Starting phenix.real_space_refine on Fri Mar 6 09:10:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r8n_24319/03_2026/7r8n_24319.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r8n_24319/03_2026/7r8n_24319.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r8n_24319/03_2026/7r8n_24319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r8n_24319/03_2026/7r8n_24319.map" model { file = "/net/cci-nas-00/data/ceres_data/7r8n_24319/03_2026/7r8n_24319.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r8n_24319/03_2026/7r8n_24319.cif" } resolution = 3.55 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= 0.021 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 135 5.16 5 C 18907 2.51 5 N 4913 2.21 5 O 5764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29719 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 7945 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 2, 'GLN:plan1': 3, 'ARG:plan': 3, 'TYR:plan': 2, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "B" Number of atoms: 7945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 7945 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 2, 'GLN:plan1': 3, 'ARG:plan': 3, 'TYR:plan': 2, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "E" Number of atoms: 7945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 7945 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 2, 'GLN:plan1': 3, 'ARG:plan': 3, 'TYR:plan': 2, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "H" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 999 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 127} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 799 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "M" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 999 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 127} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 799 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "O" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 999 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 127} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 799 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 6.77, per 1000 atoms: 0.23 Number of scatterers: 29719 At special positions: 0 Unit cell: (150.337, 137.302, 175.538, 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 135 16.00 O 5764 8.00 N 4913 7.00 C 18907 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.01 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.01 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 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 E 15 " - pdb=" SG CYS E 136 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.04 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.05 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.04 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.02 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 95 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM29493 O5 NAG B1303 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A1301 " - " ASN A 165 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A1098 " " NAG A1307 " - " ASN A1134 " " NAG A1308 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B1098 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 343 " " NAG B1309 " - " ASN B 801 " " NAG C 1 " - " ASN A 234 " " NAG D 1 " - " ASN A 717 " " NAG E1301 " - " ASN E 165 " " NAG E1302 " - " ASN E 234 " " NAG E1303 " - " ASN E 282 " " NAG E1304 " - " ASN E 616 " " NAG E1305 " - " ASN E 657 " " NAG E1306 " - " ASN E 717 " " NAG E1307 " - " ASN E 801 " " NAG E1308 " - " ASN E1098 " " NAG E1309 " - " ASN E1134 " " NAG E1310 " - " ASN E 61 " " NAG F 1 " - " ASN B 234 " " NAG G 1 " - " ASN B 717 " Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.4 seconds 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7068 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 69 sheets defined 20.6% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 389 removed outlier: 4.082A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 389' Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.608A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (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 782 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.860A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.408A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.791A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.451A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 389 removed outlier: 4.234A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 386 through 389' Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.630A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 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 782 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 850 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.604A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 891' Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.512A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.817A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.513A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 416 through 422 removed outlier: 3.634A pdb=" N TYR E 421 " --> pdb=" O LYS E 417 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN E 422 " --> pdb=" O ILE E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 616 through 620 Processing helix chain 'E' and resid 737 through 744 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 782 Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 850 through 855 Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 886 through 891 removed outlier: 4.065A pdb=" N GLY E 891 " --> pdb=" O PHE E 888 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 909 Processing helix chain 'E' and resid 912 through 919 removed outlier: 4.378A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'E' and resid 945 through 967 Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 5.223A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 102 through 106 Processing helix chain 'M' and resid 86 through 90 removed outlier: 3.609A pdb=" N ASP M 89 " --> pdb=" O ARG M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 102 through 106 Processing helix chain 'N' and resid 82 through 86 removed outlier: 3.506A pdb=" N ASP N 85 " --> pdb=" O GLN N 82 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU N 86 " --> pdb=" O ALA N 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 82 through 86' Processing helix chain 'O' and resid 86 through 90 removed outlier: 3.596A pdb=" N ASP O 89 " --> pdb=" O ARG O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 102 through 106 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.931A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 44 removed outlier: 3.740A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE E 587 " --> pdb=" O ASP E 574 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU E 324 " --> pdb=" O CYS E 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.531A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.743A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE A 238 " --> pdb=" O LEU A 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 229 removed outlier: 6.649A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 101 through 104 removed outlier: 6.437A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 118 through 120 removed outlier: 4.101A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.988A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 595 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY A 593 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.922A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.748A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 376 through 378 removed outlier: 4.090A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.043A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS A 671 " --> pdb=" O TYR A 695 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 703 through 704 removed outlier: 3.714A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB7, first strand: chain 'A' and resid 719 through 728 removed outlier: 3.518A pdb=" N THR A 723 " --> pdb=" O HIS A1064 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS A1064 " --> pdb=" O THR A 723 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 727 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A1060 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.693A 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: 4.110A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 859 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 789 through 790 removed outlier: 3.795A pdb=" N LYS A 790 " --> pdb=" O ASN E 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 4.745A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.527A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.506A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.421A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 118 through 120 removed outlier: 3.576A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 201 through 205 removed outlier: 3.971A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 314 through 319 removed outlier: 6.922A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER B 596 " --> pdb=" O LEU B 611 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.396A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN B 540 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE B 565 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AD1, 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) Processing sheet with id=AD2, first strand: chain 'B' and resid 376 through 379 removed outlier: 4.453A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.000A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N CYS B 671 " --> pdb=" O TYR B 695 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.860A pdb=" N LYS E 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.505A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR B 723 " --> pdb=" O HIS B1064 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B1062 " --> pdb=" O GLU B 725 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 727 " --> pdb=" O VAL B1060 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.280A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 3.528A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE2, first strand: chain 'E' and resid 27 through 30 removed outlier: 8.159A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR E 63 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL E 267 " --> pdb=" O THR E 63 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE E 65 " --> pdb=" O TYR E 265 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR E 265 " --> pdb=" O PHE E 65 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG E 190 " --> pdb=" O SER E 94 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU E 96 " --> pdb=" O ASN E 188 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN E 188 " --> pdb=" O GLU E 96 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 36 through 37 removed outlier: 8.006A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'E' and resid 48 through 55 removed outlier: 3.505A pdb=" N PHE E 55 " --> pdb=" O GLN E 271 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN E 271 " --> pdb=" O PHE E 55 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 84 through 85 removed outlier: 4.334A pdb=" N LEU E 84 " --> pdb=" O PHE E 238 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE E 238 " --> pdb=" O LEU E 84 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG E 237 " --> pdb=" O PHE E 106 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE E 106 " --> pdb=" O ARG E 237 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLN E 239 " --> pdb=" O TRP E 104 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N TRP E 104 " --> pdb=" O GLN E 239 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU E 241 " --> pdb=" O ARG E 102 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 118 through 120 removed outlier: 4.297A pdb=" N VAL E 127 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL E 126 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR E 170 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE E 168 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU E 132 " --> pdb=" O CYS E 166 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N CYS E 166 " --> pdb=" O GLU E 132 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLN E 134 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ASN E 164 " --> pdb=" O GLN E 134 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 201 through 204 removed outlier: 3.763A pdb=" N ILE E 203 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL E 227 " --> pdb=" O ILE E 203 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 313 through 319 removed outlier: 6.751A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL E 595 " --> pdb=" O SER E 316 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY E 593 " --> pdb=" O PHE E 318 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS E 649 " --> pdb=" O TYR E 612 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.693A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 376 through 378 removed outlier: 4.081A pdb=" N LYS E 378 " --> pdb=" O VAL E 433 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL E 433 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE E 402 " --> pdb=" O TYR E 508 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AF3, first strand: chain 'E' and resid 654 through 655 removed outlier: 5.973A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 711 through 713 Processing sheet with id=AF5, first strand: chain 'E' and resid 718 through 728 removed outlier: 3.589A pdb=" N SER E 721 " --> pdb=" O THR E1066 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR E 723 " --> pdb=" O HIS E1064 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS E1064 " --> pdb=" O THR E 723 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU E 725 " --> pdb=" O PHE E1062 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE E1062 " --> pdb=" O GLU E 725 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU E 727 " --> pdb=" O VAL E1060 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL E1060 " --> pdb=" O LEU E 727 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.155A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR E 859 " --> pdb=" O SER E 735 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 1081 through 1082 removed outlier: 4.511A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 1093 through 1096 Processing sheet with id=AF9, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.596A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS H 22 " --> pdb=" O VAL H 78 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.083A pdb=" N ILE H 12 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL H 50 " --> pdb=" O TYR H 58 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N TYR H 58 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.083A pdb=" N ILE H 12 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N CYS H 95 " --> pdb=" O TRP H 121 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N TRP H 121 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ARG H 97 " --> pdb=" O ASP H 119 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 11 through 13 Processing sheet with id=AG4, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AG5, first strand: chain 'L' and resid 48 through 52 removed outlier: 5.129A pdb=" N LEU L 49 " --> pdb=" O GLN L 40 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLN L 40 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.835A pdb=" N THR M 68 " --> pdb=" O GLN M 81 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 45 through 51 removed outlier: 5.042A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AG9, first strand: chain 'N' and resid 48 through 52 removed outlier: 5.256A pdb=" N LEU N 49 " --> pdb=" O GLN N 40 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLN N 40 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN N 41 " --> pdb=" O ASP N 88 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP N 88 " --> pdb=" O GLN N 41 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.511A pdb=" N MET O 82 " --> pdb=" O LEU O 18 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR O 68 " --> pdb=" O GLN O 81 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'O' and resid 58 through 59 removed outlier: 4.486A pdb=" N TYR O 58 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL O 50 " --> pdb=" O TYR O 58 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N CYS O 95 " --> pdb=" O TRP O 121 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N TRP O 121 " --> pdb=" O CYS O 95 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ARG O 97 " --> pdb=" O ASP O 119 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'O' and resid 58 through 59 removed outlier: 4.486A pdb=" N TYR O 58 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL O 50 " --> pdb=" O TYR O 58 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'P' and resid 11 through 13 Processing sheet with id=AH5, first strand: chain 'P' and resid 19 through 24 Processing sheet with id=AH6, first strand: chain 'P' and resid 48 through 52 removed outlier: 6.570A pdb=" N TRP P 38 " --> pdb=" O LEU P 50 " (cutoff:3.500A) 1005 hydrogen bonds defined for protein. 2742 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.40 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 8617 1.34 - 1.47: 8566 1.47 - 1.60: 13039 1.60 - 1.73: 1 1.73 - 1.87: 171 Bond restraints: 30394 Sorted by residual: bond pdb=" N GLN N 6 " pdb=" CA GLN N 6 " ideal model delta sigma weight residual 1.455 1.489 -0.034 7.00e-03 2.04e+04 2.40e+01 bond pdb=" N GLN A 498 " pdb=" CA GLN A 498 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.75e+01 bond pdb=" N PHE E 329 " pdb=" CA PHE E 329 " ideal model delta sigma weight residual 1.453 1.488 -0.034 8.30e-03 1.45e+04 1.72e+01 bond pdb=" N VAL L 11 " pdb=" CA VAL L 11 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.20e+01 bond pdb=" N VAL P 54 " pdb=" CA VAL P 54 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.25e-02 6.40e+03 1.16e+01 ... (remaining 30389 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.81: 40735 4.81 - 9.62: 572 9.62 - 14.43: 76 14.43 - 19.23: 8 19.23 - 24.04: 2 Bond angle restraints: 41393 Sorted by residual: angle pdb=" CA PRO A 272 " pdb=" N PRO A 272 " pdb=" CD PRO A 272 " ideal model delta sigma weight residual 112.00 98.56 13.44 1.40e+00 5.10e-01 9.21e+01 angle pdb=" N CYS E 525 " pdb=" CA CYS E 525 " pdb=" C CYS E 525 " ideal model delta sigma weight residual 107.73 118.60 -10.87 1.34e+00 5.57e-01 6.58e+01 angle pdb=" CA GLY A 502 " pdb=" C GLY A 502 " pdb=" O GLY A 502 " ideal model delta sigma weight residual 122.22 117.15 5.07 6.50e-01 2.37e+00 6.09e+01 angle pdb=" CA GLN E 563 " pdb=" CB GLN E 563 " pdb=" CG GLN E 563 " ideal model delta sigma weight residual 114.10 128.70 -14.60 2.00e+00 2.50e-01 5.33e+01 angle pdb=" N ARG B1014 " pdb=" CA ARG B1014 " pdb=" C ARG B1014 " ideal model delta sigma weight residual 111.36 103.70 7.66 1.09e+00 8.42e-01 4.94e+01 ... (remaining 41388 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16876 17.98 - 35.97: 1123 35.97 - 53.95: 303 53.95 - 71.94: 80 71.94 - 89.92: 44 Dihedral angle restraints: 18426 sinusoidal: 7398 harmonic: 11028 Sorted by residual: dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -4.05 -81.95 1 1.00e+01 1.00e-02 8.26e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -8.43 -77.57 1 1.00e+01 1.00e-02 7.53e+01 dihedral pdb=" CB CYS E 291 " pdb=" SG CYS E 291 " pdb=" SG CYS E 301 " pdb=" CB CYS E 301 " ideal model delta sinusoidal sigma weight residual -86.00 -10.03 -75.97 1 1.00e+01 1.00e-02 7.27e+01 ... (remaining 18423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.177: 4556 0.177 - 0.354: 202 0.354 - 0.531: 14 0.531 - 0.708: 7 0.708 - 0.885: 1 Chirality restraints: 4780 Sorted by residual: chirality pdb=" CB ILE B 882 " pdb=" CA ILE B 882 " pdb=" CG1 ILE B 882 " pdb=" CG2 ILE B 882 " both_signs ideal model delta sigma weight residual False 2.64 1.76 0.89 2.00e-01 2.50e+01 1.96e+01 chirality pdb=" CB ILE B 666 " pdb=" CA ILE B 666 " pdb=" CG1 ILE B 666 " pdb=" CG2 ILE B 666 " both_signs ideal model delta sigma weight residual False 2.64 1.99 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" C1 NAG E1302 " pdb=" ND2 ASN E 234 " pdb=" C2 NAG E1302 " pdb=" O5 NAG E1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.67e+00 ... (remaining 4777 not shown) Planarity restraints: 5355 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 271 " 0.102 5.00e-02 4.00e+02 1.45e-01 3.36e+01 pdb=" N PRO A 272 " -0.250 5.00e-02 4.00e+02 pdb=" CA PRO A 272 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 272 " 0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER P 14 " -0.093 5.00e-02 4.00e+02 1.41e-01 3.16e+01 pdb=" N PRO P 15 " 0.243 5.00e-02 4.00e+02 pdb=" CA PRO P 15 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO P 15 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E1052 " -0.091 5.00e-02 4.00e+02 1.40e-01 3.13e+01 pdb=" N PRO E1053 " 0.242 5.00e-02 4.00e+02 pdb=" CA PRO E1053 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO E1053 " -0.073 5.00e-02 4.00e+02 ... (remaining 5352 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1233 2.70 - 3.25: 28937 3.25 - 3.80: 47504 3.80 - 4.35: 59311 4.35 - 4.90: 98126 Nonbonded interactions: 235111 Sorted by model distance: nonbonded pdb=" OG1 THR B 393 " pdb=" O GLU B 516 " model vdw 2.148 3.040 nonbonded pdb=" O GLU A 484 " pdb=" OH TYR H 58 " model vdw 2.188 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.188 3.040 nonbonded pdb=" O TYR E 38 " pdb=" OH TYR E 204 " model vdw 2.196 3.040 nonbonded pdb=" O GLU E 484 " pdb=" OH TYR M 58 " model vdw 2.216 3.040 ... (remaining 235106 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 15 through 1308) selection = (chain 'E' and resid 15 through 1308) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.070 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: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 28.280 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 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 : 0.008 0.125 30472 Z= 0.399 Angle : 1.590 26.147 41584 Z= 0.865 Chirality : 0.089 0.885 4780 Planarity : 0.011 0.145 5324 Dihedral : 14.068 89.924 11229 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.48 % Allowed : 1.23 % Favored : 97.30 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.12), residues: 3753 helix: -0.05 (0.17), residues: 681 sheet: 0.18 (0.19), residues: 669 loop : -1.37 (0.12), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG A 34 TYR 0.078 0.004 TYR A 904 PHE 0.074 0.005 PHE L 102 TRP 0.056 0.005 TRP P 38 HIS 0.033 0.003 HIS E1048 Details of bonding type rmsd covalent geometry : bond 0.00801 (30394) covalent geometry : angle 1.52842 (41393) SS BOND : bond 0.00804 ( 43) SS BOND : angle 3.94424 ( 86) hydrogen bonds : bond 0.21786 ( 991) hydrogen bonds : angle 9.38231 ( 2742) link_BETA1-4 : bond 0.01760 ( 4) link_BETA1-4 : angle 4.51969 ( 12) link_NAG-ASN : bond 0.01717 ( 31) link_NAG-ASN : angle 8.60069 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 618 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.5968 (m-30) cc_final: 0.5512 (m-30) REVERT: A 506 GLN cc_start: 0.6516 (OUTLIER) cc_final: 0.6144 (mt0) REVERT: A 740 MET cc_start: 0.5664 (tpp) cc_final: 0.5277 (tpp) REVERT: A 814 LYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6748 (mmtt) REVERT: A 928 ASN cc_start: 0.7419 (m110) cc_final: 0.7110 (m-40) REVERT: A 977 LEU cc_start: 0.7538 (tp) cc_final: 0.7315 (tp) REVERT: B 349 SER cc_start: 0.7766 (t) cc_final: 0.7540 (p) REVERT: B 529 LYS cc_start: 0.8112 (mppt) cc_final: 0.7580 (tptp) REVERT: B 977 LEU cc_start: 0.7503 (tp) cc_final: 0.7132 (tp) REVERT: B 1048 HIS cc_start: 0.6745 (t70) cc_final: 0.6296 (t70) REVERT: E 118 LEU cc_start: 0.7069 (tp) cc_final: 0.6846 (tp) REVERT: E 759 PHE cc_start: 0.6961 (OUTLIER) cc_final: 0.6240 (t80) REVERT: E 810 SER cc_start: 0.7617 (OUTLIER) cc_final: 0.7367 (p) REVERT: E 814 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7290 (mmtt) REVERT: L 94 PHE cc_start: 0.4021 (t80) cc_final: 0.3252 (t80) outliers start: 47 outliers final: 8 residues processed: 646 average time/residue: 0.1703 time to fit residues: 179.1952 Evaluate side-chains 419 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 406 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 810 SER Chi-restraints excluded: chain E residue 811 LYS Chi-restraints excluded: chain E residue 813 SER Chi-restraints excluded: chain E residue 814 LYS Chi-restraints excluded: chain L residue 41 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.0770 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1011 GLN A1108 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS B 901 GLN B1023 ASN B1101 HIS E 66 HIS ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 GLN E 856 ASN E 901 GLN ** E1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1011 GLN ** E1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1058 HIS E1083 HIS ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN O 31 ASN O 73 ASN ** P 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 98 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.165764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.142033 restraints weight = 71505.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.145359 restraints weight = 37282.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.147527 restraints weight = 23512.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.148907 restraints weight = 16928.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.149851 restraints weight = 13534.867| |-----------------------------------------------------------------------------| r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6412 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 30472 Z= 0.185 Angle : 0.859 17.342 41584 Z= 0.431 Chirality : 0.053 0.607 4780 Planarity : 0.007 0.083 5324 Dihedral : 8.470 76.099 4854 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.45 % Allowed : 11.60 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.13), residues: 3753 helix: 0.10 (0.19), residues: 684 sheet: -0.10 (0.18), residues: 717 loop : -1.37 (0.12), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 577 TYR 0.029 0.002 TYR E 37 PHE 0.030 0.002 PHE B 898 TRP 0.037 0.002 TRP H 47 HIS 0.011 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00402 (30394) covalent geometry : angle 0.80632 (41393) SS BOND : bond 0.00418 ( 43) SS BOND : angle 2.45820 ( 86) hydrogen bonds : bond 0.06259 ( 991) hydrogen bonds : angle 7.66128 ( 2742) link_BETA1-4 : bond 0.01100 ( 4) link_BETA1-4 : angle 2.79864 ( 12) link_NAG-ASN : bond 0.00860 ( 31) link_NAG-ASN : angle 5.80767 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 498 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7357 (t0) cc_final: 0.7098 (t0) REVERT: A 177 MET cc_start: 0.1861 (mmp) cc_final: 0.1558 (mmt) REVERT: A 506 GLN cc_start: 0.6935 (OUTLIER) cc_final: 0.6657 (mt0) REVERT: B 375 SER cc_start: 0.8487 (t) cc_final: 0.8163 (m) REVERT: B 529 LYS cc_start: 0.8180 (mppt) cc_final: 0.7336 (mmmt) REVERT: B 751 ASN cc_start: 0.8162 (m-40) cc_final: 0.7897 (m-40) REVERT: B 1048 HIS cc_start: 0.6908 (t70) cc_final: 0.6515 (t70) REVERT: E 118 LEU cc_start: 0.6986 (tp) cc_final: 0.6779 (tp) REVERT: E 269 TYR cc_start: 0.3367 (OUTLIER) cc_final: 0.3026 (m-10) REVERT: E 1077 THR cc_start: 0.6620 (t) cc_final: 0.6072 (t) REVERT: H 89 ASP cc_start: 0.4661 (m-30) cc_final: 0.4337 (m-30) REVERT: L 40 GLN cc_start: 0.5889 (OUTLIER) cc_final: 0.5543 (tm-30) REVERT: M 19 ARG cc_start: 0.6412 (tpt170) cc_final: 0.6177 (tpp80) REVERT: M 89 ASP cc_start: 0.4994 (m-30) cc_final: 0.4552 (m-30) REVERT: N 17 GLN cc_start: 0.7854 (pp30) cc_final: 0.7488 (pp30) REVERT: P 90 TYR cc_start: 0.6724 (m-80) cc_final: 0.6297 (m-80) REVERT: P 100 ARG cc_start: 0.6517 (ptp-170) cc_final: 0.6165 (mtt-85) outliers start: 78 outliers final: 50 residues processed: 542 average time/residue: 0.1637 time to fit residues: 147.7785 Evaluate side-chains 457 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 404 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 204 TYR Chi-restraints excluded: chain E residue 269 TYR Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 313 TYR Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 727 LEU Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain E residue 873 TYR Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 979 ASP Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 105 SER Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain P residue 40 GLN Chi-restraints excluded: chain P residue 63 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 180 optimal weight: 2.9990 chunk 272 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 303 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 348 optimal weight: 4.9990 chunk 286 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 99 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN A 969 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 907 ASN B 955 ASN B1119 ASN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS E 99 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 675 GLN E 955 ASN E1010 GLN ** E1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 81 GLN ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 32 ASN P 82 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.162189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.137796 restraints weight = 71904.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.142204 restraints weight = 39183.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.143292 restraints weight = 21678.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.144212 restraints weight = 17251.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.144696 restraints weight = 14399.840| |-----------------------------------------------------------------------------| r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 30472 Z= 0.208 Angle : 0.796 16.463 41584 Z= 0.399 Chirality : 0.051 0.517 4780 Planarity : 0.006 0.065 5324 Dihedral : 7.671 63.844 4837 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.28 % Allowed : 14.03 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.13), residues: 3753 helix: 0.13 (0.19), residues: 684 sheet: -0.18 (0.18), residues: 720 loop : -1.36 (0.12), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 100 TYR 0.023 0.002 TYR E 37 PHE 0.028 0.002 PHE B 898 TRP 0.036 0.002 TRP B 886 HIS 0.009 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00459 (30394) covalent geometry : angle 0.75332 (41393) SS BOND : bond 0.01195 ( 43) SS BOND : angle 2.03144 ( 86) hydrogen bonds : bond 0.05708 ( 991) hydrogen bonds : angle 7.14205 ( 2742) link_BETA1-4 : bond 0.01237 ( 4) link_BETA1-4 : angle 2.42643 ( 12) link_NAG-ASN : bond 0.00827 ( 31) link_NAG-ASN : angle 5.11276 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 468 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.6625 (m) cc_final: 0.6362 (m) REVERT: A 177 MET cc_start: 0.2286 (mmp) cc_final: 0.1679 (mmt) REVERT: A 651 ILE cc_start: 0.7541 (pt) cc_final: 0.7277 (pt) REVERT: B 529 LYS cc_start: 0.8313 (mppt) cc_final: 0.7406 (mmmt) REVERT: B 563 GLN cc_start: 0.5398 (tt0) cc_final: 0.5075 (tt0) REVERT: B 802 PHE cc_start: 0.6727 (m-80) cc_final: 0.6471 (m-80) REVERT: B 898 PHE cc_start: 0.6788 (OUTLIER) cc_final: 0.5279 (t80) REVERT: B 900 MET cc_start: 0.5378 (mpp) cc_final: 0.4931 (mpp) REVERT: B 1048 HIS cc_start: 0.7026 (t70) cc_final: 0.5682 (t70) REVERT: E 118 LEU cc_start: 0.7443 (tp) cc_final: 0.7217 (tp) REVERT: E 269 TYR cc_start: 0.3648 (OUTLIER) cc_final: 0.2929 (m-10) REVERT: E 298 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6583 (mm-30) REVERT: E 759 PHE cc_start: 0.7541 (OUTLIER) cc_final: 0.6712 (t80) REVERT: E 1077 THR cc_start: 0.7519 (t) cc_final: 0.7159 (t) REVERT: H 51 ILE cc_start: 0.7097 (OUTLIER) cc_final: 0.6880 (mp) REVERT: H 89 ASP cc_start: 0.4825 (m-30) cc_final: 0.4409 (m-30) REVERT: L 17 GLN cc_start: 0.7516 (pp30) cc_final: 0.7157 (pp30) REVERT: L 90 TYR cc_start: 0.7427 (m-80) cc_final: 0.6805 (m-80) REVERT: M 89 ASP cc_start: 0.5189 (m-30) cc_final: 0.4597 (m-30) REVERT: N 17 GLN cc_start: 0.8175 (pp30) cc_final: 0.7814 (pp30) REVERT: O 19 ARG cc_start: 0.6268 (tpt170) cc_final: 0.5409 (tpp80) REVERT: P 39 TYR cc_start: 0.7691 (m-80) cc_final: 0.7478 (m-80) REVERT: P 90 TYR cc_start: 0.6869 (m-80) cc_final: 0.6496 (m-80) REVERT: P 94 PHE cc_start: 0.4176 (t80) cc_final: 0.3097 (t80) outliers start: 136 outliers final: 84 residues processed: 551 average time/residue: 0.1581 time to fit residues: 146.2000 Evaluate side-chains 492 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 403 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 269 TYR Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 313 TYR Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain E residue 860 VAL Chi-restraints excluded: chain E residue 873 TYR Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 979 ASP Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 29 ASP Chi-restraints excluded: chain N residue 63 ASP Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain O residue 32 ASN Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 63 ASP Chi-restraints excluded: chain P residue 73 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 113 optimal weight: 8.9990 chunk 198 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 141 optimal weight: 0.0570 chunk 244 optimal weight: 2.9990 overall best weight: 2.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 928 ASN A 949 GLN A 955 ASN A1023 ASN A1106 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B 613 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS E 409 GLN ** E 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN N 6 GLN ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.157337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.132380 restraints weight = 71782.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.135551 restraints weight = 37625.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.137622 restraints weight = 24080.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.138978 restraints weight = 17678.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.139839 restraints weight = 14380.219| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 30472 Z= 0.244 Angle : 0.804 15.995 41584 Z= 0.407 Chirality : 0.052 0.519 4780 Planarity : 0.006 0.064 5324 Dihedral : 7.240 60.027 4831 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.98 % Favored : 92.99 % Rotamer: Outliers : 4.65 % Allowed : 16.73 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.13), residues: 3753 helix: -0.00 (0.20), residues: 669 sheet: -0.16 (0.20), residues: 663 loop : -1.46 (0.12), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 100 TYR 0.023 0.002 TYR E 37 PHE 0.026 0.002 PHE A1052 TRP 0.045 0.002 TRP H 47 HIS 0.009 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00547 (30394) covalent geometry : angle 0.76565 (41393) SS BOND : bond 0.00424 ( 43) SS BOND : angle 2.05411 ( 86) hydrogen bonds : bond 0.05748 ( 991) hydrogen bonds : angle 7.12761 ( 2742) link_BETA1-4 : bond 0.01098 ( 4) link_BETA1-4 : angle 2.50443 ( 12) link_NAG-ASN : bond 0.00750 ( 31) link_NAG-ASN : angle 4.86326 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 444 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7665 (p) REVERT: A 858 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8553 (pp) REVERT: A 870 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.8016 (mt) REVERT: A 900 MET cc_start: 0.6825 (mtp) cc_final: 0.6357 (mtm) REVERT: B 118 LEU cc_start: 0.7635 (mp) cc_final: 0.6927 (tp) REVERT: B 214 ARG cc_start: 0.2661 (mmm160) cc_final: 0.1651 (mmm160) REVERT: B 529 LYS cc_start: 0.8304 (mppt) cc_final: 0.7433 (mmmt) REVERT: B 870 ILE cc_start: 0.8147 (mm) cc_final: 0.7848 (mt) REVERT: B 898 PHE cc_start: 0.6863 (OUTLIER) cc_final: 0.5418 (t80) REVERT: E 203 ILE cc_start: 0.8376 (mt) cc_final: 0.7808 (tp) REVERT: E 298 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6481 (mm-30) REVERT: E 376 THR cc_start: 0.8052 (OUTLIER) cc_final: 0.7638 (p) REVERT: E 1077 THR cc_start: 0.7674 (t) cc_final: 0.7454 (t) REVERT: H 51 ILE cc_start: 0.6997 (OUTLIER) cc_final: 0.6764 (mp) REVERT: H 67 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.7473 (t80) REVERT: H 93 TYR cc_start: 0.6997 (m-80) cc_final: 0.6687 (m-80) REVERT: H 123 GLN cc_start: 0.5971 (mp10) cc_final: 0.5393 (tm-30) REVERT: L 17 GLN cc_start: 0.7646 (pp30) cc_final: 0.7369 (pp30) REVERT: L 81 LEU cc_start: 0.5593 (OUTLIER) cc_final: 0.5391 (tt) REVERT: L 90 TYR cc_start: 0.7653 (m-80) cc_final: 0.7002 (m-80) REVERT: M 19 ARG cc_start: 0.6596 (tpt170) cc_final: 0.6329 (tpp80) REVERT: M 89 ASP cc_start: 0.5155 (m-30) cc_final: 0.4782 (m-30) REVERT: N 17 GLN cc_start: 0.8118 (pp30) cc_final: 0.7790 (pp30) REVERT: N 82 GLN cc_start: 0.6146 (OUTLIER) cc_final: 0.5946 (mp10) REVERT: O 19 ARG cc_start: 0.6337 (tpt170) cc_final: 0.5782 (tpp80) REVERT: P 90 TYR cc_start: 0.7192 (m-80) cc_final: 0.6925 (m-80) outliers start: 148 outliers final: 97 residues processed: 545 average time/residue: 0.1573 time to fit residues: 143.2975 Evaluate side-chains 497 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 390 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 200 TYR Chi-restraints excluded: chain E residue 231 ILE Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 655 HIS Chi-restraints excluded: chain E residue 692 ILE Chi-restraints excluded: chain E residue 716 THR Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain E residue 860 VAL Chi-restraints excluded: chain E residue 873 TYR Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 979 ASP Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 114 ASP Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 63 ASP Chi-restraints excluded: chain P residue 73 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 273 optimal weight: 0.9980 chunk 348 optimal weight: 20.0000 chunk 136 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 294 optimal weight: 2.9990 chunk 361 optimal weight: 20.0000 chunk 162 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS E 439 ASN ** E 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 613 GLN ** E 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 955 ASN N 40 GLN O 32 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.158497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.133613 restraints weight = 71977.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.136822 restraints weight = 37894.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.138899 restraints weight = 24279.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.140186 restraints weight = 17870.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.141140 restraints weight = 14574.944| |-----------------------------------------------------------------------------| r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30472 Z= 0.181 Angle : 0.747 15.771 41584 Z= 0.373 Chirality : 0.050 0.512 4780 Planarity : 0.005 0.065 5324 Dihedral : 6.940 58.349 4827 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.72 % Allowed : 17.96 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.13), residues: 3753 helix: 0.03 (0.20), residues: 678 sheet: -0.28 (0.19), residues: 699 loop : -1.42 (0.12), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 237 TYR 0.023 0.002 TYR H 116 PHE 0.024 0.002 PHE B 898 TRP 0.042 0.002 TRP H 47 HIS 0.009 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00406 (30394) covalent geometry : angle 0.70911 (41393) SS BOND : bond 0.00385 ( 43) SS BOND : angle 1.86921 ( 86) hydrogen bonds : bond 0.05286 ( 991) hydrogen bonds : angle 6.94595 ( 2742) link_BETA1-4 : bond 0.01112 ( 4) link_BETA1-4 : angle 2.39133 ( 12) link_NAG-ASN : bond 0.00727 ( 31) link_NAG-ASN : angle 4.68295 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 427 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 THR cc_start: 0.8065 (OUTLIER) cc_final: 0.7637 (p) REVERT: A 740 MET cc_start: 0.5409 (tpt) cc_final: 0.5144 (mmt) REVERT: A 858 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8485 (pp) REVERT: A 870 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7919 (mt) REVERT: A 967 SER cc_start: 0.8106 (OUTLIER) cc_final: 0.7807 (t) REVERT: B 118 LEU cc_start: 0.7693 (mp) cc_final: 0.6979 (tp) REVERT: B 214 ARG cc_start: 0.2719 (mmm160) cc_final: 0.1505 (mmm160) REVERT: B 529 LYS cc_start: 0.8306 (mppt) cc_final: 0.7467 (mmmt) REVERT: B 870 ILE cc_start: 0.8269 (mm) cc_final: 0.7915 (mt) REVERT: B 898 PHE cc_start: 0.6724 (OUTLIER) cc_final: 0.5155 (t80) REVERT: E 118 LEU cc_start: 0.7636 (mp) cc_final: 0.7134 (tp) REVERT: E 203 ILE cc_start: 0.8330 (mt) cc_final: 0.7723 (tp) REVERT: E 376 THR cc_start: 0.8050 (OUTLIER) cc_final: 0.7585 (p) REVERT: E 428 ASP cc_start: 0.8019 (p0) cc_final: 0.7799 (p0) REVERT: E 511 VAL cc_start: 0.8661 (t) cc_final: 0.8432 (t) REVERT: E 740 MET cc_start: 0.6870 (tpp) cc_final: 0.6663 (mmm) REVERT: E 759 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7058 (t80) REVERT: E 955 ASN cc_start: 0.7490 (OUTLIER) cc_final: 0.7237 (m110) REVERT: H 3 GLN cc_start: 0.7696 (mm-40) cc_final: 0.7444 (mp10) REVERT: H 51 ILE cc_start: 0.6899 (OUTLIER) cc_final: 0.6682 (mp) REVERT: H 67 PHE cc_start: 0.7801 (OUTLIER) cc_final: 0.7539 (t80) REVERT: H 93 TYR cc_start: 0.6985 (m-80) cc_final: 0.6677 (m-80) REVERT: L 17 GLN cc_start: 0.7695 (pp30) cc_final: 0.7424 (pp30) REVERT: L 81 LEU cc_start: 0.5490 (OUTLIER) cc_final: 0.5276 (tt) REVERT: L 90 TYR cc_start: 0.7705 (m-80) cc_final: 0.7241 (m-80) REVERT: M 89 ASP cc_start: 0.5023 (m-30) cc_final: 0.4650 (m-30) REVERT: N 17 GLN cc_start: 0.8080 (pp30) cc_final: 0.7815 (pp30) REVERT: N 85 ASP cc_start: 0.6243 (t0) cc_final: 0.5239 (m-30) REVERT: O 19 ARG cc_start: 0.6470 (tpt170) cc_final: 0.5918 (tpp80) REVERT: P 41 GLN cc_start: 0.7245 (pm20) cc_final: 0.6841 (pm20) REVERT: P 90 TYR cc_start: 0.7212 (m-80) cc_final: 0.6286 (m-80) REVERT: P 94 PHE cc_start: 0.4595 (t80) cc_final: 0.3360 (t80) REVERT: P 100 ARG cc_start: 0.6715 (ptp-170) cc_final: 0.6341 (mtt180) outliers start: 150 outliers final: 106 residues processed: 529 average time/residue: 0.1615 time to fit residues: 142.6410 Evaluate side-chains 505 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 388 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 231 ILE Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 716 THR Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain E residue 860 VAL Chi-restraints excluded: chain E residue 907 ASN Chi-restraints excluded: chain E residue 955 ASN Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 979 ASP Chi-restraints excluded: chain E residue 1032 CYS Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 120 TYR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 29 ASP Chi-restraints excluded: chain N residue 63 ASP Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 95 CYS Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 63 ASP Chi-restraints excluded: chain P residue 73 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 122 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 220 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 158 optimal weight: 0.2980 chunk 176 optimal weight: 3.9990 chunk 362 optimal weight: 10.0000 chunk 224 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 210 optimal weight: 10.0000 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS E 409 GLN E 439 ASN ** E 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN N 82 GLN O 32 ASN ** P 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.156987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.131876 restraints weight = 72041.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.135085 restraints weight = 37828.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.137167 restraints weight = 24293.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.138513 restraints weight = 17833.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.139439 restraints weight = 14487.311| |-----------------------------------------------------------------------------| r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 30472 Z= 0.206 Angle : 0.758 15.434 41584 Z= 0.381 Chirality : 0.051 0.507 4780 Planarity : 0.005 0.064 5324 Dihedral : 6.846 58.023 4827 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.83 % Favored : 92.11 % Rotamer: Outliers : 5.28 % Allowed : 18.84 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.13), residues: 3753 helix: 0.01 (0.20), residues: 675 sheet: -0.45 (0.19), residues: 717 loop : -1.48 (0.12), residues: 2361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 577 TYR 0.022 0.002 TYR E1067 PHE 0.024 0.002 PHE A1042 TRP 0.037 0.002 TRP H 47 HIS 0.008 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00468 (30394) covalent geometry : angle 0.72211 (41393) SS BOND : bond 0.00403 ( 43) SS BOND : angle 1.89960 ( 86) hydrogen bonds : bond 0.05339 ( 991) hydrogen bonds : angle 6.95541 ( 2742) link_BETA1-4 : bond 0.00945 ( 4) link_BETA1-4 : angle 2.61153 ( 12) link_NAG-ASN : bond 0.00690 ( 31) link_NAG-ASN : angle 4.55079 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 422 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 ILE cc_start: 0.3510 (OUTLIER) cc_final: 0.3298 (pt) REVERT: A 376 THR cc_start: 0.8070 (OUTLIER) cc_final: 0.7679 (p) REVERT: A 493 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.7096 (tm-30) REVERT: A 612 TYR cc_start: 0.7193 (m-80) cc_final: 0.6836 (m-80) REVERT: A 858 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8542 (pp) REVERT: A 870 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.8008 (mt) REVERT: A 967 SER cc_start: 0.8119 (OUTLIER) cc_final: 0.7871 (t) REVERT: B 214 ARG cc_start: 0.2601 (mmm160) cc_final: 0.1498 (mmm160) REVERT: B 529 LYS cc_start: 0.8287 (mppt) cc_final: 0.7453 (mmmt) REVERT: B 651 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7329 (tt) REVERT: B 870 ILE cc_start: 0.8376 (mm) cc_final: 0.8106 (mt) REVERT: B 900 MET cc_start: 0.5483 (mpp) cc_final: 0.5253 (mpp) REVERT: E 118 LEU cc_start: 0.7729 (mp) cc_final: 0.7147 (tp) REVERT: E 203 ILE cc_start: 0.8390 (mt) cc_final: 0.7799 (tp) REVERT: E 376 THR cc_start: 0.8161 (OUTLIER) cc_final: 0.7698 (p) REVERT: E 428 ASP cc_start: 0.8093 (p0) cc_final: 0.7803 (p0) REVERT: E 500 THR cc_start: 0.6933 (OUTLIER) cc_final: 0.6635 (t) REVERT: E 511 VAL cc_start: 0.8697 (t) cc_final: 0.8472 (t) REVERT: E 740 MET cc_start: 0.6853 (tpp) cc_final: 0.6601 (mmm) REVERT: E 759 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7104 (t80) REVERT: H 82 MET cc_start: 0.4583 (pmm) cc_final: 0.3127 (ttt) REVERT: L 17 GLN cc_start: 0.7841 (pp30) cc_final: 0.7578 (pp30) REVERT: L 41 GLN cc_start: 0.7328 (pt0) cc_final: 0.7102 (pt0) REVERT: L 90 TYR cc_start: 0.7618 (m-80) cc_final: 0.6994 (m-80) REVERT: M 89 ASP cc_start: 0.5130 (m-30) cc_final: 0.4737 (m-30) REVERT: M 117 TYR cc_start: 0.8347 (p90) cc_final: 0.8059 (p90) REVERT: N 17 GLN cc_start: 0.8089 (pp30) cc_final: 0.7842 (pp30) REVERT: N 41 GLN cc_start: 0.7136 (pm20) cc_final: 0.6899 (pm20) REVERT: O 19 ARG cc_start: 0.6457 (tpt170) cc_final: 0.5874 (tpp80) REVERT: O 29 VAL cc_start: 0.7864 (OUTLIER) cc_final: 0.7645 (t) REVERT: P 94 PHE cc_start: 0.4820 (t80) cc_final: 0.3612 (t80) REVERT: P 100 ARG cc_start: 0.6640 (ptp-170) cc_final: 0.6332 (mtt180) outliers start: 168 outliers final: 124 residues processed: 542 average time/residue: 0.1613 time to fit residues: 145.4564 Evaluate side-chains 512 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 377 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 200 TYR Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 231 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 409 GLN Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 699 LEU Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 716 THR Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 768 THR Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain E residue 860 VAL Chi-restraints excluded: chain E residue 907 ASN Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 979 ASP Chi-restraints excluded: chain E residue 1032 CYS Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1055 SER Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 63 ASP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 29 ASP Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 32 ASN Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 95 CYS Chi-restraints excluded: chain O residue 105 SER Chi-restraints excluded: chain O residue 114 ASP Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 63 ASP Chi-restraints excluded: chain P residue 73 THR Chi-restraints excluded: chain P residue 110 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 188 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 266 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 307 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 328 optimal weight: 9.9990 chunk 371 optimal weight: 10.0000 chunk 176 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B1058 HIS ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS ** E 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 32 ASN O 32 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.153089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.128399 restraints weight = 72223.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.132741 restraints weight = 40309.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.133725 restraints weight = 23029.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.134550 restraints weight = 18074.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.134820 restraints weight = 15408.040| |-----------------------------------------------------------------------------| r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 30472 Z= 0.272 Angle : 0.814 15.984 41584 Z= 0.413 Chirality : 0.053 0.512 4780 Planarity : 0.006 0.067 5324 Dihedral : 6.986 58.666 4827 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 21.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.97 % Favored : 91.95 % Rotamer: Outliers : 5.79 % Allowed : 19.62 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.13), residues: 3753 helix: -0.23 (0.19), residues: 687 sheet: -0.64 (0.19), residues: 717 loop : -1.58 (0.12), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 100 TYR 0.023 0.002 TYR E 873 PHE 0.024 0.002 PHE A 456 TRP 0.055 0.003 TRP H 47 HIS 0.010 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00619 (30394) covalent geometry : angle 0.77934 (41393) SS BOND : bond 0.00449 ( 43) SS BOND : angle 2.18972 ( 86) hydrogen bonds : bond 0.05746 ( 991) hydrogen bonds : angle 7.12232 ( 2742) link_BETA1-4 : bond 0.01211 ( 4) link_BETA1-4 : angle 2.59233 ( 12) link_NAG-ASN : bond 0.00674 ( 31) link_NAG-ASN : angle 4.54952 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 409 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 858 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8668 (pp) REVERT: B 214 ARG cc_start: 0.2604 (mmm160) cc_final: 0.1582 (mmm160) REVERT: B 529 LYS cc_start: 0.8374 (mppt) cc_final: 0.7491 (mmmt) REVERT: B 651 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7426 (tt) REVERT: B 902 MET cc_start: 0.7379 (mmp) cc_final: 0.7138 (mmp) REVERT: B 1089 PHE cc_start: 0.7121 (OUTLIER) cc_final: 0.6143 (m-80) REVERT: E 118 LEU cc_start: 0.7779 (mp) cc_final: 0.7187 (tp) REVERT: E 189 LEU cc_start: 0.5800 (OUTLIER) cc_final: 0.5103 (mp) REVERT: E 203 ILE cc_start: 0.8460 (mt) cc_final: 0.7837 (tp) REVERT: E 298 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.6229 (mm-30) REVERT: E 376 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.7883 (p) REVERT: E 428 ASP cc_start: 0.8115 (p0) cc_final: 0.7794 (p0) REVERT: E 500 THR cc_start: 0.6991 (OUTLIER) cc_final: 0.6688 (t) REVERT: E 511 VAL cc_start: 0.8685 (t) cc_final: 0.8451 (t) REVERT: E 699 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.7075 (mm) REVERT: E 740 MET cc_start: 0.6763 (tpp) cc_final: 0.6525 (mmm) REVERT: E 759 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7168 (t80) REVERT: E 1050 MET cc_start: 0.7393 (ptt) cc_final: 0.7050 (ptt) REVERT: H 82 MET cc_start: 0.4867 (pmm) cc_final: 0.3551 (ttm) REVERT: H 123 GLN cc_start: 0.6542 (mp10) cc_final: 0.5682 (tp-100) REVERT: L 17 GLN cc_start: 0.7989 (pp30) cc_final: 0.7697 (pp30) REVERT: L 41 GLN cc_start: 0.7499 (pt0) cc_final: 0.7205 (pt0) REVERT: L 90 TYR cc_start: 0.7686 (m-80) cc_final: 0.7041 (m-80) REVERT: N 17 GLN cc_start: 0.8287 (pp30) cc_final: 0.8034 (pp30) REVERT: N 111 LEU cc_start: 0.5969 (mm) cc_final: 0.5626 (tp) REVERT: O 19 ARG cc_start: 0.6554 (tpt170) cc_final: 0.6264 (tpt90) REVERT: O 29 VAL cc_start: 0.8081 (OUTLIER) cc_final: 0.7849 (t) REVERT: P 41 GLN cc_start: 0.7320 (pm20) cc_final: 0.7028 (pm20) REVERT: P 90 TYR cc_start: 0.7457 (m-80) cc_final: 0.6678 (m-80) REVERT: P 94 PHE cc_start: 0.4926 (t80) cc_final: 0.3447 (t80) REVERT: P 100 ARG cc_start: 0.6851 (ptp-170) cc_final: 0.6633 (mtt180) REVERT: P 111 LEU cc_start: 0.5963 (mm) cc_final: 0.5432 (tp) outliers start: 184 outliers final: 132 residues processed: 538 average time/residue: 0.1634 time to fit residues: 145.5626 Evaluate side-chains 512 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 370 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 928 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1019 ARG Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 231 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 409 GLN Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 699 LEU Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 716 THR Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 734 THR Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 768 THR Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain E residue 860 VAL Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 979 ASP Chi-restraints excluded: chain E residue 1032 CYS Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1055 SER Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 63 ASP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 29 ASP Chi-restraints excluded: chain N residue 63 ASP Chi-restraints excluded: chain N residue 68 SER Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 95 CYS Chi-restraints excluded: chain O residue 105 SER Chi-restraints excluded: chain O residue 114 ASP Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 40 GLN Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 73 THR Chi-restraints excluded: chain P residue 110 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 323 optimal weight: 0.3980 chunk 307 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 360 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 319 optimal weight: 0.7980 chunk 373 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 969 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN B1108 ASN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS E 409 GLN ** E 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.157531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.132476 restraints weight = 71637.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.137020 restraints weight = 39558.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.138115 restraints weight = 21717.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.139059 restraints weight = 17096.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.139428 restraints weight = 14449.406| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30472 Z= 0.160 Angle : 0.751 15.589 41584 Z= 0.376 Chirality : 0.050 0.506 4780 Planarity : 0.005 0.065 5324 Dihedral : 6.709 57.989 4826 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.85 % Favored : 93.07 % Rotamer: Outliers : 4.28 % Allowed : 21.51 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 are not related in a simple way. whole: -1.57 (0.13), residues: 3753 helix: -0.13 (0.19), residues: 690 sheet: -0.62 (0.19), residues: 711 loop : -1.51 (0.12), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 64 TYR 0.026 0.002 TYR E 873 PHE 0.030 0.002 PHE N 102 TRP 0.051 0.002 TRP H 47 HIS 0.010 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00360 (30394) covalent geometry : angle 0.71583 (41393) SS BOND : bond 0.00350 ( 43) SS BOND : angle 2.19580 ( 86) hydrogen bonds : bond 0.05040 ( 991) hydrogen bonds : angle 6.92329 ( 2742) link_BETA1-4 : bond 0.01337 ( 4) link_BETA1-4 : angle 2.37221 ( 12) link_NAG-ASN : bond 0.00718 ( 31) link_NAG-ASN : angle 4.38375 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 420 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 THR cc_start: 0.8123 (OUTLIER) cc_final: 0.7695 (p) REVERT: A 551 VAL cc_start: 0.5839 (OUTLIER) cc_final: 0.5626 (p) REVERT: A 612 TYR cc_start: 0.7213 (m-80) cc_final: 0.6780 (m-80) REVERT: A 858 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8565 (pp) REVERT: A 997 ILE cc_start: 0.7672 (mm) cc_final: 0.7440 (tp) REVERT: B 214 ARG cc_start: 0.2684 (mmm160) cc_final: 0.1638 (mmt-90) REVERT: B 529 LYS cc_start: 0.8388 (mppt) cc_final: 0.7512 (mmmt) REVERT: B 651 ILE cc_start: 0.7549 (OUTLIER) cc_final: 0.7176 (tt) REVERT: B 784 GLN cc_start: 0.7644 (tm-30) cc_final: 0.7231 (tm-30) REVERT: B 920 GLN cc_start: 0.2393 (OUTLIER) cc_final: 0.1676 (tt0) REVERT: E 118 LEU cc_start: 0.7763 (mp) cc_final: 0.7169 (tp) REVERT: E 189 LEU cc_start: 0.5893 (OUTLIER) cc_final: 0.5230 (mp) REVERT: E 376 THR cc_start: 0.8177 (OUTLIER) cc_final: 0.7678 (p) REVERT: E 428 ASP cc_start: 0.8128 (p0) cc_final: 0.7788 (p0) REVERT: E 511 VAL cc_start: 0.8649 (t) cc_final: 0.8400 (t) REVERT: E 759 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.7324 (t80) REVERT: E 955 ASN cc_start: 0.7713 (m110) cc_final: 0.7479 (m-40) REVERT: H 19 ARG cc_start: 0.6074 (tpt-90) cc_final: 0.5667 (tpt-90) REVERT: H 82 MET cc_start: 0.4993 (pmm) cc_final: 0.3869 (ttp) REVERT: L 17 GLN cc_start: 0.8038 (pp30) cc_final: 0.7792 (pp30) REVERT: L 90 TYR cc_start: 0.7688 (m-80) cc_final: 0.7275 (m-80) REVERT: M 82 MET cc_start: 0.2714 (tpt) cc_final: 0.2427 (tpt) REVERT: M 89 ASP cc_start: 0.4520 (m-30) cc_final: 0.4305 (m-30) REVERT: N 17 GLN cc_start: 0.8195 (pp30) cc_final: 0.7950 (pp30) REVERT: N 41 GLN cc_start: 0.7120 (pm20) cc_final: 0.6683 (pm20) REVERT: N 111 LEU cc_start: 0.5983 (mm) cc_final: 0.5657 (tp) REVERT: O 19 ARG cc_start: 0.6511 (tpt170) cc_final: 0.6187 (tpt90) REVERT: O 29 VAL cc_start: 0.7867 (OUTLIER) cc_final: 0.7624 (t) REVERT: O 46 GLU cc_start: 0.7431 (tm-30) cc_final: 0.7097 (tm-30) REVERT: O 49 SER cc_start: 0.8704 (t) cc_final: 0.8068 (m) REVERT: O 85 LEU cc_start: 0.4069 (pp) cc_final: 0.3687 (mm) REVERT: P 41 GLN cc_start: 0.7245 (pm20) cc_final: 0.6938 (pm20) REVERT: P 90 TYR cc_start: 0.7434 (m-80) cc_final: 0.6655 (m-80) REVERT: P 100 ARG cc_start: 0.6744 (ptp-170) cc_final: 0.6411 (mtt180) REVERT: P 111 LEU cc_start: 0.5954 (mm) cc_final: 0.5421 (tp) outliers start: 136 outliers final: 96 residues processed: 522 average time/residue: 0.1657 time to fit residues: 143.2484 Evaluate side-chains 475 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 370 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 920 GLN Chi-restraints excluded: chain B residue 928 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1019 ARG Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 186 PHE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain E residue 860 VAL Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 979 ASP Chi-restraints excluded: chain E residue 994 ASP Chi-restraints excluded: chain E residue 1032 CYS Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 120 TYR Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 63 ASP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain N residue 29 ASP Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 95 CYS Chi-restraints excluded: chain O residue 105 SER Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 40 GLN Chi-restraints excluded: chain P residue 73 THR Chi-restraints excluded: chain P residue 110 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 73 optimal weight: 0.2980 chunk 251 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 223 optimal weight: 0.0770 chunk 182 optimal weight: 0.6980 chunk 117 optimal weight: 7.9990 chunk 271 optimal weight: 0.8980 chunk 220 optimal weight: 10.0000 chunk 147 optimal weight: 4.9990 chunk 254 optimal weight: 7.9990 chunk 221 optimal weight: 2.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS ** E 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 784 GLN ** E 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.157982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.133699 restraints weight = 71800.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.138045 restraints weight = 40171.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.139130 restraints weight = 22644.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.139960 restraints weight = 17638.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.140197 restraints weight = 14941.591| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 30472 Z= 0.159 Angle : 0.742 15.374 41584 Z= 0.371 Chirality : 0.050 0.501 4780 Planarity : 0.005 0.066 5324 Dihedral : 6.580 57.562 4826 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.30 % Favored : 92.65 % Rotamer: Outliers : 3.87 % Allowed : 21.98 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.13), residues: 3753 helix: -0.19 (0.19), residues: 690 sheet: -0.60 (0.19), residues: 711 loop : -1.49 (0.12), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 64 TYR 0.042 0.002 TYR E 873 PHE 0.033 0.002 PHE A 186 TRP 0.064 0.002 TRP H 47 HIS 0.010 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00365 (30394) covalent geometry : angle 0.70847 (41393) SS BOND : bond 0.00329 ( 43) SS BOND : angle 2.12455 ( 86) hydrogen bonds : bond 0.04944 ( 991) hydrogen bonds : angle 6.80698 ( 2742) link_BETA1-4 : bond 0.01087 ( 4) link_BETA1-4 : angle 2.27822 ( 12) link_NAG-ASN : bond 0.00702 ( 31) link_NAG-ASN : angle 4.27103 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 421 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 THR cc_start: 0.8098 (OUTLIER) cc_final: 0.7680 (p) REVERT: A 612 TYR cc_start: 0.7201 (m-80) cc_final: 0.6778 (m-80) REVERT: A 784 GLN cc_start: 0.7634 (pp30) cc_final: 0.7381 (pp30) REVERT: A 858 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8530 (pp) REVERT: B 189 LEU cc_start: 0.4576 (OUTLIER) cc_final: 0.4122 (mp) REVERT: B 529 LYS cc_start: 0.8362 (mppt) cc_final: 0.7504 (mmmt) REVERT: B 651 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7239 (tt) REVERT: B 759 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.7298 (t80) REVERT: B 784 GLN cc_start: 0.7522 (tm-30) cc_final: 0.7153 (tm-30) REVERT: B 920 GLN cc_start: 0.2255 (OUTLIER) cc_final: 0.1482 (tt0) REVERT: E 118 LEU cc_start: 0.7733 (mp) cc_final: 0.7128 (tp) REVERT: E 189 LEU cc_start: 0.5855 (OUTLIER) cc_final: 0.5222 (mp) REVERT: E 203 ILE cc_start: 0.8348 (mt) cc_final: 0.7662 (tp) REVERT: E 376 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7707 (p) REVERT: E 428 ASP cc_start: 0.8002 (p0) cc_final: 0.7674 (p0) REVERT: E 511 VAL cc_start: 0.8625 (t) cc_final: 0.8386 (t) REVERT: E 740 MET cc_start: 0.6961 (tpp) cc_final: 0.6585 (mmm) REVERT: E 759 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7220 (t80) REVERT: E 994 ASP cc_start: 0.7172 (OUTLIER) cc_final: 0.6873 (m-30) REVERT: H 82 MET cc_start: 0.4869 (pmm) cc_final: 0.4046 (ttp) REVERT: L 17 GLN cc_start: 0.8007 (pp30) cc_final: 0.7785 (pp30) REVERT: M 89 ASP cc_start: 0.4636 (m-30) cc_final: 0.4315 (m-30) REVERT: N 17 GLN cc_start: 0.8164 (pp30) cc_final: 0.7892 (pp30) REVERT: N 41 GLN cc_start: 0.7098 (pm20) cc_final: 0.6648 (pm20) REVERT: N 111 LEU cc_start: 0.6018 (mm) cc_final: 0.5672 (tp) REVERT: O 29 VAL cc_start: 0.7738 (OUTLIER) cc_final: 0.7482 (t) REVERT: O 46 GLU cc_start: 0.7333 (tm-30) cc_final: 0.7030 (tm-30) REVERT: P 41 GLN cc_start: 0.7230 (pm20) cc_final: 0.6916 (pm20) REVERT: P 90 TYR cc_start: 0.7480 (m-80) cc_final: 0.6720 (m-80) REVERT: P 100 ARG cc_start: 0.6615 (ptp-170) cc_final: 0.6109 (mtt90) REVERT: P 111 LEU cc_start: 0.5904 (mm) cc_final: 0.5359 (tp) outliers start: 123 outliers final: 95 residues processed: 517 average time/residue: 0.1672 time to fit residues: 142.7058 Evaluate side-chains 487 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 381 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 920 GLN Chi-restraints excluded: chain B residue 928 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1019 ARG Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 186 PHE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain E residue 860 VAL Chi-restraints excluded: chain E residue 898 PHE Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 979 ASP Chi-restraints excluded: chain E residue 994 ASP Chi-restraints excluded: chain E residue 1032 CYS Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain N residue 29 ASP Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 95 CYS Chi-restraints excluded: chain O residue 105 SER Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 40 GLN Chi-restraints excluded: chain P residue 73 THR Chi-restraints excluded: chain P residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 292 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 313 optimal weight: 10.0000 chunk 237 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 172 optimal weight: 0.6980 chunk 339 optimal weight: 1.9990 chunk 226 optimal weight: 0.7980 chunk 213 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS E 409 GLN ** E 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1058 HIS N 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.155273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.131012 restraints weight = 71583.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.134152 restraints weight = 38308.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.135823 restraints weight = 22134.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.136163 restraints weight = 18042.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.136386 restraints weight = 16084.623| |-----------------------------------------------------------------------------| r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.5402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 30472 Z= 0.224 Angle : 0.785 15.251 41584 Z= 0.399 Chirality : 0.052 0.501 4780 Planarity : 0.006 0.075 5324 Dihedral : 6.740 58.209 4826 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.23 % Favored : 91.66 % Rotamer: Outliers : 3.87 % Allowed : 22.33 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 are not related in a simple way. whole: -1.72 (0.13), residues: 3753 helix: -0.32 (0.19), residues: 687 sheet: -0.77 (0.19), residues: 711 loop : -1.56 (0.12), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E1000 TYR 0.050 0.002 TYR E 873 PHE 0.034 0.002 PHE E1052 TRP 0.088 0.003 TRP H 47 HIS 0.010 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00518 (30394) covalent geometry : angle 0.75145 (41393) SS BOND : bond 0.00392 ( 43) SS BOND : angle 2.16840 ( 86) hydrogen bonds : bond 0.05281 ( 991) hydrogen bonds : angle 7.00360 ( 2742) link_BETA1-4 : bond 0.01176 ( 4) link_BETA1-4 : angle 2.43808 ( 12) link_NAG-ASN : bond 0.00675 ( 31) link_NAG-ASN : angle 4.33001 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 391 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 784 GLN cc_start: 0.7860 (pp30) cc_final: 0.7610 (pp30) REVERT: A 858 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8665 (pp) REVERT: B 214 ARG cc_start: 0.2710 (mmm160) cc_final: 0.1759 (mmt-90) REVERT: B 529 LYS cc_start: 0.8476 (mppt) cc_final: 0.7512 (mmmt) REVERT: B 651 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7327 (tt) REVERT: B 802 PHE cc_start: 0.6872 (m-80) cc_final: 0.6366 (m-80) REVERT: B 920 GLN cc_start: 0.2436 (OUTLIER) cc_final: 0.1570 (tt0) REVERT: B 1125 ASN cc_start: 0.7052 (p0) cc_final: 0.6834 (p0) REVERT: E 118 LEU cc_start: 0.7777 (mp) cc_final: 0.7174 (tp) REVERT: E 189 LEU cc_start: 0.5698 (OUTLIER) cc_final: 0.5151 (mp) REVERT: E 376 THR cc_start: 0.8227 (OUTLIER) cc_final: 0.7739 (p) REVERT: E 428 ASP cc_start: 0.8077 (p0) cc_final: 0.7742 (p0) REVERT: E 511 VAL cc_start: 0.8673 (t) cc_final: 0.8435 (t) REVERT: E 740 MET cc_start: 0.6893 (tpp) cc_final: 0.6463 (mmm) REVERT: H 19 ARG cc_start: 0.6241 (tpt-90) cc_final: 0.5851 (tpt-90) REVERT: H 82 MET cc_start: 0.4865 (pmm) cc_final: 0.4443 (ttp) REVERT: L 41 GLN cc_start: 0.8000 (pt0) cc_final: 0.7194 (pm20) REVERT: L 90 TYR cc_start: 0.7537 (m-80) cc_final: 0.6732 (m-80) REVERT: M 89 ASP cc_start: 0.4537 (m-30) cc_final: 0.4206 (m-30) REVERT: N 17 GLN cc_start: 0.8192 (pp30) cc_final: 0.7899 (pp30) REVERT: N 41 GLN cc_start: 0.6948 (pm20) cc_final: 0.6697 (pm20) REVERT: N 111 LEU cc_start: 0.5752 (mm) cc_final: 0.5473 (tp) REVERT: O 29 VAL cc_start: 0.7988 (OUTLIER) cc_final: 0.7707 (t) REVERT: P 41 GLN cc_start: 0.7177 (pm20) cc_final: 0.6846 (pm20) REVERT: P 90 TYR cc_start: 0.7581 (m-80) cc_final: 0.6809 (m-80) REVERT: P 94 PHE cc_start: 0.4893 (t80) cc_final: 0.3466 (t80) REVERT: P 100 ARG cc_start: 0.6756 (ptp-170) cc_final: 0.6331 (mtt90) REVERT: P 111 LEU cc_start: 0.5816 (mm) cc_final: 0.5241 (tp) outliers start: 123 outliers final: 103 residues processed: 487 average time/residue: 0.1644 time to fit residues: 132.5316 Evaluate side-chains 483 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 374 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 920 GLN Chi-restraints excluded: chain B residue 928 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1019 ARG Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 186 PHE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 200 TYR Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 409 GLN Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 780 GLU Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain E residue 860 VAL Chi-restraints excluded: chain E residue 973 ILE Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 979 ASP Chi-restraints excluded: chain E residue 1032 CYS Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1136 THR Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain N residue 29 ASP Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 95 CYS Chi-restraints excluded: chain O residue 105 SER Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 40 GLN Chi-restraints excluded: chain P residue 73 THR Chi-restraints excluded: chain P residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 255 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 201 optimal weight: 0.0870 chunk 104 optimal weight: 0.9980 chunk 110 optimal weight: 9.9990 chunk 281 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 196 optimal weight: 0.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS ** E 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.155313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.130101 restraints weight = 71876.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.134551 restraints weight = 39219.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.135677 restraints weight = 21761.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.136531 restraints weight = 17199.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.136709 restraints weight = 14451.900| |-----------------------------------------------------------------------------| r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.5423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.362 30472 Z= 0.240 Angle : 0.869 59.030 41584 Z= 0.464 Chirality : 0.052 0.571 4780 Planarity : 0.006 0.079 5324 Dihedral : 6.743 58.213 4826 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 22.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.21 % Favored : 91.69 % Rotamer: Outliers : 3.77 % Allowed : 22.58 % Favored : 73.65 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 are not related in a simple way. whole: -1.72 (0.13), residues: 3753 helix: -0.29 (0.19), residues: 687 sheet: -0.78 (0.19), residues: 711 loop : -1.58 (0.12), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E1000 TYR 0.040 0.002 TYR E 873 PHE 0.057 0.002 PHE E 329 TRP 0.070 0.003 TRP H 47 HIS 0.010 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00578 (30394) covalent geometry : angle 0.83987 (41393) SS BOND : bond 0.00364 ( 43) SS BOND : angle 2.14256 ( 86) hydrogen bonds : bond 0.05288 ( 991) hydrogen bonds : angle 7.00424 ( 2742) link_BETA1-4 : bond 0.01367 ( 4) link_BETA1-4 : angle 2.52303 ( 12) link_NAG-ASN : bond 0.00683 ( 31) link_NAG-ASN : angle 4.32462 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5404.04 seconds wall clock time: 94 minutes 12.82 seconds (5652.82 seconds total)