Starting phenix.real_space_refine on Mon Aug 25 19:40:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dxs_27775/08_2025/8dxs_27775.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dxs_27775/08_2025/8dxs_27775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dxs_27775/08_2025/8dxs_27775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dxs_27775/08_2025/8dxs_27775.map" model { file = "/net/cci-nas-00/data/ceres_data/8dxs_27775/08_2025/8dxs_27775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dxs_27775/08_2025/8dxs_27775.cif" } resolution = 3.76 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= 0.010 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 132 5.16 5 C 19137 2.51 5 N 4985 2.21 5 O 5877 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30131 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7999 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7985 Classifications: {'peptide': 1021} Link IDs: {'PTRANS': 49, 'TRANS': 971} Chain breaks: 8 Conformer: "B" Number of residues, atoms: 1021, 7985 Classifications: {'peptide': 1021} Link IDs: {'PTRANS': 49, 'TRANS': 971} Chain breaks: 8 bond proxies already assigned to first conformer: 8152 Chain: "B" Number of atoms: 8205 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1047, 8191 Classifications: {'peptide': 1047} Link IDs: {'PTRANS': 51, 'TRANS': 995} Chain breaks: 8 Conformer: "B" Number of residues, atoms: 1047, 8191 Classifications: {'peptide': 1047} Link IDs: {'PTRANS': 51, 'TRANS': 995} Chain breaks: 8 bond proxies already assigned to first conformer: 8361 Chain: "C" Number of atoms: 8097 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1033, 8083 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 50, 'TRANS': 982} Chain breaks: 8 Conformer: "B" Number of residues, atoms: 1033, 8083 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 50, 'TRANS': 982} Chain breaks: 8 bond proxies already assigned to first conformer: 8251 Chain: "H" Number of atoms: 923 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 123, 923 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 923 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 123, 923 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 923 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 123, 923 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "J" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ATYR A 365 " occ=0.91 ... (22 atoms not shown) pdb=" OH BTYR A 365 " occ=0.09 residue: pdb=" N ATYR B 365 " occ=0.90 ... (22 atoms not shown) pdb=" OH BTYR B 365 " occ=0.10 residue: pdb=" N ATYR C 365 " occ=0.72 ... (22 atoms not shown) pdb=" OH BTYR C 365 " occ=0.28 Time building chain proxies: 12.26, per 1000 atoms: 0.41 Number of scatterers: 30131 At special positions: 0 Unit cell: (159.309, 193.779, 223.591, 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 132 16.00 O 5877 8.00 N 4985 7.00 C 19137 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 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=2.04 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 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=2.02 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 B 131 " - 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 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=2.61 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 C 131 " - 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=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " 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 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=1.92 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 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 Atom "HETATM29793 O5 NAG B1304 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 122 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 234 " " NAG A1306 " - " ASN A 282 " " NAG A1307 " - " ASN A 331 " " NAG A1308 " - " ASN A 343 " " NAG A1309 " - " ASN A 603 " " NAG A1310 " - " ASN A 616 " " NAG A1311 " - " ASN A 657 " " NAG A1312 " - " ASN A 709 " " NAG A1313 " - " ASN A 717 " " NAG A1314 " - " ASN A 801 " " NAG A1315 " - " ASN A1098 " " NAG A1316 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 717 " " NAG B1310 " - " ASN B 801 " " NAG B1311 " - " ASN B1074 " " NAG B1312 " - " ASN B1098 " " NAG B1313 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C 717 " " NAG C1312 " - " ASN C 801 " " NAG C1313 " - " ASN C1074 " " NAG C1314 " - " ASN C1098 " " NAG C1315 " - " ASN C1134 " Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 2.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7050 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 67 sheets defined 18.5% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.866A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.592A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 389 removed outlier: 4.385A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 389' Processing helix chain 'A' and resid 502 through 506 removed outlier: 4.028A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 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: 3.807A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.656A pdb=" N LEU A 877 " --> pdb=" O TYR A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.538A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.948A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 919 removed outlier: 3.563A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 924 removed outlier: 3.716A pdb=" N ALA A 924 " --> pdb=" O GLN A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 941 removed outlier: 3.621A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.648A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR A 961 " --> pdb=" O GLN A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.655A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1031 removed outlier: 4.682A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.858A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.518A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.650A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.784A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.851A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.570A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.640A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.530A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (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 966 removed outlier: 4.243A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.983A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.292A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 738 through 744 removed outlier: 3.677A pdb=" N GLY C 744 " --> pdb=" O MET C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.569A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.626A 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: 3.590A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA C 771 " --> pdb=" O LEU C 767 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.892A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.504A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 941 removed outlier: 3.877A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.806A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 988 through 1032 removed outlier: 4.314A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU C1031 " --> pdb=" O THR C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.864A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.551A pdb=" N ASP H 86 " --> pdb=" O ARG H 83 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR H 87 " --> pdb=" O THR H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.945A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.082A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.394A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.308A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.520A pdb=" N VAL C 576 " --> pdb=" O LEU C 585 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.931A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 49 removed outlier: 8.008A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.735A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A 237 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 117 removed outlier: 3.791A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 156 through 157 removed outlier: 3.746A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 318 removed outlier: 3.590A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 597 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 334 through 335 removed outlier: 6.391A pdb=" N ASN A 334 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.578A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 551 through 552 removed outlier: 5.723A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.404A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.882A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.603A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.201A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.859A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AC3, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.839A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 65 through 66 removed outlier: 3.676A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.520A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 140 through 142 Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 318 removed outlier: 5.589A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 609 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.593A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.877A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 453 through 454 removed outlier: 3.746A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 551 through 553 removed outlier: 4.561A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP B 578 " --> pdb=" O GLU B 583 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.906A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 693 " --> pdb=" O SER B 673 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE B 666 " --> pdb=" O ILE B 670 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 719 removed outlier: 6.703A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 719 removed outlier: 6.703A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE1, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.613A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.613A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.122A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 277 " --> pdb=" O HIS C 49 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN C 271 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.924A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE C 238 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE C 128 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 121 through 122 Processing sheet with id=AE6, first strand: chain 'C' and resid 153 through 160 removed outlier: 4.243A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 10.578A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 318 removed outlier: 5.621A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.205A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY C 431 " --> pdb=" O CYS C 379 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N CYS C 379 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL C 433 " --> pdb=" O PHE C 377 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N PHE C 377 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ALA C 435 " --> pdb=" O SER C 375 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.137A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.559A pdb=" N PHE C1075 " --> pdb=" O ILE C 712 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.549A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.022A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 3.514A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.650A pdb=" N LEU H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS H 22 " --> pdb=" O LEU H 78 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP H 72 " --> pdb=" O SER H 77 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR H 79 " --> pdb=" O SER H 70 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 58 through 59 removed outlier: 3.832A pdb=" N GLU H 58 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.524A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AG1, first strand: chain 'L' and resid 19 through 20 removed outlier: 4.269A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.110A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN L 89 " --> pdb=" O SER L 34 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TYR L 36 " --> pdb=" O TYR L 87 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN L 38 " --> pdb=" O THR L 85 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.541A pdb=" N LEU F 20 " --> pdb=" O LEU F 80 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU F 80 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS F 22 " --> pdb=" O LEU F 78 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER F 77 " --> pdb=" O ASP F 72 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP F 72 " --> pdb=" O SER F 77 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR F 79 " --> pdb=" O SER F 70 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER F 70 " --> pdb=" O TYR F 79 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AG5, first strand: chain 'F' and resid 57 through 58 removed outlier: 3.703A pdb=" N GLU F 58 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY F 50 " --> pdb=" O GLU F 58 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE F 51 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET F 34 " --> pdb=" O ILE F 51 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR F 91 " --> pdb=" O ALA F 37 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 5 through 7 removed outlier: 4.203A pdb=" N THR I 5 " --> pdb=" O ARG I 24 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG I 24 " --> pdb=" O THR I 5 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR I 22 " --> pdb=" O SER I 7 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL I 19 " --> pdb=" O ILE I 75 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE I 21 " --> pdb=" O LEU I 73 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS I 23 " --> pdb=" O PHE I 71 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE I 71 " --> pdb=" O CYS I 23 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER I 67 " --> pdb=" O ASP I 70 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 11 through 13 removed outlier: 6.647A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'I' and resid 35 through 38 removed outlier: 6.600A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.756A pdb=" N VAL G 5 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER G 77 " --> pdb=" O ASP G 72 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP G 72 " --> pdb=" O SER G 77 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR G 79 " --> pdb=" O SER G 70 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER G 70 " --> pdb=" O TYR G 79 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.603A pdb=" N VAL G 12 " --> pdb=" O THR G 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.829A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLY G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N MET G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR G 90 " --> pdb=" O THR G 107 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR G 107 " --> pdb=" O TYR G 90 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 4 through 7 removed outlier: 4.088A pdb=" N THR J 5 " --> pdb=" O ARG J 24 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG J 24 " --> pdb=" O THR J 5 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER J 65 " --> pdb=" O THR J 72 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.543A pdb=" N THR J 102 " --> pdb=" O TYR J 86 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR J 85 " --> pdb=" O GLN J 38 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN J 38 " --> pdb=" O THR J 85 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU J 33 " --> pdb=" O ASN J 49 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ASN J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) 907 hydrogen bonds defined for protein. 2523 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: 8.08 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.35: 9605 1.35 - 1.62: 21032 1.62 - 1.90: 174 1.90 - 2.17: 1 2.17 - 2.45: 1 Bond restraints: 30813 Sorted by residual: bond pdb=" N PRO C 987 " pdb=" CD PRO C 987 " ideal model delta sigma weight residual 1.473 1.994 -0.521 1.40e-02 5.10e+03 1.39e+03 bond pdb=" N PRO B 463 " pdb=" CD PRO B 463 " ideal model delta sigma weight residual 1.473 1.787 -0.314 1.40e-02 5.10e+03 5.02e+02 bond pdb=" CB PRO A 322 " pdb=" CG PRO A 322 " ideal model delta sigma weight residual 1.492 2.446 -0.954 5.00e-02 4.00e+02 3.64e+02 bond pdb=" CG PRO A 322 " pdb=" CD PRO A 322 " ideal model delta sigma weight residual 1.503 1.070 0.433 3.40e-02 8.65e+02 1.62e+02 bond pdb=" C1 NAG C1305 " pdb=" C2 NAG C1305 " ideal model delta sigma weight residual 1.532 1.700 -0.168 2.00e-02 2.50e+03 7.07e+01 ... (remaining 30808 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.21: 41897 21.21 - 42.42: 2 42.42 - 63.63: 0 63.63 - 84.84: 0 84.84 - 106.05: 1 Bond angle restraints: 41900 Sorted by residual: angle pdb=" CB PRO A 322 " pdb=" CG PRO A 322 " pdb=" CD PRO A 322 " ideal model delta sigma weight residual 106.10 0.05 106.05 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA PRO C 987 " pdb=" N PRO C 987 " pdb=" CD PRO C 987 " ideal model delta sigma weight residual 112.00 86.08 25.92 1.40e+00 5.10e-01 3.43e+02 angle pdb=" N PRO A 322 " pdb=" CA PRO A 322 " pdb=" CB PRO A 322 " ideal model delta sigma weight residual 103.25 86.84 16.41 1.05e+00 9.07e-01 2.44e+02 angle pdb=" CA PRO B 463 " pdb=" N PRO B 463 " pdb=" CD PRO B 463 " ideal model delta sigma weight residual 112.00 91.04 20.96 1.40e+00 5.10e-01 2.24e+02 angle pdb=" CA PRO A 322 " pdb=" N PRO A 322 " pdb=" CD PRO A 322 " ideal model delta sigma weight residual 112.00 92.03 19.97 1.40e+00 5.10e-01 2.03e+02 ... (remaining 41895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.77: 17220 22.77 - 45.53: 1378 45.53 - 68.30: 212 68.30 - 91.06: 45 91.06 - 113.83: 1 Dihedral angle restraints: 18856 sinusoidal: 7874 harmonic: 10982 Sorted by residual: dihedral pdb=" CB CYS I 23 " pdb=" SG CYS I 23 " pdb=" SG CYS I 88 " pdb=" CB CYS I 88 " ideal model delta sinusoidal sigma weight residual -86.00 -172.80 86.80 1 1.00e+01 1.00e-02 9.06e+01 dihedral pdb=" CB CYS J 23 " pdb=" SG CYS J 23 " pdb=" SG CYS J 88 " pdb=" CB CYS J 88 " ideal model delta sinusoidal sigma weight residual -86.00 -170.93 84.93 1 1.00e+01 1.00e-02 8.75e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 172.55 -79.55 1 1.00e+01 1.00e-02 7.86e+01 ... (remaining 18853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.400: 4829 0.400 - 0.800: 5 0.800 - 1.200: 0 1.200 - 1.600: 0 1.600 - 2.000: 1 Chirality restraints: 4835 Sorted by residual: chirality pdb=" C1 NAG A1315 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1315 " pdb=" O5 NAG A1315 " both_signs ideal model delta sigma weight residual False -2.40 -0.40 -2.00 2.00e-01 2.50e+01 1.00e+02 chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C 603 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.60e+00 chirality pdb=" CA PRO A 322 " pdb=" N PRO A 322 " pdb=" C PRO A 322 " pdb=" CB PRO A 322 " both_signs ideal model delta sigma weight residual False 2.72 2.20 0.52 2.00e-01 2.50e+01 6.70e+00 ... (remaining 4832 not shown) Planarity restraints: 5398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.081 2.00e-02 2.50e+03 6.91e-02 5.96e+01 pdb=" CG ASN C 331 " -0.087 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.062 2.00e-02 2.50e+03 pdb=" C1 NAG C1305 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 462 " -0.133 5.00e-02 4.00e+02 1.71e-01 4.68e+01 pdb=" N PRO B 463 " 0.294 5.00e-02 4.00e+02 pdb=" CA PRO B 463 " -0.087 5.00e-02 4.00e+02 pdb=" CD PRO B 463 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " -0.113 5.00e-02 4.00e+02 1.34e-01 2.88e+01 pdb=" N PRO C 987 " 0.229 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " -0.065 5.00e-02 4.00e+02 ... (remaining 5395 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 252 2.57 - 3.15: 22358 3.15 - 3.73: 46178 3.73 - 4.32: 61381 4.32 - 4.90: 101759 Nonbonded interactions: 231928 Sorted by model distance: nonbonded pdb=" ND2 ASN B 343 " pdb=" O5 NAG B1304 " model vdw 1.986 3.120 nonbonded pdb=" ND2 ASN B 343 " pdb=" C1 NAG B1304 " model vdw 2.019 3.550 nonbonded pdb=" OD1 ASP B 287 " pdb=" CE2 PHE B 306 " model vdw 2.072 3.340 nonbonded pdb=" O THR B 236 " pdb=" NE ARG B 237 " model vdw 2.080 3.120 nonbonded pdb=" O ASP B 796 " pdb=" OD1 ASP B 796 " model vdw 2.147 3.040 ... (remaining 231923 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 171 or resid 187 through 364 or resid 366 throu \ gh 476 or resid 478 through 1313)) selection = (chain 'B' and (resid 26 through 171 or resid 187 through 364 or resid 366 throu \ gh 476 or resid 478 through 676 or resid 690 through 827 or resid 855 through 13 \ 13)) selection = (chain 'C' and (resid 26 through 171 or resid 187 through 364 or resid 366 throu \ gh 476 or resid 478 through 676 or resid 690 through 827 or resid 855 through 13 \ 13)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.960 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: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 37.470 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 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 : 0.009 0.954 30898 Z= 0.407 Angle : 1.045 106.046 42113 Z= 0.490 Chirality : 0.060 2.000 4835 Planarity : 0.007 0.171 5355 Dihedral : 15.678 113.827 11680 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.21 % Favored : 94.60 % Rotamer: Outliers : 0.27 % Allowed : 24.57 % Favored : 75.15 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.28 (0.12), residues: 3734 helix: -1.63 (0.17), residues: 620 sheet: -0.07 (0.19), residues: 770 loop : -2.10 (0.11), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 273 TYR 0.020 0.001 TYR B 674 PHE 0.040 0.002 PHE B 306 TRP 0.019 0.001 TRP A 104 HIS 0.007 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00857 (30813) covalent geometry : angle 0.99354 (41900) SS BOND : bond 0.09156 ( 42) SS BOND : angle 3.48623 ( 84) hydrogen bonds : bond 0.25925 ( 885) hydrogen bonds : angle 9.98769 ( 2523) link_NAG-ASN : bond 0.01337 ( 43) link_NAG-ASN : angle 5.30640 ( 129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 282 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 980 ILE cc_start: 0.7764 (mm) cc_final: 0.7371 (tt) outliers start: 8 outliers final: 8 residues processed: 283 average time/residue: 0.1832 time to fit residues: 87.8152 Evaluate side-chains 290 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 282 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain H residue 16 ARG Chi-restraints excluded: chain H residue 46 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 0.4980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.4980 chunk 298 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 655 HIS ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN C 762 GLN ** L 38 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 = 0.4444 r_free = 0.4444 target = 0.162064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.118879 restraints weight = 206265.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.122076 restraints weight = 81361.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.122880 restraints weight = 45534.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.123113 restraints weight = 42821.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.123962 restraints weight = 32790.229| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3843 r_free = 0.3843 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3843 r_free = 0.3843 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.0362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.995 30898 Z= 0.237 Angle : 0.945 106.100 42113 Z= 0.441 Chirality : 0.051 1.225 4835 Planarity : 0.006 0.102 5355 Dihedral : 6.914 58.683 5009 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.48 % Favored : 94.36 % Rotamer: Outliers : 1.59 % Allowed : 23.14 % Favored : 75.27 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.13), residues: 3734 helix: -0.41 (0.20), residues: 622 sheet: 0.13 (0.18), residues: 779 loop : -2.06 (0.11), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 237 TYR 0.016 0.001 TYR B 674 PHE 0.053 0.001 PHE B 306 TRP 0.016 0.001 TRP B 104 HIS 0.004 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00746 (30813) covalent geometry : angle 0.91325 (41900) SS BOND : bond 0.00740 ( 42) SS BOND : angle 1.94400 ( 84) hydrogen bonds : bond 0.08338 ( 885) hydrogen bonds : angle 8.12670 ( 2523) link_NAG-ASN : bond 0.00781 ( 43) link_NAG-ASN : angle 4.25564 ( 129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 291 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.7387 (mmt) cc_final: 0.6973 (mtt) REVERT: B 748 GLU cc_start: 0.7771 (tp30) cc_final: 0.7390 (mt-10) REVERT: C 493 GLN cc_start: 0.3562 (OUTLIER) cc_final: 0.3093 (tp-100) REVERT: I 65 SER cc_start: 0.0105 (OUTLIER) cc_final: -0.0530 (p) outliers start: 51 outliers final: 30 residues processed: 319 average time/residue: 0.1822 time to fit residues: 97.3210 Evaluate side-chains 307 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 275 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 61 TRP Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain I residue 65 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 100 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 318 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 285 optimal weight: 1.9990 chunk 242 optimal weight: 7.9990 chunk 203 optimal weight: 0.9980 chunk 142 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 655 HIS ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** L 38 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 = 0.4443 r_free = 0.4443 target = 0.162001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.119200 restraints weight = 151873.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.121804 restraints weight = 70152.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.122109 restraints weight = 39564.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.122793 restraints weight = 38033.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.123291 restraints weight = 30056.897| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3837 r_free = 0.3837 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3837 r_free = 0.3837 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.0451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.995 30898 Z= 0.253 Angle : 0.963 106.100 42113 Z= 0.448 Chirality : 0.052 1.225 4835 Planarity : 0.006 0.102 5355 Dihedral : 6.821 58.683 4997 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.48 % Favored : 94.36 % Rotamer: Outliers : 1.01 % Allowed : 23.84 % Favored : 75.15 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.13), residues: 3734 helix: -0.41 (0.20), residues: 622 sheet: 0.13 (0.18), residues: 779 loop : -2.06 (0.11), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 237 TYR 0.016 0.001 TYR B 674 PHE 0.053 0.001 PHE B 306 TRP 0.016 0.001 TRP B 104 HIS 0.004 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00746 (30813) covalent geometry : angle 0.91325 (41900) SS BOND : bond 0.04711 ( 42) SS BOND : angle 3.70043 ( 84) hydrogen bonds : bond 0.08338 ( 885) hydrogen bonds : angle 8.12670 ( 2523) link_NAG-ASN : bond 0.01615 ( 43) link_NAG-ASN : angle 4.77113 ( 129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 274 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.7295 (mmt) cc_final: 0.6897 (mtt) REVERT: B 748 GLU cc_start: 0.7719 (tp30) cc_final: 0.7359 (mt-10) REVERT: C 493 GLN cc_start: 0.3548 (OUTLIER) cc_final: 0.3078 (tp-100) REVERT: I 65 SER cc_start: 0.0132 (OUTLIER) cc_final: -0.0514 (p) outliers start: 32 outliers final: 30 residues processed: 289 average time/residue: 0.1727 time to fit residues: 84.3777 Evaluate side-chains 305 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 273 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 61 TRP Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain I residue 65 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 277 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 136 optimal weight: 20.0000 chunk 141 optimal weight: 7.9990 chunk 369 optimal weight: 30.0000 chunk 354 optimal weight: 20.0000 chunk 239 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 324 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 225 optimal weight: 8.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.161997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.120131 restraints weight = 186798.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.122564 restraints weight = 72425.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.123573 restraints weight = 43567.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.123933 restraints weight = 40606.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.124220 restraints weight = 34395.012| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3858 r_free = 0.3858 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3858 r_free = 0.3858 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.0451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.995 30898 Z= 0.249 Angle : 0.981 106.100 42113 Z= 0.457 Chirality : 0.052 1.225 4835 Planarity : 0.006 0.102 5355 Dihedral : 6.821 58.683 4997 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.48 % Favored : 94.36 % Rotamer: Outliers : 1.01 % Allowed : 23.87 % Favored : 75.12 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.13), residues: 3734 helix: -0.41 (0.20), residues: 622 sheet: 0.13 (0.18), residues: 779 loop : -2.06 (0.11), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 237 TYR 0.016 0.001 TYR B 674 PHE 0.053 0.001 PHE B 306 TRP 0.016 0.001 TRP B 104 HIS 0.004 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00746 (30813) covalent geometry : angle 0.91325 (41900) SS BOND : bond 0.04020 ( 42) SS BOND : angle 5.63139 ( 84) hydrogen bonds : bond 0.08338 ( 885) hydrogen bonds : angle 8.12670 ( 2523) link_NAG-ASN : bond 0.01615 ( 43) link_NAG-ASN : angle 4.77113 ( 129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 273 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.7352 (mmt) cc_final: 0.6942 (mtt) REVERT: B 748 GLU cc_start: 0.7743 (tp30) cc_final: 0.7379 (mt-10) REVERT: C 493 GLN cc_start: 0.3453 (OUTLIER) cc_final: 0.2982 (tp-100) REVERT: I 65 SER cc_start: 0.0225 (OUTLIER) cc_final: -0.0450 (p) outliers start: 32 outliers final: 30 residues processed: 288 average time/residue: 0.1748 time to fit residues: 85.4477 Evaluate side-chains 305 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 273 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 61 TRP Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain I residue 65 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 250 optimal weight: 7.9990 chunk 235 optimal weight: 7.9990 chunk 328 optimal weight: 6.9990 chunk 361 optimal weight: 9.9990 chunk 271 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 365 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 278 optimal weight: 4.9990 chunk 317 optimal weight: 6.9990 chunk 370 optimal weight: 30.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.161999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.119729 restraints weight = 145600.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.121678 restraints weight = 68623.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.122493 restraints weight = 40832.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.123220 restraints weight = 36790.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.123324 restraints weight = 28751.085| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3841 r_free = 0.3841 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3841 r_free = 0.3841 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.0451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.995 30898 Z= 0.249 Angle : 0.981 106.100 42113 Z= 0.457 Chirality : 0.052 1.225 4835 Planarity : 0.006 0.102 5355 Dihedral : 6.821 58.683 4997 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.48 % Favored : 94.36 % Rotamer: Outliers : 1.01 % Allowed : 23.87 % Favored : 75.12 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.13), residues: 3734 helix: -0.41 (0.20), residues: 622 sheet: 0.13 (0.18), residues: 779 loop : -2.06 (0.11), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 237 TYR 0.016 0.001 TYR B 674 PHE 0.053 0.001 PHE B 306 TRP 0.016 0.001 TRP B 104 HIS 0.004 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00746 (30813) covalent geometry : angle 0.91325 (41900) SS BOND : bond 0.04020 ( 42) SS BOND : angle 5.63139 ( 84) hydrogen bonds : bond 0.08338 ( 885) hydrogen bonds : angle 8.12670 ( 2523) link_NAG-ASN : bond 0.01615 ( 43) link_NAG-ASN : angle 4.77113 ( 129) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 273 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.7312 (mmt) cc_final: 0.6906 (mtt) REVERT: B 748 GLU cc_start: 0.7677 (tp30) cc_final: 0.7341 (mt-10) REVERT: C 493 GLN cc_start: 0.3520 (OUTLIER) cc_final: 0.3047 (tp-100) REVERT: I 65 SER cc_start: 0.0140 (OUTLIER) cc_final: -0.0508 (p) outliers start: 32 outliers final: 30 residues processed: 288 average time/residue: 0.1726 time to fit residues: 84.4154 Evaluate side-chains 305 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 273 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 61 TRP Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain I residue 65 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 162 optimal weight: 4.9990 chunk 322 optimal weight: 9.9990 chunk 159 optimal weight: 1.9990 chunk 361 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 chunk 323 optimal weight: 30.0000 chunk 120 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 54 optimal weight: 0.0570 chunk 307 optimal weight: 0.8980 chunk 185 optimal weight: 0.8980 overall best weight: 1.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.162002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.120306 restraints weight = 165606.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.122442 restraints weight = 71098.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.123005 restraints weight = 43943.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.123435 restraints weight = 41685.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.124395 restraints weight = 32889.749| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3853 r_free = 0.3853 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3853 r_free = 0.3853 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.0451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.995 30898 Z= 0.249 Angle : 0.981 106.100 42113 Z= 0.457 Chirality : 0.052 1.225 4835 Planarity : 0.006 0.102 5355 Dihedral : 6.821 58.683 4997 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.48 % Favored : 94.36 % Rotamer: Outliers : 1.01 % Allowed : 23.87 % Favored : 75.12 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.13), residues: 3734 helix: -0.41 (0.20), residues: 622 sheet: 0.13 (0.18), residues: 779 loop : -2.06 (0.11), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 237 TYR 0.016 0.001 TYR B 674 PHE 0.053 0.001 PHE B 306 TRP 0.016 0.001 TRP B 104 HIS 0.004 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00746 (30813) covalent geometry : angle 0.91325 (41900) SS BOND : bond 0.04020 ( 42) SS BOND : angle 5.63139 ( 84) hydrogen bonds : bond 0.08338 ( 885) hydrogen bonds : angle 8.12670 ( 2523) link_NAG-ASN : bond 0.01615 ( 43) link_NAG-ASN : angle 4.77113 ( 129) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 273 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.7369 (mmt) cc_final: 0.6959 (mtt) REVERT: B 748 GLU cc_start: 0.7707 (tp30) cc_final: 0.7353 (mt-10) REVERT: C 493 GLN cc_start: 0.3554 (OUTLIER) cc_final: 0.3085 (tp-100) REVERT: I 65 SER cc_start: 0.0094 (OUTLIER) cc_final: -0.0540 (p) outliers start: 32 outliers final: 30 residues processed: 288 average time/residue: 0.1688 time to fit residues: 82.4371 Evaluate side-chains 305 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 273 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 61 TRP Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain I residue 65 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 204 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 247 optimal weight: 8.9990 chunk 220 optimal weight: 5.9990 chunk 243 optimal weight: 0.0040 chunk 353 optimal weight: 40.0000 chunk 13 optimal weight: 6.9990 chunk 352 optimal weight: 30.0000 chunk 359 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.162000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.120809 restraints weight = 161248.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.121929 restraints weight = 72561.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.123055 restraints weight = 46356.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.123210 restraints weight = 42186.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.124427 restraints weight = 33791.095| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3858 r_free = 0.3858 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3858 r_free = 0.3858 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.0451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.995 30898 Z= 0.249 Angle : 0.981 106.100 42113 Z= 0.457 Chirality : 0.052 1.225 4835 Planarity : 0.006 0.102 5355 Dihedral : 6.821 58.683 4997 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.48 % Favored : 94.36 % Rotamer: Outliers : 1.01 % Allowed : 23.87 % Favored : 75.12 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.13), residues: 3734 helix: -0.41 (0.20), residues: 622 sheet: 0.13 (0.18), residues: 779 loop : -2.06 (0.11), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 237 TYR 0.016 0.001 TYR B 674 PHE 0.053 0.001 PHE B 306 TRP 0.016 0.001 TRP B 104 HIS 0.004 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00746 (30813) covalent geometry : angle 0.91325 (41900) SS BOND : bond 0.04020 ( 42) SS BOND : angle 5.63139 ( 84) hydrogen bonds : bond 0.08338 ( 885) hydrogen bonds : angle 8.12670 ( 2523) link_NAG-ASN : bond 0.01615 ( 43) link_NAG-ASN : angle 4.77113 ( 129) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 273 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.7327 (mmt) cc_final: 0.6911 (mtt) REVERT: B 748 GLU cc_start: 0.7713 (tp30) cc_final: 0.7362 (mt-10) REVERT: C 493 GLN cc_start: 0.3473 (OUTLIER) cc_final: 0.3001 (tp-100) REVERT: I 65 SER cc_start: 0.0184 (OUTLIER) cc_final: -0.0481 (p) outliers start: 32 outliers final: 30 residues processed: 288 average time/residue: 0.1805 time to fit residues: 88.3809 Evaluate side-chains 305 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 273 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 61 TRP Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain I residue 65 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 341 optimal weight: 40.0000 chunk 226 optimal weight: 20.0000 chunk 140 optimal weight: 0.0060 chunk 4 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 217 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 309 optimal weight: 20.0000 chunk 185 optimal weight: 0.9980 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.162002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.118445 restraints weight = 213232.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.122101 restraints weight = 80797.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.122826 restraints weight = 42545.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.122913 restraints weight = 39238.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.124046 restraints weight = 30918.060| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3850 r_free = 0.3850 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3850 r_free = 0.3850 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.0451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.995 30898 Z= 0.249 Angle : 0.981 106.100 42113 Z= 0.457 Chirality : 0.052 1.225 4835 Planarity : 0.006 0.102 5355 Dihedral : 6.821 58.683 4997 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.48 % Favored : 94.36 % Rotamer: Outliers : 1.01 % Allowed : 23.87 % Favored : 75.12 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.13), residues: 3734 helix: -0.41 (0.20), residues: 622 sheet: 0.13 (0.18), residues: 779 loop : -2.06 (0.11), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 237 TYR 0.016 0.001 TYR B 674 PHE 0.053 0.001 PHE B 306 TRP 0.016 0.001 TRP B 104 HIS 0.004 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00746 (30813) covalent geometry : angle 0.91325 (41900) SS BOND : bond 0.04020 ( 42) SS BOND : angle 5.63139 ( 84) hydrogen bonds : bond 0.08338 ( 885) hydrogen bonds : angle 8.12670 ( 2523) link_NAG-ASN : bond 0.01615 ( 43) link_NAG-ASN : angle 4.77113 ( 129) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 273 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.7391 (mmt) cc_final: 0.6980 (mtt) REVERT: B 748 GLU cc_start: 0.7710 (tp30) cc_final: 0.7350 (mt-10) REVERT: C 493 GLN cc_start: 0.3531 (OUTLIER) cc_final: 0.3059 (tp-100) REVERT: I 65 SER cc_start: 0.0130 (OUTLIER) cc_final: -0.0516 (p) outliers start: 32 outliers final: 30 residues processed: 288 average time/residue: 0.1760 time to fit residues: 86.0451 Evaluate side-chains 305 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 273 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 61 TRP Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain I residue 65 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 335 optimal weight: 0.4980 chunk 220 optimal weight: 8.9990 chunk 218 optimal weight: 20.0000 chunk 252 optimal weight: 20.0000 chunk 345 optimal weight: 40.0000 chunk 32 optimal weight: 2.9990 chunk 227 optimal weight: 10.0000 chunk 241 optimal weight: 30.0000 chunk 81 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.161999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.120676 restraints weight = 175934.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.122234 restraints weight = 71701.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.122675 restraints weight = 48310.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.123340 restraints weight = 43498.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.124159 restraints weight = 35423.613| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3851 r_free = 0.3851 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3851 r_free = 0.3851 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.0451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.995 30898 Z= 0.249 Angle : 0.981 106.100 42113 Z= 0.457 Chirality : 0.052 1.225 4835 Planarity : 0.006 0.102 5355 Dihedral : 6.821 58.683 4997 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.48 % Favored : 94.36 % Rotamer: Outliers : 1.01 % Allowed : 23.87 % Favored : 75.12 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.13), residues: 3734 helix: -0.41 (0.20), residues: 622 sheet: 0.13 (0.18), residues: 779 loop : -2.06 (0.11), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 237 TYR 0.016 0.001 TYR B 674 PHE 0.053 0.001 PHE B 306 TRP 0.016 0.001 TRP B 104 HIS 0.004 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00746 (30813) covalent geometry : angle 0.91325 (41900) SS BOND : bond 0.04020 ( 42) SS BOND : angle 5.63139 ( 84) hydrogen bonds : bond 0.08338 ( 885) hydrogen bonds : angle 8.12670 ( 2523) link_NAG-ASN : bond 0.01615 ( 43) link_NAG-ASN : angle 4.77113 ( 129) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 273 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.7309 (mmt) cc_final: 0.6908 (mtt) REVERT: B 748 GLU cc_start: 0.7738 (tp30) cc_final: 0.7377 (mt-10) REVERT: C 493 GLN cc_start: 0.3481 (OUTLIER) cc_final: 0.3009 (tp-100) REVERT: I 65 SER cc_start: 0.0170 (OUTLIER) cc_final: -0.0491 (p) outliers start: 32 outliers final: 30 residues processed: 288 average time/residue: 0.1808 time to fit residues: 88.3990 Evaluate side-chains 305 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 273 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 61 TRP Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain I residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 354 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 100 optimal weight: 0.0670 chunk 367 optimal weight: 7.9990 chunk 331 optimal weight: 30.0000 chunk 317 optimal weight: 7.9990 chunk 265 optimal weight: 6.9990 chunk 256 optimal weight: 0.3980 chunk 261 optimal weight: 1.9990 chunk 79 optimal weight: 0.0270 chunk 60 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.162001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.119770 restraints weight = 188532.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.122552 restraints weight = 74024.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.122792 restraints weight = 46060.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.123568 restraints weight = 42936.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.124123 restraints weight = 34027.404| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3850 r_free = 0.3850 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3850 r_free = 0.3850 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.0451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.995 30898 Z= 0.249 Angle : 0.981 106.100 42113 Z= 0.457 Chirality : 0.052 1.225 4835 Planarity : 0.006 0.102 5355 Dihedral : 6.821 58.683 4997 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.48 % Favored : 94.36 % Rotamer: Outliers : 1.01 % Allowed : 23.87 % Favored : 75.12 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.13), residues: 3734 helix: -0.41 (0.20), residues: 622 sheet: 0.13 (0.18), residues: 779 loop : -2.06 (0.11), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 237 TYR 0.016 0.001 TYR B 674 PHE 0.053 0.001 PHE B 306 TRP 0.016 0.001 TRP B 104 HIS 0.004 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00746 (30813) covalent geometry : angle 0.91325 (41900) SS BOND : bond 0.04020 ( 42) SS BOND : angle 5.63139 ( 84) hydrogen bonds : bond 0.08338 ( 885) hydrogen bonds : angle 8.12670 ( 2523) link_NAG-ASN : bond 0.01615 ( 43) link_NAG-ASN : angle 4.77113 ( 129) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 273 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.7375 (mmt) cc_final: 0.6961 (mtt) REVERT: B 748 GLU cc_start: 0.7730 (tp30) cc_final: 0.7372 (mt-10) REVERT: C 493 GLN cc_start: 0.3526 (OUTLIER) cc_final: 0.3054 (tp-100) REVERT: I 65 SER cc_start: 0.0134 (OUTLIER) cc_final: -0.0512 (p) outliers start: 32 outliers final: 30 residues processed: 288 average time/residue: 0.1831 time to fit residues: 89.5671 Evaluate side-chains 305 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 273 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 61 TRP Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain I residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 293 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 340 optimal weight: 20.0000 chunk 184 optimal weight: 2.9990 chunk 292 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 257 optimal weight: 0.8980 chunk 308 optimal weight: 1.9990 chunk 240 optimal weight: 30.0000 chunk 14 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.162000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.120668 restraints weight = 161739.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.121877 restraints weight = 72790.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.122997 restraints weight = 45984.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.123166 restraints weight = 41856.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.124531 restraints weight = 33480.911| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3860 r_free = 0.3860 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3860 r_free = 0.3860 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.0451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.995 30898 Z= 0.249 Angle : 0.981 106.100 42113 Z= 0.457 Chirality : 0.052 1.225 4835 Planarity : 0.006 0.102 5355 Dihedral : 6.821 58.683 4997 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.48 % Favored : 94.36 % Rotamer: Outliers : 1.01 % Allowed : 23.87 % Favored : 75.12 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.13), residues: 3734 helix: -0.41 (0.20), residues: 622 sheet: 0.13 (0.18), residues: 779 loop : -2.06 (0.11), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 237 TYR 0.016 0.001 TYR B 674 PHE 0.053 0.001 PHE B 306 TRP 0.016 0.001 TRP B 104 HIS 0.004 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00746 (30813) covalent geometry : angle 0.91325 (41900) SS BOND : bond 0.04020 ( 42) SS BOND : angle 5.63139 ( 84) hydrogen bonds : bond 0.08338 ( 885) hydrogen bonds : angle 8.12670 ( 2523) link_NAG-ASN : bond 0.01615 ( 43) link_NAG-ASN : angle 4.77113 ( 129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6312.59 seconds wall clock time: 109 minutes 45.17 seconds (6585.17 seconds total)