Starting phenix.real_space_refine on Mon Jul 6 14:10:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fer_31561/07_2026/7fer_31561.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fer_31561/07_2026/7fer_31561.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7fer_31561/07_2026/7fer_31561.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fer_31561/07_2026/7fer_31561.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fer_31561/07_2026/7fer_31561.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fer_31561/07_2026/7fer_31561.map" model { file = "/net/cci-nas-00/data/ceres_data/7fer_31561/07_2026/7fer_31561.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fer_31561/07_2026/7fer_31561.cif" } resolution = 3.4 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= 0.022 sd= 0.132 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: 5 Type Number sf(0) Gaussians S 98 5.16 5 C 11856 2.51 5 N 3070 2.21 5 O 3570 1.98 5 H 18142 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 101 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36736 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2568 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "B" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2568 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "C" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2568 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2583 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2568 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "F" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2568 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "G" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2568 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "H" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2568 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "I" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2568 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "J" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2568 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "K" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2568 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "L" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2568 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "M" Number of atoms: 2609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2609 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 1 Chain: "N" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2568 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "O" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT O 1 " pdbres="PHE O 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT P 1 " pdbres="PHE P 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Q" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT Q 1 " pdbres="PHE Q 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT R 1 " pdbres="PHE R 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT S 1 " pdbres="PHE S 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "T" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT T 1 " pdbres="PHE T 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "U" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT U 1 " pdbres="PHE U 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "V" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT V 1 " pdbres="PHE V 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "W" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT W 1 " pdbres="PHE W 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "X" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT X 1 " pdbres="PHE X 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Y" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT Y 1 " pdbres="PHE Y 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Z" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT Z 1 " pdbres="PHE Z 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "a" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT a 1 " pdbres="PHE a 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "b" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT b 1 " pdbres="PHE b 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 6.18, per 1000 atoms: 0.17 Number of scatterers: 36736 At special positions: 0 Unit cell: (120.4, 122.12, 103.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 98 16.00 O 3570 8.00 N 3070 7.00 C 11856 6.00 H 18142 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=42, symmetry=0 Number of additional bonds: simple=42, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 772.0 milliseconds 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4508 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 14 sheets defined 46.3% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 18 through 25 Processing helix chain 'A' and resid 36 through 54 removed outlier: 3.931A pdb=" N SER A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 81 removed outlier: 3.502A pdb=" N GLY A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA A 75 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP A 78 " --> pdb=" O MET A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 104 removed outlier: 3.816A pdb=" N LEU A 102 " --> pdb=" O MET A 98 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 158 removed outlier: 3.669A pdb=" N LEU A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 156 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.995A pdb=" N ILE A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.902A pdb=" N LEU A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 25 Processing helix chain 'B' and resid 36 through 54 removed outlier: 3.932A pdb=" N SER B 42 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 52 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU B 53 " --> pdb=" O PHE B 49 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 81 removed outlier: 3.501A pdb=" N GLY B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP B 78 " --> pdb=" O MET B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 104 removed outlier: 3.902A pdb=" N ALA B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 158 removed outlier: 3.669A pdb=" N LEU B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP B 147 " --> pdb=" O LEU B 143 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU B 155 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG B 156 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR B 157 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 165 removed outlier: 3.995A pdb=" N ILE B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 180 removed outlier: 3.902A pdb=" N LEU B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 25 Processing helix chain 'C' and resid 36 through 54 removed outlier: 3.930A pdb=" N SER C 42 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN C 46 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU C 53 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 81 removed outlier: 3.500A pdb=" N GLY C 73 " --> pdb=" O SER C 69 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET C 74 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA C 75 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR C 77 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP C 78 " --> pdb=" O MET C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 104 removed outlier: 3.613A pdb=" N LEU C 102 " --> pdb=" O MET C 98 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 104' Processing helix chain 'C' and resid 138 through 158 removed outlier: 3.669A pdb=" N LEU C 144 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP C 147 " --> pdb=" O LEU C 143 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU C 155 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG C 156 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR C 157 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 165 removed outlier: 3.996A pdb=" N ILE C 164 " --> pdb=" O PRO C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 180 removed outlier: 3.901A pdb=" N LEU C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 25 Processing helix chain 'D' and resid 36 through 54 removed outlier: 3.930A pdb=" N SER D 42 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN D 46 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA D 52 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU D 53 " --> pdb=" O PHE D 49 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 81 removed outlier: 3.501A pdb=" N GLY D 73 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR D 77 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP D 78 " --> pdb=" O MET D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 104 removed outlier: 3.690A pdb=" N LEU D 103 " --> pdb=" O GLY D 99 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA D 104 " --> pdb=" O ALA D 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 99 through 104' Processing helix chain 'D' and resid 138 through 158 removed outlier: 3.670A pdb=" N LEU D 144 " --> pdb=" O LYS D 140 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP D 147 " --> pdb=" O LEU D 143 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU D 155 " --> pdb=" O LYS D 151 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG D 156 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR D 157 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY D 158 " --> pdb=" O ALA D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 165 removed outlier: 3.995A pdb=" N ILE D 164 " --> pdb=" O PRO D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 180 removed outlier: 3.900A pdb=" N LEU D 180 " --> pdb=" O ALA D 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 25 Processing helix chain 'E' and resid 36 through 54 removed outlier: 3.931A pdb=" N SER E 42 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN E 46 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU E 53 " --> pdb=" O PHE E 49 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 81 removed outlier: 3.501A pdb=" N GLY E 73 " --> pdb=" O SER E 69 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA E 75 " --> pdb=" O THR E 71 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR E 77 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP E 78 " --> pdb=" O MET E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 104 removed outlier: 3.664A pdb=" N LEU E 102 " --> pdb=" O MET E 98 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU E 103 " --> pdb=" O GLY E 99 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 98 through 104' Processing helix chain 'E' and resid 138 through 158 removed outlier: 3.669A pdb=" N LEU E 144 " --> pdb=" O LYS E 140 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA E 154 " --> pdb=" O ASN E 150 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU E 155 " --> pdb=" O LYS E 151 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG E 156 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR E 157 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY E 158 " --> pdb=" O ALA E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 165 removed outlier: 3.996A pdb=" N ILE E 164 " --> pdb=" O PRO E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 180 removed outlier: 3.902A pdb=" N LEU E 180 " --> pdb=" O ALA E 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 25 Processing helix chain 'F' and resid 36 through 54 removed outlier: 3.931A pdb=" N SER F 42 " --> pdb=" O ASN F 38 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN F 46 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU F 53 " --> pdb=" O PHE F 49 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 81 removed outlier: 3.500A pdb=" N GLY F 73 " --> pdb=" O SER F 69 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET F 74 " --> pdb=" O ILE F 70 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE F 76 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR F 77 " --> pdb=" O GLY F 73 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP F 78 " --> pdb=" O MET F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 106 removed outlier: 3.951A pdb=" N LEU F 103 " --> pdb=" O ALA F 100 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY F 106 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 158 removed outlier: 3.670A pdb=" N LEU F 144 " --> pdb=" O LYS F 140 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP F 147 " --> pdb=" O LEU F 143 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU F 149 " --> pdb=" O LEU F 145 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA F 154 " --> pdb=" O ASN F 150 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU F 155 " --> pdb=" O LYS F 151 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG F 156 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY F 158 " --> pdb=" O ALA F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 165 removed outlier: 3.996A pdb=" N ILE F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 180 removed outlier: 3.901A pdb=" N LEU F 180 " --> pdb=" O ALA F 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 25 Processing helix chain 'G' and resid 36 through 54 removed outlier: 3.931A pdb=" N SER G 42 " --> pdb=" O ASN G 38 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN G 46 " --> pdb=" O SER G 42 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA G 52 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU G 53 " --> pdb=" O PHE G 49 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 81 removed outlier: 3.501A pdb=" N GLY G 73 " --> pdb=" O SER G 69 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET G 74 " --> pdb=" O ILE G 70 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA G 75 " --> pdb=" O THR G 71 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE G 76 " --> pdb=" O ALA G 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR G 77 " --> pdb=" O GLY G 73 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ASP G 78 " --> pdb=" O MET G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 104 removed outlier: 3.609A pdb=" N ALA G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 158 removed outlier: 3.669A pdb=" N LEU G 144 " --> pdb=" O LYS G 140 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP G 147 " --> pdb=" O LEU G 143 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU G 149 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN G 150 " --> pdb=" O ARG G 146 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA G 154 " --> pdb=" O ASN G 150 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU G 155 " --> pdb=" O LYS G 151 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG G 156 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR G 157 " --> pdb=" O LEU G 153 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY G 158 " --> pdb=" O ALA G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 165 removed outlier: 3.995A pdb=" N ILE G 164 " --> pdb=" O PRO G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 180 removed outlier: 3.901A pdb=" N LEU G 180 " --> pdb=" O ALA G 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 25 Processing helix chain 'H' and resid 36 through 54 removed outlier: 3.931A pdb=" N SER H 42 " --> pdb=" O ASN H 38 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN H 46 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA H 52 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU H 53 " --> pdb=" O PHE H 49 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP H 54 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 81 removed outlier: 3.501A pdb=" N GLY H 73 " --> pdb=" O SER H 69 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET H 74 " --> pdb=" O ILE H 70 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR H 77 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP H 78 " --> pdb=" O MET H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 104 removed outlier: 3.670A pdb=" N LEU H 102 " --> pdb=" O MET H 98 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU H 103 " --> pdb=" O GLY H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 158 removed outlier: 3.669A pdb=" N LEU H 144 " --> pdb=" O LYS H 140 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP H 147 " --> pdb=" O LEU H 143 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU H 149 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN H 150 " --> pdb=" O ARG H 146 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA H 154 " --> pdb=" O ASN H 150 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU H 155 " --> pdb=" O LYS H 151 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG H 156 " --> pdb=" O VAL H 152 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR H 157 " --> pdb=" O LEU H 153 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY H 158 " --> pdb=" O ALA H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 165 removed outlier: 3.995A pdb=" N ILE H 164 " --> pdb=" O PRO H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 180 removed outlier: 3.901A pdb=" N LEU H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 25 Processing helix chain 'I' and resid 36 through 54 removed outlier: 3.931A pdb=" N SER I 42 " --> pdb=" O ASN I 38 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN I 46 " --> pdb=" O SER I 42 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA I 52 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU I 53 " --> pdb=" O PHE I 49 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP I 54 " --> pdb=" O LEU I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 81 removed outlier: 3.501A pdb=" N GLY I 73 " --> pdb=" O SER I 69 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET I 74 " --> pdb=" O ILE I 70 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA I 75 " --> pdb=" O THR I 71 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE I 76 " --> pdb=" O ALA I 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR I 77 " --> pdb=" O GLY I 73 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP I 78 " --> pdb=" O MET I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 104 removed outlier: 3.872A pdb=" N LEU I 102 " --> pdb=" O MET I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 158 removed outlier: 3.669A pdb=" N LEU I 144 " --> pdb=" O LYS I 140 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP I 147 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU I 149 " --> pdb=" O LEU I 145 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN I 150 " --> pdb=" O ARG I 146 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA I 154 " --> pdb=" O ASN I 150 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU I 155 " --> pdb=" O LYS I 151 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG I 156 " --> pdb=" O VAL I 152 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR I 157 " --> pdb=" O LEU I 153 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY I 158 " --> pdb=" O ALA I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 165 removed outlier: 3.995A pdb=" N ILE I 164 " --> pdb=" O PRO I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 175 through 180 removed outlier: 3.900A pdb=" N LEU I 180 " --> pdb=" O ALA I 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 25 Processing helix chain 'J' and resid 36 through 54 removed outlier: 3.931A pdb=" N SER J 42 " --> pdb=" O ASN J 38 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN J 46 " --> pdb=" O SER J 42 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA J 52 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU J 53 " --> pdb=" O PHE J 49 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP J 54 " --> pdb=" O LEU J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 81 removed outlier: 3.500A pdb=" N GLY J 73 " --> pdb=" O SER J 69 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET J 74 " --> pdb=" O ILE J 70 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA J 75 " --> pdb=" O THR J 71 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE J 76 " --> pdb=" O ALA J 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR J 77 " --> pdb=" O GLY J 73 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP J 78 " --> pdb=" O MET J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 106 removed outlier: 4.114A pdb=" N GLY J 106 " --> pdb=" O LEU J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 158 removed outlier: 3.669A pdb=" N LEU J 144 " --> pdb=" O LYS J 140 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP J 147 " --> pdb=" O LEU J 143 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU J 149 " --> pdb=" O LEU J 145 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN J 150 " --> pdb=" O ARG J 146 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA J 154 " --> pdb=" O ASN J 150 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU J 155 " --> pdb=" O LYS J 151 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG J 156 " --> pdb=" O VAL J 152 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR J 157 " --> pdb=" O LEU J 153 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY J 158 " --> pdb=" O ALA J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 165 removed outlier: 3.996A pdb=" N ILE J 164 " --> pdb=" O PRO J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 180 removed outlier: 3.902A pdb=" N LEU J 180 " --> pdb=" O ALA J 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 25 Processing helix chain 'K' and resid 36 through 54 removed outlier: 3.931A pdb=" N SER K 42 " --> pdb=" O ASN K 38 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN K 46 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA K 52 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU K 53 " --> pdb=" O PHE K 49 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP K 54 " --> pdb=" O LEU K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 81 removed outlier: 3.502A pdb=" N GLY K 73 " --> pdb=" O SER K 69 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET K 74 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR K 77 " --> pdb=" O GLY K 73 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP K 78 " --> pdb=" O MET K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 106 removed outlier: 4.115A pdb=" N GLY K 106 " --> pdb=" O LEU K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 158 removed outlier: 3.669A pdb=" N LEU K 144 " --> pdb=" O LYS K 140 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP K 147 " --> pdb=" O LEU K 143 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU K 149 " --> pdb=" O LEU K 145 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN K 150 " --> pdb=" O ARG K 146 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA K 154 " --> pdb=" O ASN K 150 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU K 155 " --> pdb=" O LYS K 151 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG K 156 " --> pdb=" O VAL K 152 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR K 157 " --> pdb=" O LEU K 153 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY K 158 " --> pdb=" O ALA K 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 165 removed outlier: 4.212A pdb=" N ILE K 164 " --> pdb=" O PRO K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 175 through 180 removed outlier: 3.901A pdb=" N LEU K 180 " --> pdb=" O ALA K 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 25 Processing helix chain 'L' and resid 36 through 54 removed outlier: 3.931A pdb=" N SER L 42 " --> pdb=" O ASN L 38 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN L 46 " --> pdb=" O SER L 42 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA L 52 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU L 53 " --> pdb=" O PHE L 49 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP L 54 " --> pdb=" O LEU L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 81 removed outlier: 3.501A pdb=" N GLY L 73 " --> pdb=" O SER L 69 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET L 74 " --> pdb=" O ILE L 70 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA L 75 " --> pdb=" O THR L 71 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE L 76 " --> pdb=" O ALA L 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR L 77 " --> pdb=" O GLY L 73 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP L 78 " --> pdb=" O MET L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 104 removed outlier: 3.807A pdb=" N LEU L 102 " --> pdb=" O MET L 98 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU L 103 " --> pdb=" O GLY L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 158 removed outlier: 3.670A pdb=" N LEU L 144 " --> pdb=" O LYS L 140 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP L 147 " --> pdb=" O LEU L 143 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU L 149 " --> pdb=" O LEU L 145 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA L 154 " --> pdb=" O ASN L 150 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU L 155 " --> pdb=" O LYS L 151 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG L 156 " --> pdb=" O VAL L 152 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR L 157 " --> pdb=" O LEU L 153 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY L 158 " --> pdb=" O ALA L 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 165 removed outlier: 3.995A pdb=" N ILE L 164 " --> pdb=" O PRO L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 175 through 180 removed outlier: 3.901A pdb=" N LEU L 180 " --> pdb=" O ALA L 176 " (cutoff:3.500A) Processing helix chain 'M' and resid 18 through 25 Processing helix chain 'M' and resid 36 through 54 removed outlier: 3.931A pdb=" N SER M 42 " --> pdb=" O ASN M 38 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN M 46 " --> pdb=" O SER M 42 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA M 52 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU M 53 " --> pdb=" O PHE M 49 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP M 54 " --> pdb=" O LEU M 50 " (cutoff:3.500A) Processing helix chain 'M' and resid 69 through 81 removed outlier: 3.501A pdb=" N GLY M 73 " --> pdb=" O SER M 69 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET M 74 " --> pdb=" O ILE M 70 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA M 75 " --> pdb=" O THR M 71 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE M 76 " --> pdb=" O ALA M 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR M 77 " --> pdb=" O GLY M 73 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP M 78 " --> pdb=" O MET M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 104 removed outlier: 3.693A pdb=" N LEU M 102 " --> pdb=" O MET M 98 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU M 103 " --> pdb=" O GLY M 99 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA M 104 " --> pdb=" O ALA M 100 " (cutoff:3.500A) Processing helix chain 'M' and resid 138 through 158 removed outlier: 3.670A pdb=" N LEU M 144 " --> pdb=" O LYS M 140 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP M 147 " --> pdb=" O LEU M 143 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU M 149 " --> pdb=" O LEU M 145 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN M 150 " --> pdb=" O ARG M 146 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA M 154 " --> pdb=" O ASN M 150 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU M 155 " --> pdb=" O LYS M 151 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG M 156 " --> pdb=" O VAL M 152 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR M 157 " --> pdb=" O LEU M 153 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY M 158 " --> pdb=" O ALA M 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 165 removed outlier: 3.995A pdb=" N ILE M 164 " --> pdb=" O PRO M 160 " (cutoff:3.500A) Processing helix chain 'M' and resid 175 through 180 removed outlier: 3.901A pdb=" N LEU M 180 " --> pdb=" O ALA M 176 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 25 Processing helix chain 'N' and resid 36 through 54 removed outlier: 3.931A pdb=" N SER N 42 " --> pdb=" O ASN N 38 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN N 46 " --> pdb=" O SER N 42 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA N 52 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU N 53 " --> pdb=" O PHE N 49 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP N 54 " --> pdb=" O LEU N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 69 through 81 removed outlier: 3.501A pdb=" N GLY N 73 " --> pdb=" O SER N 69 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET N 74 " --> pdb=" O ILE N 70 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA N 75 " --> pdb=" O THR N 71 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE N 76 " --> pdb=" O ALA N 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR N 77 " --> pdb=" O GLY N 73 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP N 78 " --> pdb=" O MET N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 104 removed outlier: 3.656A pdb=" N LEU N 102 " --> pdb=" O MET N 98 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU N 103 " --> pdb=" O GLY N 99 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA N 104 " --> pdb=" O ALA N 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 138 through 158 removed outlier: 3.669A pdb=" N LEU N 144 " --> pdb=" O LYS N 140 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP N 147 " --> pdb=" O LEU N 143 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU N 149 " --> pdb=" O LEU N 145 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN N 150 " --> pdb=" O ARG N 146 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA N 154 " --> pdb=" O ASN N 150 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU N 155 " --> pdb=" O LYS N 151 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG N 156 " --> pdb=" O VAL N 152 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR N 157 " --> pdb=" O LEU N 153 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY N 158 " --> pdb=" O ALA N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 160 through 165 removed outlier: 3.995A pdb=" N ILE N 164 " --> pdb=" O PRO N 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 180 removed outlier: 3.901A pdb=" N LEU N 180 " --> pdb=" O ALA N 176 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 31 removed outlier: 7.083A pdb=" N ILE A 59 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ILE A 90 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU A 61 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE A 92 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE A 63 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N MET A 94 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A 65 " --> pdb=" O MET A 94 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU A 118 " --> pdb=" O CYS A 91 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLY A 93 " --> pdb=" O GLU A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 30 through 31 removed outlier: 7.083A pdb=" N ILE B 59 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ILE B 90 " --> pdb=" O ILE B 59 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU B 61 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE B 92 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE B 63 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N MET B 94 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 65 " --> pdb=" O MET B 94 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU B 118 " --> pdb=" O CYS B 91 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLY B 93 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 30 through 31 removed outlier: 7.083A pdb=" N ILE C 59 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ILE C 90 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU C 61 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE C 92 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ILE C 63 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N MET C 94 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER C 65 " --> pdb=" O MET C 94 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU C 118 " --> pdb=" O CYS C 91 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLY C 93 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 30 through 31 removed outlier: 7.084A pdb=" N ILE D 59 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ILE D 90 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU D 61 " --> pdb=" O ILE D 90 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE D 92 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ILE D 63 " --> pdb=" O ILE D 92 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N MET D 94 " --> pdb=" O ILE D 63 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER D 65 " --> pdb=" O MET D 94 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU D 118 " --> pdb=" O CYS D 91 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLY D 93 " --> pdb=" O GLU D 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 30 through 31 removed outlier: 7.083A pdb=" N ILE E 59 " --> pdb=" O SER E 88 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ILE E 90 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU E 61 " --> pdb=" O ILE E 90 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE E 92 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE E 63 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N MET E 94 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER E 65 " --> pdb=" O MET E 94 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU E 118 " --> pdb=" O CYS E 91 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLY E 93 " --> pdb=" O GLU E 118 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 30 through 31 removed outlier: 7.084A pdb=" N ILE F 59 " --> pdb=" O SER F 88 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ILE F 90 " --> pdb=" O ILE F 59 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU F 61 " --> pdb=" O ILE F 90 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE F 92 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE F 63 " --> pdb=" O ILE F 92 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N MET F 94 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER F 65 " --> pdb=" O MET F 94 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU F 118 " --> pdb=" O CYS F 91 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLY F 93 " --> pdb=" O GLU F 118 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 30 through 31 removed outlier: 7.083A pdb=" N ILE G 59 " --> pdb=" O SER G 88 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ILE G 90 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU G 61 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE G 92 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ILE G 63 " --> pdb=" O ILE G 92 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N MET G 94 " --> pdb=" O ILE G 63 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER G 65 " --> pdb=" O MET G 94 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU G 118 " --> pdb=" O CYS G 91 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLY G 93 " --> pdb=" O GLU G 118 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 30 through 31 removed outlier: 7.083A pdb=" N ILE H 59 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N ILE H 90 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU H 61 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE H 92 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ILE H 63 " --> pdb=" O ILE H 92 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N MET H 94 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER H 65 " --> pdb=" O MET H 94 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU H 118 " --> pdb=" O CYS H 91 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLY H 93 " --> pdb=" O GLU H 118 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 30 through 31 removed outlier: 7.083A pdb=" N ILE I 59 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N ILE I 90 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU I 61 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE I 92 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE I 63 " --> pdb=" O ILE I 92 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N MET I 94 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER I 65 " --> pdb=" O MET I 94 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU I 118 " --> pdb=" O CYS I 91 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLY I 93 " --> pdb=" O GLU I 118 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 30 through 31 removed outlier: 7.083A pdb=" N ILE J 59 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ILE J 90 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU J 61 " --> pdb=" O ILE J 90 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE J 92 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE J 63 " --> pdb=" O ILE J 92 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N MET J 94 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER J 65 " --> pdb=" O MET J 94 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU J 118 " --> pdb=" O CYS J 91 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLY J 93 " --> pdb=" O GLU J 118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 30 through 31 removed outlier: 7.084A pdb=" N ILE K 59 " --> pdb=" O SER K 88 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ILE K 90 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU K 61 " --> pdb=" O ILE K 90 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE K 92 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ILE K 63 " --> pdb=" O ILE K 92 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N MET K 94 " --> pdb=" O ILE K 63 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER K 65 " --> pdb=" O MET K 94 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU K 118 " --> pdb=" O CYS K 91 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLY K 93 " --> pdb=" O GLU K 118 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 30 through 31 removed outlier: 7.083A pdb=" N ILE L 59 " --> pdb=" O SER L 88 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ILE L 90 " --> pdb=" O ILE L 59 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU L 61 " --> pdb=" O ILE L 90 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE L 92 " --> pdb=" O LEU L 61 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE L 63 " --> pdb=" O ILE L 92 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N MET L 94 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER L 65 " --> pdb=" O MET L 94 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU L 118 " --> pdb=" O CYS L 91 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLY L 93 " --> pdb=" O GLU L 118 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 30 through 31 removed outlier: 7.083A pdb=" N ILE M 59 " --> pdb=" O SER M 88 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ILE M 90 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU M 61 " --> pdb=" O ILE M 90 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE M 92 " --> pdb=" O LEU M 61 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ILE M 63 " --> pdb=" O ILE M 92 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N MET M 94 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER M 65 " --> pdb=" O MET M 94 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 30 through 31 removed outlier: 7.083A pdb=" N ILE N 59 " --> pdb=" O SER N 88 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ILE N 90 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU N 61 " --> pdb=" O ILE N 90 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE N 92 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE N 63 " --> pdb=" O ILE N 92 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N MET N 94 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER N 65 " --> pdb=" O MET N 94 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU N 118 " --> pdb=" O CYS N 91 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLY N 93 " --> pdb=" O GLU N 118 " (cutoff:3.500A) 431 hydrogen bonds defined for protein. 1251 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: 6.54 Time building geometry restraints manager: 4.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 0.99: 18071 0.99 - 1.20: 62 1.20 - 1.40: 7121 1.40 - 1.61: 11510 1.61 - 1.81: 196 Bond restraints: 36960 Sorted by residual: bond pdb=" C ALA b 6 " pdb=" N MP8 b 7 " ideal model delta sigma weight residual 1.329 1.467 -0.138 1.40e-02 5.10e+03 9.71e+01 bond pdb=" C ALA Y 6 " pdb=" N MP8 Y 7 " ideal model delta sigma weight residual 1.329 1.467 -0.138 1.40e-02 5.10e+03 9.71e+01 bond pdb=" C ALA P 6 " pdb=" N MP8 P 7 " ideal model delta sigma weight residual 1.329 1.467 -0.138 1.40e-02 5.10e+03 9.70e+01 bond pdb=" C ALA O 6 " pdb=" N MP8 O 7 " ideal model delta sigma weight residual 1.329 1.467 -0.138 1.40e-02 5.10e+03 9.66e+01 bond pdb=" C ALA R 6 " pdb=" N MP8 R 7 " ideal model delta sigma weight residual 1.329 1.467 -0.138 1.40e-02 5.10e+03 9.65e+01 ... (remaining 36955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.63: 66563 11.63 - 23.26: 60 23.26 - 34.89: 51 34.89 - 46.52: 52 46.52 - 58.16: 10 Bond angle restraints: 66736 Sorted by residual: angle pdb=" C ALA M 104 " pdb=" N ALA M 105 " pdb=" H ALA M 105 " ideal model delta sigma weight residual 124.24 66.09 58.16 3.00e+00 1.11e-01 3.76e+02 angle pdb=" C LEU J 161 " pdb=" N GLU J 162 " pdb=" H GLU J 162 " ideal model delta sigma weight residual 124.39 66.50 57.89 3.00e+00 1.11e-01 3.72e+02 angle pdb=" C ASN J 116 " pdb=" N SER J 117 " pdb=" H SER J 117 " ideal model delta sigma weight residual 124.11 66.38 57.73 3.00e+00 1.11e-01 3.70e+02 angle pdb=" C ASP J 169 " pdb=" N ARG J 170 " pdb=" H ARG J 170 " ideal model delta sigma weight residual 123.49 66.13 57.36 3.00e+00 1.11e-01 3.66e+02 angle pdb=" CA GLU J 162 " pdb=" N GLU J 162 " pdb=" H GLU J 162 " ideal model delta sigma weight residual 114.09 56.80 57.29 3.00e+00 1.11e-01 3.65e+02 ... (remaining 66731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 14658 16.03 - 32.06: 1722 32.06 - 48.09: 541 48.09 - 64.11: 262 64.11 - 80.14: 29 Dihedral angle restraints: 17212 sinusoidal: 9568 harmonic: 7644 Sorted by residual: dihedral pdb=" CA ASP F 26 " pdb=" C ASP F 26 " pdb=" N ARG F 27 " pdb=" CA ARG F 27 " ideal model delta harmonic sigma weight residual 180.00 153.07 26.93 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA ASP H 26 " pdb=" C ASP H 26 " pdb=" N ARG H 27 " pdb=" CA ARG H 27 " ideal model delta harmonic sigma weight residual 180.00 153.08 26.92 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA ASP K 26 " pdb=" C ASP K 26 " pdb=" N ARG K 27 " pdb=" CA ARG K 27 " ideal model delta harmonic sigma weight residual 180.00 153.08 26.92 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 17209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2391 0.069 - 0.139: 476 0.139 - 0.208: 31 0.208 - 0.277: 28 0.277 - 0.347: 28 Chirality restraints: 2954 Sorted by residual: chirality pdb=" CA PRO Z 4 " pdb=" N PRO Z 4 " pdb=" C PRO Z 4 " pdb=" CB PRO Z 4 " both_signs ideal model delta sigma weight residual False 2.72 3.07 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA PRO Q 4 " pdb=" N PRO Q 4 " pdb=" C PRO Q 4 " pdb=" CB PRO Q 4 " both_signs ideal model delta sigma weight residual False 2.72 3.06 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA PRO b 4 " pdb=" N PRO b 4 " pdb=" C PRO b 4 " pdb=" CB PRO b 4 " both_signs ideal model delta sigma weight residual False 2.72 3.06 -0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 2951 not shown) Planarity restraints: 5530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN K 159 " -0.244 2.00e-02 2.50e+03 2.96e-01 1.31e+03 pdb=" CD GLN K 159 " 0.015 2.00e-02 2.50e+03 pdb=" OE1 GLN K 159 " 0.237 2.00e-02 2.50e+03 pdb=" NE2 GLN K 159 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN K 159 " 0.448 2.00e-02 2.50e+03 pdb="HE22 GLN K 159 " -0.457 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY G 99 " 0.045 2.00e-02 2.50e+03 8.98e-02 8.07e+01 pdb=" N ALA G 100 " -0.154 2.00e-02 2.50e+03 pdb=" CA ALA G 100 " 0.036 2.00e-02 2.50e+03 pdb=" H ALA G 100 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 99 " -0.041 2.00e-02 2.50e+03 7.91e-02 6.25e+01 pdb=" N ALA C 100 " 0.136 2.00e-02 2.50e+03 pdb=" CA ALA C 100 " -0.033 2.00e-02 2.50e+03 pdb=" H ALA C 100 " -0.062 2.00e-02 2.50e+03 ... (remaining 5527 not shown) Histogram of nonbonded interaction distances: 1.34 - 1.99: 376 1.99 - 2.65: 49687 2.65 - 3.30: 98112 3.30 - 3.95: 123468 3.95 - 4.60: 199200 Nonbonded interactions: 470843 Sorted by model distance: nonbonded pdb=" O GLU M 107 " pdb=" H GLY M 109 " model vdw 1.343 2.450 nonbonded pdb=" H ALA M 105 " pdb=" HA ALA M 105 " model vdw 1.450 1.816 nonbonded pdb=" O GLY B 99 " pdb=" H LEU B 102 " model vdw 1.453 2.450 nonbonded pdb=" O GLY G 99 " pdb=" H LEU G 102 " model vdw 1.464 2.450 nonbonded pdb=" H ARG J 170 " pdb=" HA ARG J 170 " model vdw 1.473 1.816 ... (remaining 470838 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 17 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ or name HA )) or resid 108 through 189)) selection = (chain 'B' and (resid 17 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ or name HA )) or resid 108 through 189)) selection = (chain 'C' and (resid 17 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ or name HA )) or resid 108 through 189)) selection = (chain 'D' and (resid 17 through 83 or (resid 84 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 85 through 106 or (resid \ 107 and (name N or name CA or name C or name O or name CB or name CG or name CD \ or name OE1 or name OE2 or name H or name HA )) or resid 108 through 189)) selection = (chain 'E' and (resid 17 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ or name HA )) or resid 108 through 189)) selection = (chain 'F' and (resid 17 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ or name HA )) or resid 108 through 189)) selection = (chain 'G' and (resid 17 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ or name HA )) or resid 108 through 189)) selection = (chain 'H' and (resid 17 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ or name HA )) or resid 108 through 189)) selection = (chain 'I' and (resid 17 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ or name HA )) or resid 108 through 189)) selection = (chain 'J' and (resid 17 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ or name HA )) or resid 108 through 189)) selection = (chain 'K' and (resid 17 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ or name HA )) or resid 108 through 189)) selection = (chain 'L' and (resid 17 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ or name HA )) or resid 108 through 189)) selection = (chain 'M' and (resid 17 through 83 or (resid 84 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 85 through 139 or (resid \ 140 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 141 through 186 or (resid 187 and (name N or name CA or name C or na \ me O or name CB or name H or name HA )) or resid 188 through 189)) selection = (chain 'N' and (resid 17 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ or name HA )) or resid 108 through 189)) } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.230 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 29.690 Find NCS groups from input model: 0.550 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: 0.010 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 : 0.025 0.747 18860 Z= 2.186 Angle : 1.252 9.412 25328 Z= 0.689 Chirality : 0.065 0.347 2954 Planarity : 0.005 0.065 3290 Dihedral : 14.273 80.143 7030 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 1.04 % Allowed : 8.61 % Favored : 90.35 % Rotamer: Outliers : 2.03 % Allowed : 0.62 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 1.22 % 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: -5.31 (0.13), residues: 2310 helix: -3.80 (0.10), residues: 1008 sheet: -3.79 (0.24), residues: 238 loop : -3.05 (0.16), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 146 TYR 0.010 0.001 TYR N 20 PHE 0.008 0.002 PHE H 49 HIS 0.001 0.000 HIS L 122 Details of bonding type rmsd/Z covalent geometry : bond 0.01509 / 0.79 (18818) covalent geometry : angle 1.25216 / 0.69 (25328) hydrogen bonds : bond 0.29697 / 19.71 ( 431) hydrogen bonds : angle 8.09425 / 5.61 ( 1251) Misc. bond : bond 0.43166 / 21.96 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 1102 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 1063 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 18 ASP cc_start: 0.8570 (t0) cc_final: 0.8295 (t70) REVERT: A 78 ASP cc_start: 0.8263 (m-30) cc_final: 0.7613 (m-30) REVERT: A 116 ASN cc_start: 0.8589 (m-40) cc_final: 0.8374 (m110) REVERT: A 123 GLN cc_start: 0.8240 (pt0) cc_final: 0.7689 (pt0) REVERT: A 136 GLU cc_start: 0.6561 (pm20) cc_final: 0.6172 (pm20) REVERT: A 165 GLU cc_start: 0.8690 (mt-10) cc_final: 0.7862 (mt-10) REVERT: A 174 LYS cc_start: 0.8533 (mtmm) cc_final: 0.8178 (mtpp) REVERT: B 41 ASN cc_start: 0.9521 (m-40) cc_final: 0.9286 (m110) REVERT: B 78 ASP cc_start: 0.8229 (m-30) cc_final: 0.7518 (m-30) REVERT: B 116 ASN cc_start: 0.8594 (m-40) cc_final: 0.8268 (m110) REVERT: B 121 ILE cc_start: 0.8998 (pt) cc_final: 0.8764 (pt) REVERT: B 123 GLN cc_start: 0.8030 (pt0) cc_final: 0.7565 (pt0) REVERT: B 137 ILE cc_start: 0.8739 (mm) cc_final: 0.8191 (mm) REVERT: B 165 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8245 (mt-10) REVERT: C 18 ASP cc_start: 0.8441 (t0) cc_final: 0.7901 (t70) REVERT: C 78 ASP cc_start: 0.8194 (m-30) cc_final: 0.7844 (m-30) REVERT: C 98 MET cc_start: 0.9201 (tpp) cc_final: 0.8965 (tpp) REVERT: C 116 ASN cc_start: 0.8575 (m-40) cc_final: 0.8157 (m110) REVERT: C 117 SER cc_start: 0.8900 (m) cc_final: 0.8649 (p) REVERT: C 123 GLN cc_start: 0.8514 (pt0) cc_final: 0.7600 (pt0) REVERT: C 165 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8435 (tm-30) REVERT: C 174 LYS cc_start: 0.8412 (mtmm) cc_final: 0.8106 (mtpp) REVERT: D 18 ASP cc_start: 0.8103 (t0) cc_final: 0.7689 (t70) REVERT: D 56 GLU cc_start: 0.8588 (pm20) cc_final: 0.8148 (pp20) REVERT: D 78 ASP cc_start: 0.8229 (m-30) cc_final: 0.7623 (m-30) REVERT: D 116 ASN cc_start: 0.8433 (m-40) cc_final: 0.8182 (m110) REVERT: D 123 GLN cc_start: 0.8659 (pt0) cc_final: 0.7888 (pt0) REVERT: D 165 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8318 (mt-10) REVERT: D 174 LYS cc_start: 0.8423 (mtmm) cc_final: 0.8042 (mtpp) REVERT: E 18 ASP cc_start: 0.8246 (t0) cc_final: 0.7893 (t70) REVERT: E 56 GLU cc_start: 0.8408 (pm20) cc_final: 0.7906 (pp20) REVERT: E 98 MET cc_start: 0.9172 (tpp) cc_final: 0.8784 (tpp) REVERT: E 123 GLN cc_start: 0.8599 (pt0) cc_final: 0.7629 (pt0) REVERT: E 165 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8378 (mt-10) REVERT: E 174 LYS cc_start: 0.8513 (mtmm) cc_final: 0.8260 (mtpp) REVERT: F 18 ASP cc_start: 0.8528 (t0) cc_final: 0.8128 (t70) REVERT: F 78 ASP cc_start: 0.8363 (m-30) cc_final: 0.7756 (m-30) REVERT: F 123 GLN cc_start: 0.8490 (pt0) cc_final: 0.8196 (pt0) REVERT: F 141 ARG cc_start: 0.9124 (tpt90) cc_final: 0.8884 (tpp80) REVERT: F 165 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8239 (tm-30) REVERT: F 174 LYS cc_start: 0.8300 (mtmm) cc_final: 0.8058 (mtpp) REVERT: G 18 ASP cc_start: 0.8437 (t0) cc_final: 0.8152 (t70) REVERT: G 56 GLU cc_start: 0.8380 (pm20) cc_final: 0.8134 (pp20) REVERT: G 78 ASP cc_start: 0.8273 (m-30) cc_final: 0.7789 (m-30) REVERT: G 123 GLN cc_start: 0.8541 (pt0) cc_final: 0.7683 (pt0) REVERT: G 165 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8085 (tm-30) REVERT: G 174 LYS cc_start: 0.8501 (mtmm) cc_final: 0.8143 (mtpp) REVERT: H 57 LYS cc_start: 0.7692 (mmmm) cc_final: 0.7467 (mmmt) REVERT: H 81 GLN cc_start: 0.8897 (mt0) cc_final: 0.8645 (mt0) REVERT: H 141 ARG cc_start: 0.8363 (tpt90) cc_final: 0.7864 (tpt170) REVERT: H 151 LYS cc_start: 0.8963 (tptp) cc_final: 0.8548 (ttpt) REVERT: H 178 GLU cc_start: 0.8544 (pt0) cc_final: 0.8268 (pt0) REVERT: I 81 GLN cc_start: 0.8933 (mt0) cc_final: 0.8653 (mt0) REVERT: I 129 GLN cc_start: 0.7790 (pm20) cc_final: 0.7579 (pm20) REVERT: I 151 LYS cc_start: 0.8982 (tptp) cc_final: 0.8682 (tppt) REVERT: I 165 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8070 (tt0) REVERT: I 167 ASP cc_start: 0.8305 (m-30) cc_final: 0.7806 (m-30) REVERT: I 178 GLU cc_start: 0.8473 (pt0) cc_final: 0.8163 (pt0) REVERT: J 141 ARG cc_start: 0.8401 (tpt90) cc_final: 0.7700 (tpt170) REVERT: J 188 ILE cc_start: 0.8924 (tt) cc_final: 0.8718 (mt) REVERT: K 81 GLN cc_start: 0.8901 (mt0) cc_final: 0.8579 (mt0) REVERT: K 129 GLN cc_start: 0.7735 (pm20) cc_final: 0.7460 (pm20) REVERT: K 151 LYS cc_start: 0.8986 (tptp) cc_final: 0.8634 (ttpt) REVERT: K 165 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8301 (tt0) REVERT: L 18 ASP cc_start: 0.9354 (t0) cc_final: 0.9005 (t0) REVERT: L 57 LYS cc_start: 0.7751 (mmmm) cc_final: 0.7550 (mmmt) REVERT: L 81 GLN cc_start: 0.8881 (mt0) cc_final: 0.8588 (mt0) REVERT: L 123 GLN cc_start: 0.8569 (pt0) cc_final: 0.8329 (pt0) REVERT: L 141 ARG cc_start: 0.8376 (tpt90) cc_final: 0.7927 (tpt170) REVERT: M 57 LYS cc_start: 0.7758 (mmmm) cc_final: 0.7512 (mmmt) REVERT: M 81 GLN cc_start: 0.8803 (mt0) cc_final: 0.8493 (mt0) REVERT: M 97 SER cc_start: 0.8725 (p) cc_final: 0.8387 (t) REVERT: M 165 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8188 (tt0) REVERT: M 178 GLU cc_start: 0.8601 (pt0) cc_final: 0.8303 (pt0) REVERT: N 97 SER cc_start: 0.8717 (p) cc_final: 0.8311 (t) REVERT: N 167 ASP cc_start: 0.8390 (m-30) cc_final: 0.8106 (m-30) outliers start: 39 outliers final: 25 residues processed: 1076 average time/residue: 0.3520 time to fit residues: 546.6388 Evaluate side-chains 680 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 655 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 98 MET Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain K residue 161 LEU Chi-restraints excluded: chain K residue 174 LYS Chi-restraints excluded: chain L residue 37 ASP Chi-restraints excluded: chain L residue 98 MET Chi-restraints excluded: chain M residue 37 ASP Chi-restraints excluded: chain M residue 98 MET Chi-restraints excluded: chain N residue 98 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.8980 chunk 212 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 41 ASN H 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.110936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.095480 restraints weight = 120641.624| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 4.69 r_work: 0.3185 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 18860 Z= 0.140 Angle : 0.785 26.123 25328 Z= 0.399 Chirality : 0.085 1.599 2954 Planarity : 0.005 0.092 3290 Dihedral : 8.380 75.164 2696 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.31 % Favored : 91.43 % Rotamer: Outliers : 2.45 % Allowed : 15.92 % Favored : 81.63 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 1.22 % 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: -4.04 (0.16), residues: 2310 helix: -3.03 (0.13), residues: 966 sheet: -3.27 (0.28), residues: 238 loop : -2.06 (0.19), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 141 TYR 0.013 0.001 TYR D 77 PHE 0.019 0.001 PHE T 2 HIS 0.002 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (18818) covalent geometry : angle 0.78533 / 0.40 (25328) hydrogen bonds : bond 0.07140 / 4.81 ( 431) hydrogen bonds : angle 5.38490 / 3.64 ( 1251) Misc. bond : bond 0.00219 / 0.12 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 751 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 704 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 78 ASP cc_start: 0.8661 (m-30) cc_final: 0.7831 (m-30) REVERT: A 98 MET cc_start: 0.9298 (tpp) cc_final: 0.8880 (tpp) REVERT: A 116 ASN cc_start: 0.8871 (m-40) cc_final: 0.8616 (m110) REVERT: A 157 THR cc_start: 0.9314 (p) cc_final: 0.9006 (t) REVERT: A 164 ILE cc_start: 0.8666 (mm) cc_final: 0.8449 (mt) REVERT: B 78 ASP cc_start: 0.8577 (m-30) cc_final: 0.7767 (m-30) REVERT: B 116 ASN cc_start: 0.8821 (m-40) cc_final: 0.8490 (m110) REVERT: B 150 ASN cc_start: 0.8487 (p0) cc_final: 0.8098 (m-40) REVERT: B 152 VAL cc_start: 0.8791 (t) cc_final: 0.8575 (p) REVERT: B 165 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8257 (tm-30) REVERT: B 175 SER cc_start: 0.9119 (p) cc_final: 0.8310 (t) REVERT: C 78 ASP cc_start: 0.8514 (m-30) cc_final: 0.7933 (m-30) REVERT: C 98 MET cc_start: 0.9254 (tpp) cc_final: 0.8956 (tpp) REVERT: C 116 ASN cc_start: 0.8702 (m-40) cc_final: 0.8377 (m110) REVERT: C 123 GLN cc_start: 0.8405 (pt0) cc_final: 0.8044 (pt0) REVERT: C 165 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8549 (tm-30) REVERT: D 56 GLU cc_start: 0.8619 (pm20) cc_final: 0.8232 (pp20) REVERT: D 116 ASN cc_start: 0.8785 (m-40) cc_final: 0.8346 (m110) REVERT: D 123 GLN cc_start: 0.8702 (pt0) cc_final: 0.8220 (pt0) REVERT: D 165 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8459 (mt-10) REVERT: D 169 ASP cc_start: 0.8270 (t0) cc_final: 0.7952 (t0) REVERT: D 185 ILE cc_start: 0.8882 (pt) cc_final: 0.8649 (mm) REVERT: E 56 GLU cc_start: 0.8516 (pm20) cc_final: 0.8027 (pp20) REVERT: E 123 GLN cc_start: 0.8479 (pt0) cc_final: 0.8017 (pt0) REVERT: E 155 GLU cc_start: 0.8284 (mm-30) cc_final: 0.8071 (mp0) REVERT: E 165 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8415 (mt-10) REVERT: E 169 ASP cc_start: 0.8371 (t0) cc_final: 0.8077 (t0) REVERT: F 48 LEU cc_start: 0.9524 (mt) cc_final: 0.9174 (tp) REVERT: F 57 LYS cc_start: 0.9087 (mmtt) cc_final: 0.8837 (mmmt) REVERT: F 123 GLN cc_start: 0.8646 (pt0) cc_final: 0.8393 (pt0) REVERT: F 165 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8276 (tm-30) REVERT: G 48 LEU cc_start: 0.9549 (mt) cc_final: 0.9296 (tp) REVERT: G 56 GLU cc_start: 0.8534 (pm20) cc_final: 0.8277 (pp20) REVERT: G 78 ASP cc_start: 0.8839 (m-30) cc_final: 0.8126 (m-30) REVERT: G 152 VAL cc_start: 0.9123 (t) cc_final: 0.8854 (p) REVERT: G 165 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8370 (tm-30) REVERT: G 170 ARG cc_start: 0.7750 (ptm-80) cc_final: 0.7469 (ptm160) REVERT: H 57 LYS cc_start: 0.7640 (mmmm) cc_final: 0.7341 (mmmt) REVERT: H 107 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7510 (mm-30) REVERT: H 159 GLN cc_start: 0.8520 (mm-40) cc_final: 0.7984 (mp10) REVERT: H 165 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8392 (pt0) REVERT: H 178 GLU cc_start: 0.8680 (pt0) cc_final: 0.8470 (pt0) REVERT: I 107 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7415 (mm-30) REVERT: I 129 GLN cc_start: 0.8073 (pm20) cc_final: 0.7583 (pm20) REVERT: I 165 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8302 (tt0) REVERT: I 167 ASP cc_start: 0.8186 (m-30) cc_final: 0.7846 (m-30) REVERT: J 107 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7271 (mm-30) REVERT: J 123 GLN cc_start: 0.8898 (pt0) cc_final: 0.8664 (pt0) REVERT: J 159 GLN cc_start: 0.8550 (mm-40) cc_final: 0.7597 (mp10) REVERT: J 185 ILE cc_start: 0.9328 (pt) cc_final: 0.8995 (tt) REVERT: J 188 ILE cc_start: 0.8951 (tt) cc_final: 0.8745 (mt) REVERT: K 81 GLN cc_start: 0.9033 (mt0) cc_final: 0.8536 (mt0) REVERT: K 165 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8552 (tt0) REVERT: L 81 GLN cc_start: 0.9004 (mt0) cc_final: 0.8755 (mt0) REVERT: M 118 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8240 (mt-10) REVERT: M 165 GLU cc_start: 0.8602 (mt-10) cc_final: 0.7956 (tm-30) REVERT: N 148 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8262 (tmtt) outliers start: 47 outliers final: 34 residues processed: 723 average time/residue: 0.2674 time to fit residues: 302.4309 Evaluate side-chains 649 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 614 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain K residue 161 LEU Chi-restraints excluded: chain L residue 26 ASP Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 148 LYS Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 37 ASP Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 98 MET Chi-restraints excluded: chain N residue 26 ASP Chi-restraints excluded: chain N residue 98 MET Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 148 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 100 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 188 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.103806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.088377 restraints weight = 125599.580| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 4.79 r_work: 0.3067 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.5969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18860 Z= 0.251 Angle : 0.837 31.435 25328 Z= 0.426 Chirality : 0.090 1.715 2954 Planarity : 0.005 0.036 3290 Dihedral : 8.338 88.961 2659 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.96 % Favored : 89.78 % Rotamer: Outliers : 3.54 % Allowed : 18.89 % Favored : 77.58 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 1.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.67 (0.16), residues: 2310 helix: -2.64 (0.14), residues: 980 sheet: -3.03 (0.28), residues: 238 loop : -1.95 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 141 TYR 0.017 0.002 TYR E 182 PHE 0.024 0.002 PHE V 2 HIS 0.001 0.001 HIS L 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.25 (18818) covalent geometry : angle 0.83707 / 0.43 (25328) hydrogen bonds : bond 0.06045 / 4.10 ( 431) hydrogen bonds : angle 5.68745 / 3.86 ( 1251) Misc. bond : bond 0.00300 / 0.16 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 641 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 573 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 78 ASP cc_start: 0.8580 (m-30) cc_final: 0.8078 (m-30) REVERT: A 165 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8526 (mt-10) REVERT: B 78 ASP cc_start: 0.8660 (m-30) cc_final: 0.8287 (m-30) REVERT: B 116 ASN cc_start: 0.8762 (m-40) cc_final: 0.8447 (m110) REVERT: B 152 VAL cc_start: 0.9046 (t) cc_final: 0.8839 (p) REVERT: B 165 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8438 (tm-30) REVERT: C 78 ASP cc_start: 0.8455 (m-30) cc_final: 0.7844 (m-30) REVERT: C 98 MET cc_start: 0.9428 (tpp) cc_final: 0.9141 (tpp) REVERT: C 116 ASN cc_start: 0.8762 (m-40) cc_final: 0.8549 (m110) REVERT: C 165 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8682 (tm-30) REVERT: C 170 ARG cc_start: 0.7814 (ptm-80) cc_final: 0.7429 (ptm160) REVERT: C 178 GLU cc_start: 0.8799 (mp0) cc_final: 0.8567 (mp0) REVERT: D 56 GLU cc_start: 0.8636 (pm20) cc_final: 0.8279 (pp20) REVERT: D 116 ASN cc_start: 0.8761 (m-40) cc_final: 0.8404 (m110) REVERT: D 123 GLN cc_start: 0.8634 (pt0) cc_final: 0.8047 (pt0) REVERT: D 169 ASP cc_start: 0.8411 (t0) cc_final: 0.8033 (t0) REVERT: E 56 GLU cc_start: 0.8554 (pm20) cc_final: 0.8130 (pp20) REVERT: E 123 GLN cc_start: 0.8609 (pt0) cc_final: 0.8176 (pt0) REVERT: E 165 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8509 (mt-10) REVERT: F 48 LEU cc_start: 0.9623 (mt) cc_final: 0.9377 (tp) REVERT: F 57 LYS cc_start: 0.9098 (mmtt) cc_final: 0.8835 (mmmt) REVERT: F 116 ASN cc_start: 0.8721 (m-40) cc_final: 0.8408 (m110) REVERT: F 123 GLN cc_start: 0.8584 (pt0) cc_final: 0.8361 (pt0) REVERT: F 152 VAL cc_start: 0.9038 (p) cc_final: 0.8813 (p) REVERT: G 56 GLU cc_start: 0.8567 (pm20) cc_final: 0.8326 (pp20) REVERT: G 78 ASP cc_start: 0.8500 (m-30) cc_final: 0.7939 (m-30) REVERT: G 165 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8569 (tm-30) REVERT: G 170 ARG cc_start: 0.7814 (ptm-80) cc_final: 0.7304 (ptm160) REVERT: H 94 MET cc_start: 0.8721 (tpp) cc_final: 0.8473 (tpp) REVERT: H 159 GLN cc_start: 0.8604 (mm-40) cc_final: 0.7966 (mp10) REVERT: I 165 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8306 (tt0) REVERT: I 167 ASP cc_start: 0.8398 (m-30) cc_final: 0.8144 (m-30) REVERT: J 107 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7315 (mm-30) REVERT: J 118 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8308 (mt-10) REVERT: J 159 GLN cc_start: 0.8615 (mm-40) cc_final: 0.7644 (mp10) REVERT: J 167 ASP cc_start: 0.8481 (m-30) cc_final: 0.8266 (m-30) REVERT: K 81 GLN cc_start: 0.9041 (mt0) cc_final: 0.8617 (mt0) REVERT: K 165 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8551 (tt0) REVERT: L 26 ASP cc_start: 0.7599 (t70) cc_final: 0.7397 (t0) REVERT: L 61 LEU cc_start: 0.9448 (tt) cc_final: 0.9175 (tt) REVERT: L 81 GLN cc_start: 0.9030 (mt0) cc_final: 0.8610 (mt0) REVERT: L 165 GLU cc_start: 0.8600 (pt0) cc_final: 0.8386 (pt0) REVERT: M 148 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8596 (tmtt) REVERT: M 165 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8140 (tm-30) REVERT: N 148 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8480 (tmtt) outliers start: 68 outliers final: 48 residues processed: 608 average time/residue: 0.2619 time to fit residues: 252.4492 Evaluate side-chains 586 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 535 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 185 ILE Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 118 GLU Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 161 LEU Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 148 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 148 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 17 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 181 optimal weight: 0.0980 chunk 41 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 213 optimal weight: 9.9990 chunk 148 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 204 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.105722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.089948 restraints weight = 124050.741| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 4.82 r_work: 0.3096 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.6290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18860 Z= 0.118 Angle : 0.727 33.020 25328 Z= 0.361 Chirality : 0.089 1.703 2954 Planarity : 0.004 0.029 3290 Dihedral : 6.827 82.115 2650 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.79 % Favored : 91.00 % Rotamer: Outliers : 2.39 % Allowed : 20.45 % Favored : 77.16 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 1.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.55 (0.15), residues: 2310 helix: -2.23 (0.14), residues: 1120 sheet: -2.82 (0.28), residues: 238 loop : -2.18 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 141 TYR 0.007 0.001 TYR J 77 PHE 0.011 0.001 PHE J 101 HIS 0.002 0.000 HIS M 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (18818) covalent geometry : angle 0.72697 / 0.36 (25328) hydrogen bonds : bond 0.04703 / 3.17 ( 431) hydrogen bonds : angle 4.99468 / 3.38 ( 1251) Misc. bond : bond 0.00208 / 0.11 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 614 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 568 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 78 ASP cc_start: 0.8530 (m-30) cc_final: 0.7907 (m-30) REVERT: A 152 VAL cc_start: 0.9130 (t) cc_final: 0.8923 (p) REVERT: A 165 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8573 (mt-10) REVERT: B 78 ASP cc_start: 0.8647 (m-30) cc_final: 0.8210 (m-30) REVERT: B 116 ASN cc_start: 0.8766 (m-40) cc_final: 0.8400 (m110) REVERT: B 152 VAL cc_start: 0.8962 (t) cc_final: 0.8757 (p) REVERT: B 165 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8441 (tm-30) REVERT: C 78 ASP cc_start: 0.8539 (m-30) cc_final: 0.7958 (m-30) REVERT: C 116 ASN cc_start: 0.8717 (m-40) cc_final: 0.8436 (m110) REVERT: C 165 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8656 (tm-30) REVERT: C 170 ARG cc_start: 0.7710 (ptm-80) cc_final: 0.7319 (ptm160) REVERT: C 178 GLU cc_start: 0.8764 (mp0) cc_final: 0.8484 (mp0) REVERT: D 48 LEU cc_start: 0.9584 (mt) cc_final: 0.9284 (tp) REVERT: D 56 GLU cc_start: 0.8647 (pm20) cc_final: 0.8277 (pp20) REVERT: D 116 ASN cc_start: 0.8842 (m-40) cc_final: 0.8482 (m110) REVERT: D 165 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8253 (mt-10) REVERT: D 169 ASP cc_start: 0.8478 (t0) cc_final: 0.8104 (t0) REVERT: E 56 GLU cc_start: 0.8553 (pm20) cc_final: 0.8096 (pp20) REVERT: E 123 GLN cc_start: 0.8606 (pt0) cc_final: 0.8148 (pt0) REVERT: E 151 LYS cc_start: 0.8941 (ttmt) cc_final: 0.8666 (ttmm) REVERT: E 165 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8410 (mt-10) REVERT: F 48 LEU cc_start: 0.9638 (mt) cc_final: 0.9416 (tp) REVERT: F 57 LYS cc_start: 0.9097 (mmtt) cc_final: 0.8844 (mmmt) REVERT: F 116 ASN cc_start: 0.8785 (m-40) cc_final: 0.8456 (m110) REVERT: F 123 GLN cc_start: 0.8580 (pt0) cc_final: 0.8356 (pt0) REVERT: F 141 ARG cc_start: 0.9239 (tpt90) cc_final: 0.9000 (tpp80) REVERT: G 56 GLU cc_start: 0.8565 (pm20) cc_final: 0.8324 (pp20) REVERT: G 141 ARG cc_start: 0.9332 (tpt90) cc_final: 0.9049 (tpp80) REVERT: G 165 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8581 (tm-30) REVERT: G 170 ARG cc_start: 0.7606 (ptm-80) cc_final: 0.7296 (ptm160) REVERT: H 94 MET cc_start: 0.8721 (tpp) cc_final: 0.8442 (tpp) REVERT: H 159 GLN cc_start: 0.8547 (mm-40) cc_final: 0.7896 (mp10) REVERT: I 129 GLN cc_start: 0.8198 (pm20) cc_final: 0.7893 (pm20) REVERT: I 167 ASP cc_start: 0.8330 (m-30) cc_final: 0.8086 (m-30) REVERT: J 107 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7361 (mm-30) REVERT: J 123 GLN cc_start: 0.8843 (pt0) cc_final: 0.8641 (pt0) REVERT: J 159 GLN cc_start: 0.8637 (mm-40) cc_final: 0.7639 (mp10) REVERT: K 165 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8535 (tt0) REVERT: L 81 GLN cc_start: 0.8993 (mt0) cc_final: 0.8601 (mt0) REVERT: M 165 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8126 (tm-30) REVERT: N 25 LYS cc_start: 0.8716 (tppt) cc_final: 0.8371 (tttt) REVERT: N 165 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8301 (tt0) outliers start: 46 outliers final: 37 residues processed: 598 average time/residue: 0.2741 time to fit residues: 262.1642 Evaluate side-chains 563 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 526 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 119 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 9 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 173 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 142 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.101444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.085757 restraints weight = 125384.198| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 4.87 r_work: 0.3020 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.7212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 18860 Z= 0.279 Angle : 0.842 26.294 25328 Z= 0.435 Chirality : 0.092 1.786 2954 Planarity : 0.005 0.042 3290 Dihedral : 7.784 89.203 2648 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.69 % Favored : 88.10 % Rotamer: Outliers : 3.80 % Allowed : 21.33 % Favored : 74.87 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 1.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.15), residues: 2310 helix: -2.16 (0.14), residues: 1134 sheet: -2.76 (0.28), residues: 238 loop : -2.39 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 146 TYR 0.016 0.002 TYR D 77 PHE 0.017 0.002 PHE I 101 HIS 0.004 0.001 HIS I 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.28 (18818) covalent geometry : angle 0.84235 / 0.43 (25328) hydrogen bonds : bond 0.06283 / 4.23 ( 431) hydrogen bonds : angle 5.95785 / 4.03 ( 1251) Misc. bond : bond 0.00241 / 0.13 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 555 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 482 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8557 (m-30) cc_final: 0.8082 (m-30) REVERT: A 163 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.8431 (p) REVERT: B 78 ASP cc_start: 0.8764 (m-30) cc_final: 0.8453 (m-30) REVERT: B 116 ASN cc_start: 0.8630 (m-40) cc_final: 0.8260 (m110) REVERT: B 165 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8568 (tm-30) REVERT: C 78 ASP cc_start: 0.8583 (m-30) cc_final: 0.8078 (m-30) REVERT: C 116 ASN cc_start: 0.8642 (m-40) cc_final: 0.8413 (m110) REVERT: C 163 VAL cc_start: 0.8632 (m) cc_final: 0.8422 (p) REVERT: C 165 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8831 (tm-30) REVERT: D 56 GLU cc_start: 0.8714 (pm20) cc_final: 0.8399 (pp20) REVERT: D 116 ASN cc_start: 0.8734 (m-40) cc_final: 0.8482 (m110) REVERT: D 163 VAL cc_start: 0.8696 (m) cc_final: 0.8483 (p) REVERT: D 169 ASP cc_start: 0.8681 (t0) cc_final: 0.8233 (t0) REVERT: E 56 GLU cc_start: 0.8605 (pm20) cc_final: 0.8299 (pp20) REVERT: E 123 GLN cc_start: 0.8546 (pt0) cc_final: 0.8130 (pt0) REVERT: E 151 LYS cc_start: 0.8857 (ttmt) cc_final: 0.8275 (ttmm) REVERT: E 155 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8142 (mp0) REVERT: E 163 VAL cc_start: 0.8673 (OUTLIER) cc_final: 0.8451 (p) REVERT: E 169 ASP cc_start: 0.8563 (t0) cc_final: 0.7964 (t0) REVERT: F 57 LYS cc_start: 0.9113 (mmtt) cc_final: 0.8873 (mmmt) REVERT: F 116 ASN cc_start: 0.8725 (m-40) cc_final: 0.8453 (m110) REVERT: F 123 GLN cc_start: 0.8589 (pt0) cc_final: 0.8376 (pt0) REVERT: F 163 VAL cc_start: 0.8641 (OUTLIER) cc_final: 0.8333 (p) REVERT: G 56 GLU cc_start: 0.8657 (pm20) cc_final: 0.8418 (pp20) REVERT: G 165 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8612 (tm-30) REVERT: G 169 ASP cc_start: 0.8345 (t70) cc_final: 0.8036 (t0) REVERT: H 94 MET cc_start: 0.8704 (tpp) cc_final: 0.8491 (tpp) REVERT: H 118 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8416 (mt-10) REVERT: H 165 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8472 (pt0) REVERT: J 123 GLN cc_start: 0.8808 (pt0) cc_final: 0.8585 (pt0) REVERT: K 165 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8480 (tt0) REVERT: L 54 ASP cc_start: 0.8626 (m-30) cc_final: 0.8415 (m-30) REVERT: M 54 ASP cc_start: 0.8773 (m-30) cc_final: 0.8544 (m-30) REVERT: M 165 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8246 (tm-30) REVERT: N 25 LYS cc_start: 0.8928 (tppt) cc_final: 0.8697 (ttmt) REVERT: N 165 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8336 (tt0) REVERT: N 168 THR cc_start: 0.9091 (m) cc_final: 0.8805 (m) outliers start: 73 outliers final: 46 residues processed: 532 average time/residue: 0.2757 time to fit residues: 234.3996 Evaluate side-chains 492 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 442 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 41 ASN Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 155 GLU Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 119 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 73 optimal weight: 9.9990 chunk 209 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 212 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 221 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.101922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.086599 restraints weight = 126416.884| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 4.87 r_work: 0.3043 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.7353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18860 Z= 0.152 Angle : 0.714 25.766 25328 Z= 0.367 Chirality : 0.090 1.732 2954 Planarity : 0.004 0.044 3290 Dihedral : 6.980 72.193 2648 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.00 % Favored : 90.82 % Rotamer: Outliers : 3.07 % Allowed : 22.37 % Favored : 74.56 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 1.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.16), residues: 2310 helix: -1.75 (0.14), residues: 1134 sheet: -2.63 (0.29), residues: 238 loop : -2.31 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 141 TYR 0.008 0.001 TYR C 77 PHE 0.013 0.001 PHE K 101 HIS 0.001 0.000 HIS N 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (18818) covalent geometry : angle 0.71382 / 0.37 (25328) hydrogen bonds : bond 0.04641 / 3.14 ( 431) hydrogen bonds : angle 5.24600 / 3.55 ( 1251) Misc. bond : bond 0.00208 / 0.11 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 540 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 481 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8551 (m-30) cc_final: 0.8022 (m-30) REVERT: A 163 VAL cc_start: 0.8664 (OUTLIER) cc_final: 0.8432 (p) REVERT: A 165 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8362 (mt-10) REVERT: A 169 ASP cc_start: 0.7969 (t70) cc_final: 0.7418 (t0) REVERT: B 78 ASP cc_start: 0.8739 (m-30) cc_final: 0.8422 (m-30) REVERT: B 116 ASN cc_start: 0.8652 (m-40) cc_final: 0.8260 (m110) REVERT: B 165 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8591 (tm-30) REVERT: C 78 ASP cc_start: 0.8614 (m-30) cc_final: 0.8060 (m-30) REVERT: C 116 ASN cc_start: 0.8636 (m-40) cc_final: 0.8353 (m110) REVERT: C 165 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8729 (tm-30) REVERT: C 177 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8558 (mm-30) REVERT: D 56 GLU cc_start: 0.8680 (pm20) cc_final: 0.8411 (pp20) REVERT: D 116 ASN cc_start: 0.8768 (m-40) cc_final: 0.8428 (m110) REVERT: D 165 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8371 (mt-10) REVERT: D 169 ASP cc_start: 0.8643 (t0) cc_final: 0.8214 (t0) REVERT: E 56 GLU cc_start: 0.8583 (pm20) cc_final: 0.8252 (pp20) REVERT: E 123 GLN cc_start: 0.8526 (pt0) cc_final: 0.8121 (pt0) REVERT: E 151 LYS cc_start: 0.8838 (ttmt) cc_final: 0.8230 (ttmm) REVERT: E 152 VAL cc_start: 0.9165 (t) cc_final: 0.8753 (p) REVERT: E 155 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8133 (mp0) REVERT: E 163 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8424 (p) REVERT: E 169 ASP cc_start: 0.8537 (t0) cc_final: 0.7919 (t0) REVERT: E 177 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8683 (mm-30) REVERT: F 57 LYS cc_start: 0.9143 (mmtt) cc_final: 0.8919 (mmmt) REVERT: F 116 ASN cc_start: 0.8710 (m-40) cc_final: 0.8496 (m110) REVERT: F 163 VAL cc_start: 0.8589 (OUTLIER) cc_final: 0.8377 (p) REVERT: G 56 GLU cc_start: 0.8674 (pm20) cc_final: 0.8399 (pp20) REVERT: G 118 GLU cc_start: 0.8759 (pt0) cc_final: 0.8214 (pt0) REVERT: G 163 VAL cc_start: 0.8678 (m) cc_final: 0.8461 (p) REVERT: G 165 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8674 (tm-30) REVERT: G 169 ASP cc_start: 0.8378 (t70) cc_final: 0.8047 (t0) REVERT: H 94 MET cc_start: 0.8748 (tpp) cc_final: 0.8496 (tpp) REVERT: H 118 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8309 (mt-10) REVERT: H 162 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8368 (tp30) REVERT: H 165 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8371 (tt0) REVERT: I 94 MET cc_start: 0.8654 (tpp) cc_final: 0.8375 (tpp) REVERT: J 123 GLN cc_start: 0.8801 (pt0) cc_final: 0.8586 (pt0) REVERT: L 54 ASP cc_start: 0.8583 (m-30) cc_final: 0.8366 (m-30) REVERT: M 54 ASP cc_start: 0.8741 (m-30) cc_final: 0.8516 (m-30) REVERT: M 165 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8203 (tm-30) REVERT: N 25 LYS cc_start: 0.8812 (tppt) cc_final: 0.8580 (ttmt) REVERT: N 165 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8356 (tt0) outliers start: 59 outliers final: 43 residues processed: 528 average time/residue: 0.2814 time to fit residues: 237.0085 Evaluate side-chains 515 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 466 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 41 ASN Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 103 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 111 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 126 optimal weight: 8.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 122 HIS F 122 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.102866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.087636 restraints weight = 126716.450| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 4.89 r_work: 0.3044 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.7591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18860 Z= 0.156 Angle : 0.706 25.851 25328 Z= 0.362 Chirality : 0.090 1.738 2954 Planarity : 0.004 0.042 3290 Dihedral : 6.788 79.705 2648 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.35 % Favored : 89.48 % Rotamer: Outliers : 2.71 % Allowed : 22.68 % Favored : 74.61 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 1.22 % 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: -2.82 (0.16), residues: 2310 helix: -1.33 (0.15), residues: 1148 sheet: -2.40 (0.30), residues: 238 loop : -2.27 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 141 TYR 0.010 0.001 TYR C 77 PHE 0.014 0.001 PHE I 101 HIS 0.001 0.000 HIS M 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (18818) covalent geometry : angle 0.70557 / 0.36 (25328) hydrogen bonds : bond 0.04335 / 2.95 ( 431) hydrogen bonds : angle 5.10391 / 3.45 ( 1251) Misc. bond : bond 0.00203 / 0.11 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 527 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 475 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8555 (m-30) cc_final: 0.8061 (m-30) REVERT: A 163 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8460 (p) REVERT: A 165 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8355 (mt-10) REVERT: A 169 ASP cc_start: 0.8121 (t70) cc_final: 0.7851 (t70) REVERT: B 78 ASP cc_start: 0.8621 (m-30) cc_final: 0.8045 (m-30) REVERT: B 116 ASN cc_start: 0.8604 (m-40) cc_final: 0.8261 (m110) REVERT: B 165 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8482 (tm-30) REVERT: C 78 ASP cc_start: 0.8565 (m-30) cc_final: 0.8067 (m-30) REVERT: C 116 ASN cc_start: 0.8673 (m-40) cc_final: 0.8321 (m110) REVERT: C 165 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8782 (tm-30) REVERT: C 177 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8663 (mm-30) REVERT: D 56 GLU cc_start: 0.8706 (pm20) cc_final: 0.8406 (pp20) REVERT: D 81 GLN cc_start: 0.8596 (tm-30) cc_final: 0.8381 (tm-30) REVERT: D 116 ASN cc_start: 0.8702 (m-40) cc_final: 0.8386 (m-40) REVERT: D 118 GLU cc_start: 0.8353 (pt0) cc_final: 0.8086 (pt0) REVERT: D 123 GLN cc_start: 0.8516 (pt0) cc_final: 0.8225 (pt0) REVERT: D 165 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8414 (mt-10) REVERT: D 169 ASP cc_start: 0.8706 (t0) cc_final: 0.8264 (t0) REVERT: E 56 GLU cc_start: 0.8570 (pm20) cc_final: 0.8271 (pp20) REVERT: E 123 GLN cc_start: 0.8466 (pt0) cc_final: 0.8061 (pt0) REVERT: E 151 LYS cc_start: 0.8863 (ttmt) cc_final: 0.8272 (ttmm) REVERT: E 152 VAL cc_start: 0.9140 (t) cc_final: 0.8747 (p) REVERT: E 155 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8116 (mp0) REVERT: E 163 VAL cc_start: 0.8639 (OUTLIER) cc_final: 0.8435 (p) REVERT: E 169 ASP cc_start: 0.8566 (t0) cc_final: 0.7958 (t0) REVERT: F 57 LYS cc_start: 0.9136 (mmtt) cc_final: 0.8917 (mmmt) REVERT: F 116 ASN cc_start: 0.8735 (m-40) cc_final: 0.8426 (m110) REVERT: G 56 GLU cc_start: 0.8706 (pm20) cc_final: 0.8429 (pp20) REVERT: G 118 GLU cc_start: 0.8792 (pt0) cc_final: 0.8230 (pt0) REVERT: G 165 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8751 (tm-30) REVERT: G 169 ASP cc_start: 0.8289 (t70) cc_final: 0.7894 (t0) REVERT: H 94 MET cc_start: 0.8805 (tpp) cc_final: 0.8551 (tpp) REVERT: H 162 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8426 (tp30) REVERT: H 165 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8349 (tt0) REVERT: I 94 MET cc_start: 0.8712 (tpp) cc_final: 0.8440 (tpp) REVERT: J 123 GLN cc_start: 0.8815 (pt0) cc_final: 0.8513 (pt0) REVERT: L 54 ASP cc_start: 0.8673 (m-30) cc_final: 0.8450 (m-30) REVERT: M 54 ASP cc_start: 0.8789 (m-30) cc_final: 0.8554 (m-30) REVERT: M 165 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8206 (tm-30) REVERT: N 25 LYS cc_start: 0.8829 (tppt) cc_final: 0.8591 (ttmt) REVERT: N 165 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8386 (tt0) outliers start: 52 outliers final: 40 residues processed: 513 average time/residue: 0.2838 time to fit residues: 231.0813 Evaluate side-chains 506 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 463 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 41 ASN Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 70 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 162 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 208 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.102496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.087352 restraints weight = 126613.839| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 4.90 r_work: 0.3040 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.7744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 18860 Z= 0.171 Angle : 0.706 25.892 25328 Z= 0.364 Chirality : 0.090 1.740 2954 Planarity : 0.004 0.079 3290 Dihedral : 6.712 79.420 2648 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.70 % Favored : 90.17 % Rotamer: Outliers : 2.97 % Allowed : 22.79 % Favored : 74.25 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 1.22 % 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: -2.61 (0.16), residues: 2310 helix: -1.12 (0.15), residues: 1148 sheet: -2.35 (0.30), residues: 238 loop : -2.23 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 146 TYR 0.011 0.001 TYR C 77 PHE 0.015 0.001 PHE I 101 HIS 0.003 0.001 HIS F 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (18818) covalent geometry : angle 0.70560 / 0.36 (25328) hydrogen bonds : bond 0.04318 / 2.93 ( 431) hydrogen bonds : angle 5.12495 / 3.47 ( 1251) Misc. bond : bond 0.00200 / 0.11 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 529 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 472 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 78 ASP cc_start: 0.8609 (m-30) cc_final: 0.8112 (m-30) REVERT: A 163 VAL cc_start: 0.8752 (OUTLIER) cc_final: 0.8530 (p) REVERT: A 165 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8364 (mt-10) REVERT: A 169 ASP cc_start: 0.8272 (t70) cc_final: 0.7997 (t70) REVERT: B 78 ASP cc_start: 0.8637 (m-30) cc_final: 0.8086 (m-30) REVERT: B 116 ASN cc_start: 0.8736 (m-40) cc_final: 0.8254 (m110) REVERT: B 165 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8502 (tm-30) REVERT: C 78 ASP cc_start: 0.8526 (m-30) cc_final: 0.8154 (m-30) REVERT: C 116 ASN cc_start: 0.8656 (m-40) cc_final: 0.8307 (m110) REVERT: C 165 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8823 (tm-30) REVERT: C 177 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8681 (mm-30) REVERT: D 56 GLU cc_start: 0.8620 (pm20) cc_final: 0.8364 (pp20) REVERT: D 81 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8390 (tm-30) REVERT: D 116 ASN cc_start: 0.8679 (m-40) cc_final: 0.8299 (m-40) REVERT: D 118 GLU cc_start: 0.8524 (pt0) cc_final: 0.8220 (pt0) REVERT: D 123 GLN cc_start: 0.8550 (pt0) cc_final: 0.8277 (pt0) REVERT: D 165 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8374 (mt-10) REVERT: D 169 ASP cc_start: 0.8741 (t0) cc_final: 0.8278 (t0) REVERT: E 56 GLU cc_start: 0.8586 (pm20) cc_final: 0.8285 (pp20) REVERT: E 123 GLN cc_start: 0.8447 (pt0) cc_final: 0.8066 (pt0) REVERT: E 151 LYS cc_start: 0.8847 (ttmt) cc_final: 0.8266 (ttmm) REVERT: E 152 VAL cc_start: 0.9105 (t) cc_final: 0.8723 (p) REVERT: E 155 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8159 (mp0) REVERT: E 169 ASP cc_start: 0.8599 (t0) cc_final: 0.8010 (t0) REVERT: F 57 LYS cc_start: 0.9139 (mmtt) cc_final: 0.8918 (mmmt) REVERT: F 116 ASN cc_start: 0.8686 (m-40) cc_final: 0.8351 (m110) REVERT: G 56 GLU cc_start: 0.8739 (pm20) cc_final: 0.8452 (pp20) REVERT: G 118 GLU cc_start: 0.8866 (pt0) cc_final: 0.8307 (pt0) REVERT: G 165 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8810 (tm-30) REVERT: G 169 ASP cc_start: 0.8339 (t70) cc_final: 0.7929 (t0) REVERT: H 94 MET cc_start: 0.8834 (tpp) cc_final: 0.8578 (tpp) REVERT: H 118 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8228 (mt-10) REVERT: H 162 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8426 (tp30) REVERT: H 165 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8334 (tt0) REVERT: I 94 MET cc_start: 0.8770 (tpp) cc_final: 0.8474 (tpp) REVERT: J 123 GLN cc_start: 0.8860 (pt0) cc_final: 0.8592 (pt0) REVERT: K 155 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7894 (mp0) REVERT: L 54 ASP cc_start: 0.8592 (m-30) cc_final: 0.8381 (m-30) REVERT: M 54 ASP cc_start: 0.8805 (m-30) cc_final: 0.8576 (m-30) REVERT: M 165 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8192 (tm-30) REVERT: N 25 LYS cc_start: 0.8884 (tppt) cc_final: 0.8655 (ttmt) REVERT: N 165 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8419 (tt0) outliers start: 57 outliers final: 47 residues processed: 513 average time/residue: 0.2742 time to fit residues: 223.8299 Evaluate side-chains 503 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 453 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 103 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 153 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 179 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.103197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.088110 restraints weight = 125921.060| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 4.89 r_work: 0.3058 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.7847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18860 Z= 0.128 Angle : 0.692 25.809 25328 Z= 0.353 Chirality : 0.090 1.724 2954 Planarity : 0.004 0.055 3290 Dihedral : 6.211 60.230 2648 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.00 % Favored : 90.87 % Rotamer: Outliers : 2.03 % Allowed : 23.83 % Favored : 74.14 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 1.22 % 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: -2.13 (0.17), residues: 2310 helix: -0.55 (0.16), residues: 1092 sheet: -2.67 (0.29), residues: 266 loop : -1.95 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 141 TYR 0.011 0.001 TYR C 77 PHE 0.015 0.001 PHE I 101 HIS 0.001 0.000 HIS F 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (18818) covalent geometry : angle 0.69161 / 0.35 (25328) hydrogen bonds : bond 0.03893 / 2.63 ( 431) hydrogen bonds : angle 4.87159 / 3.28 ( 1251) Misc. bond : bond 0.00192 / 0.10 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 516 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 477 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8602 (m-30) cc_final: 0.8031 (m-30) REVERT: A 163 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8510 (p) REVERT: A 165 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8373 (mt-10) REVERT: A 169 ASP cc_start: 0.8229 (t70) cc_final: 0.7983 (t70) REVERT: B 78 ASP cc_start: 0.8676 (m-30) cc_final: 0.8139 (m-30) REVERT: B 116 ASN cc_start: 0.8684 (m-40) cc_final: 0.8148 (m110) REVERT: B 165 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8478 (tm-30) REVERT: C 78 ASP cc_start: 0.8605 (m-30) cc_final: 0.8014 (m-30) REVERT: C 116 ASN cc_start: 0.8614 (m-40) cc_final: 0.8249 (m110) REVERT: C 118 GLU cc_start: 0.8681 (pt0) cc_final: 0.8200 (pt0) REVERT: C 141 ARG cc_start: 0.9219 (tpt90) cc_final: 0.8853 (tpt90) REVERT: C 165 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8812 (tm-30) REVERT: D 56 GLU cc_start: 0.8609 (pm20) cc_final: 0.8367 (pp20) REVERT: D 81 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8374 (tm-30) REVERT: D 116 ASN cc_start: 0.8671 (m-40) cc_final: 0.8280 (m-40) REVERT: D 118 GLU cc_start: 0.8524 (pt0) cc_final: 0.8258 (pt0) REVERT: D 165 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8439 (mt-10) REVERT: D 169 ASP cc_start: 0.8753 (t0) cc_final: 0.8278 (t0) REVERT: E 56 GLU cc_start: 0.8599 (pm20) cc_final: 0.8305 (pp20) REVERT: E 123 GLN cc_start: 0.8442 (pt0) cc_final: 0.8027 (pt0) REVERT: E 151 LYS cc_start: 0.8854 (ttmt) cc_final: 0.8283 (ttmm) REVERT: E 152 VAL cc_start: 0.9071 (t) cc_final: 0.8695 (p) REVERT: E 155 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8143 (mp0) REVERT: E 169 ASP cc_start: 0.8643 (t0) cc_final: 0.7843 (t0) REVERT: F 57 LYS cc_start: 0.9085 (mmtt) cc_final: 0.8868 (mmmt) REVERT: F 116 ASN cc_start: 0.8666 (m-40) cc_final: 0.8339 (m110) REVERT: G 56 GLU cc_start: 0.8758 (pm20) cc_final: 0.8460 (pp20) REVERT: G 118 GLU cc_start: 0.8840 (pt0) cc_final: 0.8156 (pt0) REVERT: G 169 ASP cc_start: 0.8313 (t70) cc_final: 0.7870 (t0) REVERT: H 94 MET cc_start: 0.8822 (tpp) cc_final: 0.8563 (tpp) REVERT: H 162 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8484 (tp30) REVERT: H 165 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8316 (tt0) REVERT: I 94 MET cc_start: 0.8734 (tpp) cc_final: 0.8438 (tpp) REVERT: K 143 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8896 (mp) REVERT: K 155 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7915 (mp0) REVERT: L 54 ASP cc_start: 0.8570 (m-30) cc_final: 0.8363 (m-30) REVERT: L 81 GLN cc_start: 0.9036 (mt0) cc_final: 0.8593 (mt0) REVERT: M 54 ASP cc_start: 0.8766 (m-30) cc_final: 0.8537 (m-30) REVERT: M 165 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8190 (tm-30) REVERT: N 25 LYS cc_start: 0.8895 (tppt) cc_final: 0.8682 (ttmt) REVERT: N 165 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8362 (tt0) outliers start: 39 outliers final: 36 residues processed: 506 average time/residue: 0.2736 time to fit residues: 218.7969 Evaluate side-chains 509 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 471 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 70 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 115 optimal weight: 0.0020 chunk 152 optimal weight: 8.9990 chunk 86 optimal weight: 0.8980 chunk 187 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 206 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 overall best weight: 1.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.104519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.089292 restraints weight = 125227.643| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 4.95 r_work: 0.3073 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.7950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18860 Z= 0.110 Angle : 0.682 26.023 25328 Z= 0.346 Chirality : 0.090 1.712 2954 Planarity : 0.003 0.040 3290 Dihedral : 5.883 54.184 2648 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.23 % Favored : 91.65 % Rotamer: Outliers : 1.51 % Allowed : 24.25 % Favored : 74.25 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 1.22 % 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: -1.77 (0.17), residues: 2310 helix: -0.23 (0.17), residues: 1092 sheet: -2.54 (0.29), residues: 266 loop : -1.78 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 146 TYR 0.011 0.001 TYR J 77 PHE 0.014 0.001 PHE L 101 HIS 0.001 0.000 HIS J 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (18818) covalent geometry : angle 0.68166 / 0.35 (25328) hydrogen bonds : bond 0.03455 / 2.33 ( 431) hydrogen bonds : angle 4.59095 / 3.09 ( 1251) Misc. bond : bond 0.00186 / 0.10 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 533 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 504 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8562 (m-30) cc_final: 0.8013 (m-30) REVERT: A 165 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8345 (mt-10) REVERT: A 169 ASP cc_start: 0.8204 (t70) cc_final: 0.7913 (t70) REVERT: B 78 ASP cc_start: 0.8659 (m-30) cc_final: 0.8170 (m-30) REVERT: B 116 ASN cc_start: 0.8657 (m-40) cc_final: 0.8168 (m110) REVERT: B 165 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8477 (tm-30) REVERT: C 78 ASP cc_start: 0.8511 (m-30) cc_final: 0.8043 (m-30) REVERT: C 116 ASN cc_start: 0.8603 (m-40) cc_final: 0.8384 (m110) REVERT: C 165 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8806 (tm-30) REVERT: D 56 GLU cc_start: 0.8610 (pm20) cc_final: 0.8376 (pp20) REVERT: D 81 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8355 (tm-30) REVERT: D 116 ASN cc_start: 0.8645 (m-40) cc_final: 0.8229 (m-40) REVERT: D 118 GLU cc_start: 0.8539 (pt0) cc_final: 0.8258 (pt0) REVERT: D 165 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8450 (mt-10) REVERT: D 169 ASP cc_start: 0.8768 (t0) cc_final: 0.8045 (t0) REVERT: E 56 GLU cc_start: 0.8642 (pm20) cc_final: 0.8351 (pp20) REVERT: E 123 GLN cc_start: 0.8464 (pt0) cc_final: 0.8045 (pt0) REVERT: E 151 LYS cc_start: 0.8840 (ttmt) cc_final: 0.8261 (ttmm) REVERT: E 152 VAL cc_start: 0.9013 (t) cc_final: 0.8651 (p) REVERT: E 155 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8095 (mp0) REVERT: E 169 ASP cc_start: 0.8601 (t0) cc_final: 0.7863 (t0) REVERT: E 177 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8720 (mm-30) REVERT: F 57 LYS cc_start: 0.9078 (mmtt) cc_final: 0.8854 (mmmt) REVERT: F 116 ASN cc_start: 0.8598 (m-40) cc_final: 0.8254 (m110) REVERT: F 155 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8240 (mp0) REVERT: G 56 GLU cc_start: 0.8781 (pm20) cc_final: 0.8482 (pp20) REVERT: G 118 GLU cc_start: 0.8734 (pt0) cc_final: 0.8141 (pt0) REVERT: G 169 ASP cc_start: 0.8339 (t70) cc_final: 0.7877 (t0) REVERT: H 94 MET cc_start: 0.8812 (tpp) cc_final: 0.8523 (tpp) REVERT: I 94 MET cc_start: 0.8768 (tpp) cc_final: 0.8458 (tpp) REVERT: I 177 GLU cc_start: 0.9231 (tm-30) cc_final: 0.8978 (tm-30) REVERT: K 155 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7824 (mp0) REVERT: L 54 ASP cc_start: 0.8532 (m-30) cc_final: 0.8321 (m-30) REVERT: L 81 GLN cc_start: 0.9044 (mt0) cc_final: 0.8590 (mt0) REVERT: L 151 LYS cc_start: 0.8907 (tppt) cc_final: 0.8704 (tppt) REVERT: M 54 ASP cc_start: 0.8729 (m-30) cc_final: 0.8496 (m-30) REVERT: M 165 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8207 (tm-30) REVERT: N 25 LYS cc_start: 0.8870 (tppt) cc_final: 0.8654 (ttmt) REVERT: N 165 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8399 (tt0) outliers start: 29 outliers final: 28 residues processed: 524 average time/residue: 0.2666 time to fit residues: 219.7523 Evaluate side-chains 513 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 485 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 70 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 195 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 173 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.104256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.089053 restraints weight = 124447.681| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 4.91 r_work: 0.3077 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.8042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18860 Z= 0.116 Angle : 0.680 26.118 25328 Z= 0.347 Chirality : 0.089 1.695 2954 Planarity : 0.004 0.059 3290 Dihedral : 5.882 56.781 2648 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.53 % Favored : 91.43 % Rotamer: Outliers : 1.46 % Allowed : 24.56 % Favored : 73.99 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 1.22 % 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: -1.47 (0.18), residues: 2310 helix: -0.02 (0.17), residues: 1078 sheet: -2.45 (0.29), residues: 266 loop : -1.53 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 141 TYR 0.017 0.001 TYR J 77 PHE 0.013 0.001 PHE I 101 HIS 0.002 0.000 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (18818) covalent geometry : angle 0.68019 / 0.35 (25328) hydrogen bonds : bond 0.03464 / 2.34 ( 431) hydrogen bonds : angle 4.57455 / 3.08 ( 1251) Misc. bond : bond 0.00185 / 0.10 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7553.40 seconds wall clock time: 128 minutes 47.40 seconds (7727.40 seconds total)