: 0.8668 (t0) cc_final: 0.8321 (p0) REVERT: B 599 THR cc_start: 0.9740 (OUTLIER) cc_final: 0.9406 (p) REVERT: B 759 PHE cc_start: 0.8930 (m-80) cc_final: 0.8654 (m-80) REVERT: B 904 TYR cc_start: 0.8957 (m-10) cc_final: 0.8577 (m-10) REVERT: B 950 ASP cc_start: 0.8919 (t70) cc_final: 0.8664 (t0) REVERT: B 1010 GLN cc_start: 0.9298 (OUTLIER) cc_final: 0.8899 (mp10) REVERT: B 1017 GLU cc_start: 0.9266 (tt0) cc_final: 0.9061 (tp30) REVERT: F 170 LYS cc_start: 0.7182 (tptt) cc_final: 0.6892 (pptt) REVERT: G 203 CYS cc_start: 0.3028 (p) cc_final: 0.2702 (p) outliers start: 66 outliers final: 47 residues processed: 202 average time/residue: 0.6135 time to fit residues: 152.9285 Evaluate side-chains 198 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 140 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain I residue 32 TYR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 79 TYR Chi-restraints excluded: chain I residue 93 TYR Chi-restraints excluded: chain I residue 124 LYS Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 108 TYR Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain G residue 1 GLU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 141 optimal weight: 30.0000 chunk 174 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 36 optimal weight: 20.0000 chunk 363 optimal weight: 0.0770 chunk 275 optimal weight: 40.0000 chunk 136 optimal weight: 40.0000 chunk 295 optimal weight: 8.9990 chunk 353 optimal weight: 1.9990 chunk 362 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.144803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.089771 restraints weight = 127432.199| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 8.22 r_work: 0.2890 rms_B_bonded: 5.88 restraints_weight: 2.0000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 35688 Z= 0.152 Angle : 0.596 14.030 48600 Z= 0.294 Chirality : 0.044 0.315 5463 Planarity : 0.004 0.076 6267 Dihedral : 4.602 76.378 4861 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.79 % Favored : 93.17 % Rotamer: Outliers : 1.74 % Allowed : 14.87 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.12), residues: 4449 helix: 2.02 (0.22), residues: 630 sheet: -1.68 (0.16), residues: 997 loop : -2.04 (0.11), residues: 2822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 97 TYR 0.033 0.001 TYR E 108 PHE 0.026 0.001 PHE F 117 TRP 0.037 0.001 TRP E 36 HIS 0.004 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00350 (35637) covalent geometry : angle 0.59552 (48498) SS BOND : bond 0.00143 ( 51) SS BOND : angle 0.83365 ( 102) hydrogen bonds : bond 0.03306 ( 906) hydrogen bonds : angle 4.88128 ( 2529) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8898 Ramachandran restraints generated. 4449 Oldfield, 0 Emsley, 4449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 144 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 197 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8565 (pp) REVERT: C 336 CYS cc_start: 0.5567 (OUTLIER) cc_final: 0.5233 (m) REVERT: C 581 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8520 (p) REVERT: C 745 ASP cc_start: 0.9084 (m-30) cc_final: 0.8724 (p0) REVERT: C 855 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.6418 (p90) REVERT: C 858 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9224 (pt) REVERT: C 950 ASP cc_start: 0.8922 (t70) cc_final: 0.8689 (t0) REVERT: C 994 ASP cc_start: 0.9266 (m-30) cc_final: 0.9037 (t70) REVERT: C 1010 GLN cc_start: 0.9279 (OUTLIER) cc_final: 0.8897 (mp10) REVERT: I 59 TYR cc_start: 0.3665 (m-80) cc_final: 0.3461 (m-80) REVERT: A 54 ASP cc_start: 0.8897 (OUTLIER) cc_final: 0.8578 (t70) REVERT: A 152 TRP cc_start: 0.7738 (OUTLIER) cc_final: 0.7488 (t60) REVERT: A 200 TYR cc_start: 0.9274 (m-80) cc_final: 0.8733 (m-80) REVERT: A 854 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7517 (mppt) REVERT: E 150 LYS cc_start: -0.0289 (mmtm) cc_final: -0.0519 (mmpt) REVERT: B 569 ILE cc_start: 0.9538 (OUTLIER) cc_final: 0.9266 (mt) REVERT: B 571 ASP cc_start: 0.8944 (t0) cc_final: 0.8543 (p0) REVERT: B 759 PHE cc_start: 0.8995 (m-80) cc_final: 0.8745 (m-80) REVERT: B 904 TYR cc_start: 0.9057 (m-10) cc_final: 0.8674 (m-10) REVERT: B 950 ASP cc_start: 0.9001 (t70) cc_final: 0.8744 (t0) REVERT: B 1010 GLN cc_start: 0.9347 (OUTLIER) cc_final: 0.8957 (mp10) REVERT: B 1017 GLU cc_start: 0.9390 (tt0) cc_final: 0.9149 (tp30) REVERT: F 170 LYS cc_start: 0.7193 (tptt) cc_final: 0.6907 (pptt) REVERT: G 38 ARG cc_start: 0.8684 (ttm170) cc_final: 0.8173 (ttp80) REVERT: G 89 ASP cc_start: 0.8032 (p0) cc_final: 0.7704 (t0) outliers start: 68 outliers final: 44 residues processed: 202 average time/residue: 0.6231 time to fit residues: 155.6546 Evaluate side-chains 192 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 137 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain I residue 32 TYR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 93 TYR Chi-restraints excluded: chain I residue 124 LYS Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain G residue 1 GLU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 331 optimal weight: 0.7980 chunk 209 optimal weight: 0.2980 chunk 73 optimal weight: 0.3980 chunk 15 optimal weight: 20.0000 chunk 197 optimal weight: 9.9990 chunk 74 optimal weight: 0.5980 chunk 141 optimal weight: 50.0000 chunk 47 optimal weight: 0.0070 chunk 233 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.145854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.093280 restraints weight = 126727.510| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 7.23 r_work: 0.2937 rms_B_bonded: 5.82 restraints_weight: 2.0000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 35688 Z= 0.101 Angle : 0.587 13.618 48600 Z= 0.287 Chirality : 0.044 0.316 5463 Planarity : 0.004 0.073 6267 Dihedral : 4.534 76.633 4861 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.77 % Favored : 93.21 % Rotamer: Outliers : 1.43 % Allowed : 15.31 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.12), residues: 4449 helix: 2.08 (0.22), residues: 624 sheet: -1.53 (0.16), residues: 1000 loop : -1.96 (0.11), residues: 2825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 97 TYR 0.030 0.001 TYR E 108 PHE 0.028 0.001 PHE C 136 TRP 0.033 0.001 TRP A 105 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00233 (35637) covalent geometry : angle 0.58629 (48498) SS BOND : bond 0.00121 ( 51) SS BOND : angle 0.70580 ( 102) hydrogen bonds : bond 0.02986 ( 906) hydrogen bonds : angle 4.75565 ( 2529) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21720.17 seconds wall clock time: 368 minutes 15.03 seconds (22095.03 seconds total)