Starting phenix.real_space_refine on Sat Mar 7 00:41:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fer_31561/03_2026/7fer_31561.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fer_31561/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7fer_31561/03_2026/7fer_31561.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fer_31561/03_2026/7fer_31561.map" model { file = "/net/cci-nas-00/data/ceres_data/7fer_31561/03_2026/7fer_31561.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fer_31561/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.65, per 1000 atoms: 0.18 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: 3.19 Conformation dependent library (CDL) restraints added in 972.6 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: 0.85 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: 7.45 Time building geometry restraints manager: 4.37 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: 0.510 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: 0.220 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 31.860 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 covalent geometry : bond 0.01509 (18818) covalent geometry : angle 1.25216 (25328) hydrogen bonds : bond 0.29697 ( 431) hydrogen bonds : angle 8.09425 ( 1251) Misc. bond : bond 0.43166 ( 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 : 0.884 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: A 18 ASP cc_start: 0.8570 (t0) cc_final: 0.8294 (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: 0.7688 (pt0) REVERT: A 136 GLU cc_start: 0.6561 (pm20) cc_final: 0.6174 (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: 0.7517 (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: 0.8244 (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: 0.8158 (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: 0.7601 (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: 0.7887 (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: 0.8043 (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: 0.8885 (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: 0.8057 (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: 0.7898 (tpt170) REVERT: H 151 LYS cc_start: 0.8963 (tptp) cc_final: 0.8549 (ttpt) REVERT: H 178 GLU cc_start: 0.8544 (pt0) cc_final: 0.8269 (pt0) REVERT: I 81 GLN cc_start: 0.8933 (mt0) cc_final: 0.8654 (mt0) REVERT: I 129 GLN cc_start: 0.7790 (pm20) cc_final: 0.7580 (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: 0.7807 (m-30) REVERT: I 178 GLU cc_start: 0.8473 (pt0) cc_final: 0.8164 (pt0) REVERT: J 141 ARG cc_start: 0.8401 (tpt90) cc_final: 0.7942 (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: 0.7459 (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: M 57 LYS cc_start: 0.7758 (mmmm) cc_final: 0.7512 (mmmt) REVERT: M 81 GLN cc_start: 0.8803 (mt0) cc_final: 0.8495 (mt0) REVERT: M 97 SER cc_start: 0.8725 (p) cc_final: 0.8387 (t) REVERT: M 118 GLU cc_start: 0.8307 (pt0) cc_final: 0.7664 (pt0) REVERT: M 141 ARG cc_start: 0.8501 (tpt90) cc_final: 0.7885 (tpt170) REVERT: M 165 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8187 (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: 0.8306 (t) REVERT: N 165 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8132 (pt0) REVERT: N 167 ASP cc_start: 0.8390 (m-30) cc_final: 0.8105 (m-30) outliers start: 39 outliers final: 25 residues processed: 1076 average time/residue: 0.3631 time to fit residues: 556.6833 Evaluate side-chains 677 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 652 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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: 0.7980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.8980 chunk 212 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.111002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.095616 restraints weight = 120337.677| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 4.69 r_work: 0.3183 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 18860 Z= 0.146 Angle : 0.786 26.015 25328 Z= 0.400 Chirality : 0.085 1.597 2954 Planarity : 0.004 0.074 3290 Dihedral : 8.361 74.334 2696 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.31 % Favored : 91.43 % Rotamer: Outliers : 2.39 % Allowed : 15.92 % Favored : 81.69 % 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: -4.05 (0.16), residues: 2310 helix: -3.04 (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 0.007 0.000 ARG D 141 TYR 0.013 0.001 TYR D 77 PHE 0.020 0.001 PHE T 2 HIS 0.002 0.001 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00313 (18818) covalent geometry : angle 0.78623 (25328) hydrogen bonds : bond 0.07165 ( 431) hydrogen bonds : angle 5.39475 ( 1251) Misc. bond : bond 0.00286 ( 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 749 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 703 time to evaluate : 0.953 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: A 78 ASP cc_start: 0.8669 (m-30) cc_final: 0.7840 (m-30) REVERT: A 98 MET cc_start: 0.9309 (tpp) cc_final: 0.8893 (tpp) REVERT: A 116 ASN cc_start: 0.8875 (m-40) cc_final: 0.8616 (m110) REVERT: A 157 THR cc_start: 0.9313 (p) cc_final: 0.9005 (t) REVERT: A 164 ILE cc_start: 0.8664 (mm) cc_final: 0.8446 (mt) REVERT: B 23 LEU cc_start: 0.9052 (mt) cc_final: 0.8851 (mt) REVERT: B 78 ASP cc_start: 0.8595 (m-30) cc_final: 0.7785 (m-30) REVERT: B 116 ASN cc_start: 0.8819 (m-40) cc_final: 0.8484 (m110) REVERT: B 150 ASN cc_start: 0.8476 (p0) cc_final: 0.8088 (m-40) REVERT: B 152 VAL cc_start: 0.8790 (t) cc_final: 0.8572 (p) REVERT: B 165 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8256 (tm-30) REVERT: B 175 SER cc_start: 0.9116 (p) cc_final: 0.8305 (t) REVERT: C 78 ASP cc_start: 0.8537 (m-30) cc_final: 0.7953 (m-30) REVERT: C 98 MET cc_start: 0.9261 (tpp) cc_final: 0.8960 (tpp) REVERT: C 116 ASN cc_start: 0.8707 (m-40) cc_final: 0.8377 (m110) REVERT: C 123 GLN cc_start: 0.8405 (pt0) cc_final: 0.8042 (pt0) REVERT: C 165 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8541 (tm-30) REVERT: D 56 GLU cc_start: 0.8614 (pm20) cc_final: 0.8227 (pp20) REVERT: D 116 ASN cc_start: 0.8784 (m-40) cc_final: 0.8341 (m110) REVERT: D 123 GLN cc_start: 0.8704 (pt0) cc_final: 0.8219 (pt0) REVERT: D 165 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8464 (mt-10) REVERT: D 169 ASP cc_start: 0.8291 (t0) cc_final: 0.7974 (t0) REVERT: D 185 ILE cc_start: 0.8885 (pt) cc_final: 0.8652 (mm) REVERT: E 56 GLU cc_start: 0.8526 (pm20) cc_final: 0.8031 (pp20) REVERT: E 123 GLN cc_start: 0.8486 (pt0) cc_final: 0.8023 (pt0) REVERT: E 155 GLU cc_start: 0.8290 (mm-30) cc_final: 0.8075 (mp0) REVERT: E 165 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8407 (mt-10) REVERT: E 169 ASP cc_start: 0.8367 (t0) cc_final: 0.8071 (t0) REVERT: F 48 LEU cc_start: 0.9525 (mt) cc_final: 0.9176 (tp) REVERT: F 57 LYS cc_start: 0.9088 (mmtt) cc_final: 0.8836 (mmmt) REVERT: F 123 GLN cc_start: 0.8643 (pt0) cc_final: 0.8386 (pt0) REVERT: F 165 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8275 (tm-30) REVERT: G 48 LEU cc_start: 0.9549 (mt) cc_final: 0.9295 (tp) REVERT: G 56 GLU cc_start: 0.8523 (pm20) cc_final: 0.8270 (pp20) REVERT: G 78 ASP cc_start: 0.8853 (m-30) cc_final: 0.8141 (m-30) REVERT: G 152 VAL cc_start: 0.9123 (t) cc_final: 0.8853 (p) REVERT: G 165 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8363 (tm-30) REVERT: G 170 ARG cc_start: 0.7750 (ptm-80) cc_final: 0.7473 (ptm160) REVERT: H 57 LYS cc_start: 0.7645 (mmmm) cc_final: 0.7342 (mmmt) REVERT: H 107 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7505 (mm-30) REVERT: H 159 GLN cc_start: 0.8519 (mm-40) cc_final: 0.7987 (mp10) REVERT: H 165 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8397 (pt0) REVERT: H 178 GLU cc_start: 0.8680 (pt0) cc_final: 0.8466 (pt0) REVERT: I 81 GLN cc_start: 0.9102 (mt0) cc_final: 0.8902 (mt0) REVERT: I 107 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7407 (mm-30) REVERT: I 118 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8233 (mt-10) REVERT: I 129 GLN cc_start: 0.8074 (pm20) cc_final: 0.7586 (pm20) REVERT: I 165 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8297 (tt0) REVERT: I 167 ASP cc_start: 0.8192 (m-30) cc_final: 0.7853 (m-30) REVERT: J 107 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7257 (mm-30) REVERT: J 123 GLN cc_start: 0.8905 (pt0) cc_final: 0.8672 (pt0) REVERT: J 159 GLN cc_start: 0.8545 (mm-40) cc_final: 0.7592 (mp10) REVERT: J 185 ILE cc_start: 0.9335 (pt) cc_final: 0.8996 (tt) REVERT: J 188 ILE cc_start: 0.8948 (tt) cc_final: 0.8740 (mt) REVERT: K 81 GLN cc_start: 0.9036 (mt0) cc_final: 0.8542 (mt0) REVERT: K 165 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8551 (tt0) REVERT: L 81 GLN cc_start: 0.8995 (mt0) cc_final: 0.8745 (mt0) REVERT: M 118 GLU cc_start: 0.8598 (pt0) cc_final: 0.7711 (pt0) REVERT: M 165 GLU cc_start: 0.8607 (mt-10) cc_final: 0.7961 (tm-30) REVERT: N 148 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8261 (tmtt) outliers start: 46 outliers final: 34 residues processed: 720 average time/residue: 0.2857 time to fit residues: 319.7248 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: 10.0000 chunk 42 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 137 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 188 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.105969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.090796 restraints weight = 123476.031| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 4.68 r_work: 0.3108 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.5729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 18860 Z= 0.175 Angle : 0.773 30.231 25328 Z= 0.390 Chirality : 0.089 1.709 2954 Planarity : 0.004 0.032 3290 Dihedral : 7.730 82.078 2659 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.05 % Favored : 90.74 % Rotamer: Outliers : 2.50 % Allowed : 19.15 % Favored : 78.36 % 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: -3.56 (0.16), residues: 2310 helix: -2.57 (0.14), residues: 980 sheet: -2.97 (0.28), residues: 238 loop : -1.86 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 141 TYR 0.014 0.001 TYR E 182 PHE 0.017 0.001 PHE W 2 HIS 0.001 0.000 HIS M 122 Details of bonding type rmsd covalent geometry : bond 0.00370 (18818) covalent geometry : angle 0.77321 (25328) hydrogen bonds : bond 0.05461 ( 431) hydrogen bonds : angle 5.28163 ( 1251) Misc. bond : bond 0.00285 ( 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 658 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 610 time to evaluate : 1.013 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: A 78 ASP cc_start: 0.8528 (m-30) cc_final: 0.7960 (m-30) REVERT: A 116 ASN cc_start: 0.8853 (m-40) cc_final: 0.8616 (m110) REVERT: A 157 THR cc_start: 0.9248 (p) cc_final: 0.8967 (t) REVERT: B 78 ASP cc_start: 0.8580 (m-30) cc_final: 0.8136 (m-30) REVERT: B 116 ASN cc_start: 0.8754 (m-40) cc_final: 0.8432 (m110) REVERT: B 152 VAL cc_start: 0.8919 (t) cc_final: 0.8684 (p) REVERT: B 165 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8397 (tm-30) REVERT: B 173 PHE cc_start: 0.8564 (m-80) cc_final: 0.8224 (m-80) REVERT: C 78 ASP cc_start: 0.8438 (m-30) cc_final: 0.7864 (m-30) REVERT: C 98 MET cc_start: 0.9348 (tpp) cc_final: 0.9059 (tpp) REVERT: C 116 ASN cc_start: 0.8724 (m-40) cc_final: 0.8515 (m110) REVERT: C 123 GLN cc_start: 0.8558 (pt0) cc_final: 0.8316 (pt0) REVERT: C 165 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8609 (tm-30) REVERT: C 170 ARG cc_start: 0.7773 (ptm-80) cc_final: 0.7422 (ptm160) REVERT: C 178 GLU cc_start: 0.8703 (mp0) cc_final: 0.8493 (mp0) REVERT: D 56 GLU cc_start: 0.8622 (pm20) cc_final: 0.8250 (pp20) REVERT: D 116 ASN cc_start: 0.8772 (m-40) cc_final: 0.8396 (m110) REVERT: D 123 GLN cc_start: 0.8636 (pt0) cc_final: 0.8051 (pt0) REVERT: D 165 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8465 (mt-10) REVERT: D 169 ASP cc_start: 0.8327 (t0) cc_final: 0.7920 (t0) REVERT: E 56 GLU cc_start: 0.8554 (pm20) cc_final: 0.8121 (pp20) REVERT: E 123 GLN cc_start: 0.8575 (pt0) cc_final: 0.8152 (pt0) REVERT: E 155 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8065 (mp0) REVERT: E 165 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8533 (mt-10) REVERT: E 169 ASP cc_start: 0.8466 (t0) cc_final: 0.8217 (t70) REVERT: F 48 LEU cc_start: 0.9600 (mt) cc_final: 0.9350 (tp) REVERT: F 57 LYS cc_start: 0.9118 (mmtt) cc_final: 0.8834 (mmmt) REVERT: F 116 ASN cc_start: 0.8742 (m-40) cc_final: 0.8387 (m110) REVERT: F 123 GLN cc_start: 0.8533 (pt0) cc_final: 0.8255 (pt0) REVERT: F 152 VAL cc_start: 0.8996 (p) cc_final: 0.8764 (p) REVERT: G 48 LEU cc_start: 0.9574 (mt) cc_final: 0.9281 (tp) REVERT: G 56 GLU cc_start: 0.8483 (pm20) cc_final: 0.8260 (pp20) REVERT: G 78 ASP cc_start: 0.8569 (m-30) cc_final: 0.7978 (m-30) REVERT: G 152 VAL cc_start: 0.9128 (t) cc_final: 0.8892 (p) REVERT: G 165 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8418 (tm-30) REVERT: G 170 ARG cc_start: 0.7792 (ptm-80) cc_final: 0.7491 (ptm160) REVERT: H 159 GLN cc_start: 0.8539 (mm-40) cc_final: 0.7883 (mp10) REVERT: I 81 GLN cc_start: 0.9097 (mt0) cc_final: 0.8726 (mt0) REVERT: I 118 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8399 (mt-10) REVERT: I 129 GLN cc_start: 0.8122 (pm20) cc_final: 0.7789 (pm20) REVERT: I 165 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8309 (tt0) REVERT: I 167 ASP cc_start: 0.8315 (m-30) cc_final: 0.8019 (m-30) REVERT: J 159 GLN cc_start: 0.8641 (mm-40) cc_final: 0.7676 (mp10) REVERT: K 81 GLN cc_start: 0.9023 (mt0) cc_final: 0.8588 (mt0) REVERT: K 165 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8592 (tt0) REVERT: L 81 GLN cc_start: 0.8984 (mt0) cc_final: 0.8553 (mt0) REVERT: L 148 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8531 (tmtt) REVERT: L 165 GLU cc_start: 0.8604 (pt0) cc_final: 0.8332 (pt0) REVERT: M 165 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8089 (tm-30) REVERT: N 148 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8421 (tmtt) outliers start: 48 outliers final: 36 residues processed: 630 average time/residue: 0.2747 time to fit residues: 272.8236 Evaluate side-chains 592 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 554 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 26 ASP 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 79 THR 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 D residue 185 ILE 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 F residue 26 ASP Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain H residue 26 ASP 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 185 ILE Chi-restraints excluded: chain J residue 23 LEU 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 97 SER Chi-restraints excluded: chain L residue 148 LYS 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 N residue 26 ASP 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: 1.9990 chunk 128 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 213 optimal weight: 0.0980 chunk 148 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 204 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.104856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.089263 restraints weight = 123945.882| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 4.79 r_work: 0.3085 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.6322 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= 0.146 Angle : 0.737 32.259 25328 Z= 0.367 Chirality : 0.089 1.728 2954 Planarity : 0.004 0.031 3290 Dihedral : 6.968 83.725 2648 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.74 % Favored : 91.04 % Rotamer: Outliers : 3.23 % Allowed : 19.20 % 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: -3.45 (0.16), residues: 2310 helix: -2.09 (0.14), residues: 1078 sheet: -2.75 (0.28), residues: 238 loop : -2.23 (0.18), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 146 TYR 0.007 0.001 TYR J 77 PHE 0.012 0.001 PHE I 101 HIS 0.001 0.000 HIS N 122 Details of bonding type rmsd covalent geometry : bond 0.00314 (18818) covalent geometry : angle 0.73719 (25328) hydrogen bonds : bond 0.04626 ( 431) hydrogen bonds : angle 5.05346 ( 1251) Misc. bond : bond 0.00214 ( 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 623 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 561 time to evaluate : 0.791 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: 0.8512 (m-30) cc_final: 0.7841 (m-30) REVERT: A 116 ASN cc_start: 0.8827 (m-40) cc_final: 0.8582 (m110) REVERT: B 78 ASP cc_start: 0.8669 (m-30) cc_final: 0.8281 (m-30) REVERT: B 116 ASN cc_start: 0.8750 (m-40) cc_final: 0.8361 (m110) REVERT: B 152 VAL cc_start: 0.8938 (t) cc_final: 0.8731 (p) REVERT: B 165 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8444 (tm-30) REVERT: C 78 ASP cc_start: 0.8548 (m-30) cc_final: 0.8016 (m-30) REVERT: C 116 ASN cc_start: 0.8730 (m-40) cc_final: 0.8437 (m110) REVERT: C 165 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8686 (tm-30) REVERT: C 170 ARG cc_start: 0.7699 (ptm-80) cc_final: 0.7306 (ptm160) REVERT: C 178 GLU cc_start: 0.8776 (mp0) cc_final: 0.8507 (mp0) REVERT: D 48 LEU cc_start: 0.9603 (mt) cc_final: 0.9284 (tp) REVERT: D 56 GLU cc_start: 0.8622 (pm20) cc_final: 0.8256 (pp20) REVERT: D 116 ASN cc_start: 0.8815 (m-40) cc_final: 0.8453 (m-40) REVERT: D 123 GLN cc_start: 0.8600 (pt0) cc_final: 0.8393 (pt0) REVERT: D 141 ARG cc_start: 0.9013 (tpp80) cc_final: 0.8761 (tpp80) REVERT: D 165 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8330 (mt-10) REVERT: D 169 ASP cc_start: 0.8506 (t0) cc_final: 0.8123 (t0) REVERT: E 56 GLU cc_start: 0.8560 (pm20) cc_final: 0.8138 (pp20) REVERT: E 123 GLN cc_start: 0.8615 (pt0) cc_final: 0.8148 (pt0) REVERT: E 151 LYS cc_start: 0.8933 (ttmt) cc_final: 0.8660 (ttmm) REVERT: F 48 LEU cc_start: 0.9639 (mt) cc_final: 0.9352 (tp) REVERT: F 57 LYS cc_start: 0.9099 (mmtt) cc_final: 0.8843 (mmmt) REVERT: F 116 ASN cc_start: 0.8768 (m-40) cc_final: 0.8444 (m110) REVERT: F 123 GLN cc_start: 0.8581 (pt0) cc_final: 0.8338 (pt0) REVERT: G 48 LEU cc_start: 0.9587 (mt) cc_final: 0.9285 (tp) REVERT: G 56 GLU cc_start: 0.8558 (pm20) cc_final: 0.8316 (pp20) REVERT: G 78 ASP cc_start: 0.8638 (m-30) cc_final: 0.8055 (m-30) REVERT: G 141 ARG cc_start: 0.9337 (tpt90) cc_final: 0.9129 (tpt90) REVERT: G 165 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8553 (tm-30) REVERT: G 170 ARG cc_start: 0.7783 (ptm-80) cc_final: 0.7285 (ptm160) REVERT: H 159 GLN cc_start: 0.8545 (mm-40) cc_final: 0.7905 (mp10) REVERT: I 81 GLN cc_start: 0.9070 (mt0) cc_final: 0.8797 (mt0) REVERT: I 129 GLN cc_start: 0.8204 (pm20) cc_final: 0.7894 (pm20) REVERT: J 159 GLN cc_start: 0.8632 (mm-40) cc_final: 0.7655 (mp10) REVERT: K 165 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8533 (tt0) REVERT: L 56 GLU cc_start: 0.7377 (pm20) cc_final: 0.7147 (pm20) REVERT: L 61 LEU cc_start: 0.9412 (tt) cc_final: 0.9184 (tt) REVERT: L 81 GLN cc_start: 0.8998 (mt0) cc_final: 0.8608 (mt0) REVERT: L 177 GLU cc_start: 0.9186 (tm-30) cc_final: 0.8984 (tm-30) REVERT: M 165 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8151 (tm-30) REVERT: N 165 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8260 (pt0) outliers start: 62 outliers final: 50 residues processed: 598 average time/residue: 0.2680 time to fit residues: 255.6934 Evaluate side-chains 587 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 537 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP 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 65 SER Chi-restraints excluded: chain B residue 102 LEU 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 79 THR 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 33 SER Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 178 GLU 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 65 SER Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 185 ILE 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 79 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain J residue 41 ASN Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain K residue 33 SER 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 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 26 ASP Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 103 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 9 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 186 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 173 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 38 ASN K 81 GLN L 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.101370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.085955 restraints weight = 126488.287| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 4.83 r_work: 0.3029 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.7133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18860 Z= 0.236 Angle : 0.811 34.599 25328 Z= 0.411 Chirality : 0.091 1.774 2954 Planarity : 0.004 0.037 3290 Dihedral : 7.432 87.514 2648 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.39 % Favored : 89.39 % Rotamer: Outliers : 3.69 % Allowed : 21.07 % Favored : 75.23 % 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: -3.29 (0.16), residues: 2310 helix: -1.89 (0.14), residues: 1120 sheet: -2.68 (0.28), residues: 238 loop : -2.22 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 146 TYR 0.012 0.001 TYR D 77 PHE 0.014 0.002 PHE I 101 HIS 0.003 0.001 HIS I 122 Details of bonding type rmsd covalent geometry : bond 0.00507 (18818) covalent geometry : angle 0.81088 (25328) hydrogen bonds : bond 0.05641 ( 431) hydrogen bonds : angle 5.58986 ( 1251) Misc. bond : bond 0.00228 ( 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 577 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 506 time to evaluate : 0.678 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: A 78 ASP cc_start: 0.8449 (m-30) cc_final: 0.7970 (m-30) REVERT: A 116 ASN cc_start: 0.8725 (m-40) cc_final: 0.8491 (m110) REVERT: A 118 GLU cc_start: 0.8643 (pt0) cc_final: 0.8165 (pt0) REVERT: B 78 ASP cc_start: 0.8681 (m-30) cc_final: 0.8332 (m-30) REVERT: B 116 ASN cc_start: 0.8679 (m-40) cc_final: 0.8291 (m110) REVERT: B 165 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8560 (tm-30) REVERT: C 78 ASP cc_start: 0.8551 (m-30) cc_final: 0.8071 (m-30) REVERT: C 116 ASN cc_start: 0.8695 (m-40) cc_final: 0.8416 (m110) REVERT: C 163 VAL cc_start: 0.8637 (m) cc_final: 0.8391 (p) REVERT: C 165 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8778 (tm-30) REVERT: C 178 GLU cc_start: 0.8879 (mp0) cc_final: 0.8564 (mp0) REVERT: D 56 GLU cc_start: 0.8744 (pm20) cc_final: 0.8431 (pp20) REVERT: D 116 ASN cc_start: 0.8776 (m-40) cc_final: 0.8516 (m-40) REVERT: D 123 GLN cc_start: 0.8608 (pt0) cc_final: 0.8199 (pt0) REVERT: D 169 ASP cc_start: 0.8640 (t0) cc_final: 0.8222 (t0) REVERT: E 56 GLU cc_start: 0.8557 (pm20) cc_final: 0.8230 (pp20) REVERT: E 123 GLN cc_start: 0.8563 (pt0) cc_final: 0.8140 (pt0) REVERT: E 151 LYS cc_start: 0.8878 (ttmt) cc_final: 0.8285 (ttmm) REVERT: E 155 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8091 (mp0) REVERT: E 165 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8470 (mt-10) REVERT: E 177 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8654 (mm-30) REVERT: F 57 LYS cc_start: 0.9129 (mmtt) cc_final: 0.8900 (mmmt) REVERT: G 56 GLU cc_start: 0.8657 (pm20) cc_final: 0.8411 (pp20) REVERT: G 78 ASP cc_start: 0.8563 (m-30) cc_final: 0.8051 (m-30) REVERT: G 118 GLU cc_start: 0.8752 (pt0) cc_final: 0.8230 (pt0) REVERT: G 165 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8630 (tm-30) REVERT: G 169 ASP cc_start: 0.8424 (t70) cc_final: 0.7979 (t0) REVERT: H 165 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8524 (pt0) REVERT: I 81 GLN cc_start: 0.9083 (mt0) cc_final: 0.8737 (mt0) REVERT: I 129 GLN cc_start: 0.8222 (pm20) cc_final: 0.8018 (pm20) REVERT: K 150 ASN cc_start: 0.9546 (m-40) cc_final: 0.9338 (m110) REVERT: K 165 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8542 (tt0) REVERT: L 56 GLU cc_start: 0.7626 (pm20) cc_final: 0.7381 (pm20) REVERT: M 120 MET cc_start: 0.9006 (ppp) cc_final: 0.8781 (ppp) REVERT: M 165 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8236 (tm-30) REVERT: N 25 LYS cc_start: 0.8907 (tppt) cc_final: 0.8586 (tttt) REVERT: N 165 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8353 (tt0) outliers start: 71 outliers final: 54 residues processed: 553 average time/residue: 0.2666 time to fit residues: 233.1697 Evaluate side-chains 526 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 471 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 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 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 129 GLN Chi-restraints excluded: chain E residue 177 GLU 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 65 SER Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 165 GLU 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 185 ILE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 185 ILE 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 L residue 155 GLU Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 185 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 103 LEU 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: 8.9990 chunk 148 optimal weight: 4.9990 chunk 186 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 212 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 179 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 221 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.101405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.086078 restraints weight = 127277.091| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 4.86 r_work: 0.3034 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.7303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18860 Z= 0.193 Angle : 0.730 25.922 25328 Z= 0.377 Chirality : 0.090 1.739 2954 Planarity : 0.004 0.038 3290 Dihedral : 7.098 75.954 2648 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.13 % Favored : 89.70 % Rotamer: Outliers : 3.23 % Allowed : 21.85 % Favored : 74.92 % 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: -3.15 (0.16), residues: 2310 helix: -1.71 (0.14), residues: 1120 sheet: -2.66 (0.28), residues: 238 loop : -2.24 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 141 TYR 0.007 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 covalent geometry : bond 0.00411 (18818) covalent geometry : angle 0.73021 (25328) hydrogen bonds : bond 0.04851 ( 431) hydrogen bonds : angle 5.43185 ( 1251) Misc. bond : bond 0.00207 ( 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 545 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 483 time to evaluate : 1.113 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: A 78 ASP cc_start: 0.8497 (m-30) cc_final: 0.7958 (m-30) REVERT: A 116 ASN cc_start: 0.8731 (m-40) cc_final: 0.8491 (m110) REVERT: A 118 GLU cc_start: 0.8687 (pt0) cc_final: 0.8442 (pt0) REVERT: A 163 VAL cc_start: 0.8549 (OUTLIER) cc_final: 0.8344 (p) REVERT: A 169 ASP cc_start: 0.7999 (t70) cc_final: 0.7464 (t0) REVERT: B 78 ASP cc_start: 0.8740 (m-30) cc_final: 0.8402 (m-30) REVERT: B 116 ASN cc_start: 0.8645 (m-40) cc_final: 0.8243 (m110) REVERT: C 78 ASP cc_start: 0.8575 (m-30) cc_final: 0.8049 (m-30) REVERT: C 163 VAL cc_start: 0.8636 (m) cc_final: 0.8421 (p) REVERT: C 165 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8734 (tm-30) REVERT: C 177 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8717 (mm-30) REVERT: C 178 GLU cc_start: 0.8884 (mp0) cc_final: 0.8548 (mp0) REVERT: D 56 GLU cc_start: 0.8663 (pm20) cc_final: 0.8400 (pp20) REVERT: D 116 ASN cc_start: 0.8777 (m-40) cc_final: 0.8428 (m-40) REVERT: D 123 GLN cc_start: 0.8601 (pt0) cc_final: 0.8202 (pt0) REVERT: D 163 VAL cc_start: 0.8774 (m) cc_final: 0.8558 (p) REVERT: D 169 ASP cc_start: 0.8637 (t0) cc_final: 0.8231 (t0) REVERT: E 56 GLU cc_start: 0.8589 (pm20) cc_final: 0.8261 (pp20) REVERT: E 123 GLN cc_start: 0.8538 (pt0) cc_final: 0.8123 (pt0) REVERT: E 151 LYS cc_start: 0.8851 (ttmt) cc_final: 0.8253 (ttmm) REVERT: E 152 VAL cc_start: 0.9186 (t) cc_final: 0.8783 (p) REVERT: E 155 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8140 (mp0) REVERT: E 163 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8434 (p) REVERT: E 165 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8441 (mt-10) REVERT: E 177 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8666 (mm-30) REVERT: F 57 LYS cc_start: 0.9152 (mmtt) cc_final: 0.8922 (mmmt) REVERT: F 163 VAL cc_start: 0.8561 (OUTLIER) cc_final: 0.8332 (p) REVERT: G 56 GLU cc_start: 0.8678 (pm20) cc_final: 0.8424 (pp20) REVERT: G 78 ASP cc_start: 0.8553 (m-30) cc_final: 0.8007 (m-30) REVERT: G 118 GLU cc_start: 0.8838 (pt0) cc_final: 0.8290 (pt0) REVERT: G 163 VAL cc_start: 0.8653 (m) cc_final: 0.8417 (p) REVERT: G 165 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8658 (tm-30) REVERT: G 169 ASP cc_start: 0.8394 (t70) cc_final: 0.7953 (t0) REVERT: H 165 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8507 (pt0) REVERT: K 165 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8538 (tt0) REVERT: L 56 GLU cc_start: 0.7804 (pm20) cc_final: 0.7427 (pm20) REVERT: M 56 GLU cc_start: 0.7723 (pm20) cc_final: 0.7510 (mp0) REVERT: M 165 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8218 (tm-30) REVERT: N 25 LYS cc_start: 0.8845 (tppt) cc_final: 0.8550 (tttt) REVERT: N 165 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8368 (tt0) outliers start: 62 outliers final: 45 residues processed: 529 average time/residue: 0.2653 time to fit residues: 222.8099 Evaluate side-chains 522 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 472 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 79 THR 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 177 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 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 G residue 170 ARG Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 103 LEU 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 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: 8.9990 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 126 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 122 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.104017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.088632 restraints weight = 124031.481| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 4.87 r_work: 0.3074 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.7486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 18860 Z= 0.109 Angle : 0.683 25.674 25328 Z= 0.347 Chirality : 0.089 1.717 2954 Planarity : 0.004 0.035 3290 Dihedral : 6.329 84.015 2648 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.75 % Favored : 92.08 % Rotamer: Outliers : 2.08 % Allowed : 22.42 % Favored : 75.49 % 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: -2.56 (0.16), residues: 2310 helix: -1.13 (0.15), residues: 1120 sheet: -2.36 (0.29), residues: 238 loop : -2.08 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 141 TYR 0.008 0.001 TYR C 77 PHE 0.013 0.001 PHE I 101 HIS 0.001 0.000 HIS F 122 Details of bonding type rmsd covalent geometry : bond 0.00248 (18818) covalent geometry : angle 0.68346 (25328) hydrogen bonds : bond 0.03722 ( 431) hydrogen bonds : angle 4.77589 ( 1251) Misc. bond : bond 0.00191 ( 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 559 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 519 time to evaluate : 0.980 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: A 78 ASP cc_start: 0.8483 (m-30) cc_final: 0.7930 (m-30) REVERT: A 116 ASN cc_start: 0.8689 (m-40) cc_final: 0.8391 (m110) REVERT: A 163 VAL cc_start: 0.8566 (OUTLIER) cc_final: 0.8323 (p) REVERT: A 169 ASP cc_start: 0.7916 (t70) cc_final: 0.7611 (t70) REVERT: B 116 ASN cc_start: 0.8651 (m-40) cc_final: 0.8375 (m110) REVERT: B 123 GLN cc_start: 0.8500 (pt0) cc_final: 0.8278 (pt0) REVERT: B 165 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8438 (tm-30) REVERT: C 78 ASP cc_start: 0.8568 (m-30) cc_final: 0.8128 (m-30) REVERT: C 81 GLN cc_start: 0.8581 (tm-30) cc_final: 0.8355 (tm-30) REVERT: C 165 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8737 (tm-30) REVERT: C 169 ASP cc_start: 0.7743 (t0) cc_final: 0.7420 (t0) REVERT: C 178 GLU cc_start: 0.8859 (mp0) cc_final: 0.8522 (mp0) REVERT: D 56 GLU cc_start: 0.8711 (pm20) cc_final: 0.8386 (pp20) REVERT: D 116 ASN cc_start: 0.8804 (m-40) cc_final: 0.8448 (m-40) REVERT: D 123 GLN cc_start: 0.8566 (pt0) cc_final: 0.8184 (pt0) REVERT: D 163 VAL cc_start: 0.8780 (m) cc_final: 0.8556 (p) REVERT: D 169 ASP cc_start: 0.8670 (t0) cc_final: 0.8056 (t0) REVERT: E 56 GLU cc_start: 0.8566 (pm20) cc_final: 0.8255 (pp20) REVERT: E 123 GLN cc_start: 0.8517 (pt0) cc_final: 0.8076 (pt0) REVERT: E 151 LYS cc_start: 0.8856 (ttmt) cc_final: 0.8274 (ttmm) REVERT: E 152 VAL cc_start: 0.9053 (t) cc_final: 0.8684 (p) REVERT: E 155 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8075 (mp0) REVERT: E 163 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8361 (p) REVERT: E 165 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8413 (mt-10) REVERT: F 57 LYS cc_start: 0.9126 (mmtt) cc_final: 0.8907 (mmmt) REVERT: F 81 GLN cc_start: 0.8570 (tm-30) cc_final: 0.8368 (tm-30) REVERT: F 163 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8366 (p) REVERT: G 56 GLU cc_start: 0.8721 (pm20) cc_final: 0.8433 (pp20) REVERT: G 78 ASP cc_start: 0.8558 (m-30) cc_final: 0.8013 (m-30) REVERT: G 118 GLU cc_start: 0.8788 (pt0) cc_final: 0.8192 (pt0) REVERT: G 163 VAL cc_start: 0.8649 (m) cc_final: 0.8429 (p) REVERT: G 165 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8719 (tm-30) REVERT: G 169 ASP cc_start: 0.8405 (t70) cc_final: 0.7927 (t0) REVERT: H 94 MET cc_start: 0.8723 (tpp) cc_final: 0.8443 (tpp) REVERT: H 162 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8766 (mt-10) REVERT: H 165 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8442 (pt0) REVERT: I 81 GLN cc_start: 0.9036 (mt0) cc_final: 0.8636 (mt0) REVERT: K 24 LEU cc_start: 0.9114 (tt) cc_final: 0.8826 (tp) REVERT: K 150 ASN cc_start: 0.9491 (m-40) cc_final: 0.9262 (m110) REVERT: K 155 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7877 (mp0) REVERT: L 56 GLU cc_start: 0.7889 (pm20) cc_final: 0.7547 (pm20) REVERT: M 56 GLU cc_start: 0.7705 (pm20) cc_final: 0.7482 (mp0) REVERT: M 155 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7888 (mp0) REVERT: M 165 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8168 (tm-30) REVERT: N 25 LYS cc_start: 0.8764 (tppt) cc_final: 0.8497 (tttt) REVERT: N 165 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8411 (tt0) outliers start: 40 outliers final: 32 residues processed: 547 average time/residue: 0.2780 time to fit residues: 237.7677 Evaluate side-chains 529 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 494 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER 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 178 GLU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 79 THR 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 163 VAL 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 45 SER Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 170 ARG Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain J residue 65 SER 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 L residue 97 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 162 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 208 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.102033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.086784 restraints weight = 125998.441| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 4.85 r_work: 0.3044 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.7670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18860 Z= 0.167 Angle : 0.703 26.092 25328 Z= 0.361 Chirality : 0.090 1.738 2954 Planarity : 0.004 0.060 3290 Dihedral : 6.671 75.472 2647 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.30 % Favored : 89.57 % Rotamer: Outliers : 2.34 % Allowed : 21.80 % Favored : 75.86 % 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: -2.46 (0.17), residues: 2310 helix: -0.97 (0.15), residues: 1134 sheet: -2.76 (0.28), residues: 266 loop : -1.96 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 146 TYR 0.009 0.001 TYR J 77 PHE 0.016 0.001 PHE I 101 HIS 0.003 0.001 HIS L 122 Details of bonding type rmsd covalent geometry : bond 0.00361 (18818) covalent geometry : angle 0.70310 (25328) hydrogen bonds : bond 0.04236 ( 431) hydrogen bonds : angle 5.06880 ( 1251) Misc. bond : bond 0.00195 ( 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 531 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 486 time to evaluate : 1.041 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: A 78 ASP cc_start: 0.8504 (m-30) cc_final: 0.8015 (m-30) REVERT: A 116 ASN cc_start: 0.8705 (m-40) cc_final: 0.8421 (m110) REVERT: A 118 GLU cc_start: 0.8736 (pt0) cc_final: 0.8491 (pt0) REVERT: A 163 VAL cc_start: 0.8636 (OUTLIER) cc_final: 0.8407 (p) REVERT: A 169 ASP cc_start: 0.8125 (t70) cc_final: 0.7861 (t70) REVERT: B 116 ASN cc_start: 0.8764 (m-40) cc_final: 0.8272 (m-40) REVERT: B 165 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8436 (tm-30) REVERT: C 78 ASP cc_start: 0.8585 (m-30) cc_final: 0.8182 (m-30) REVERT: C 81 GLN cc_start: 0.8621 (tm-30) cc_final: 0.8389 (tm-30) REVERT: C 163 VAL cc_start: 0.8723 (m) cc_final: 0.8520 (p) REVERT: C 165 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8792 (tm-30) REVERT: C 169 ASP cc_start: 0.7893 (t0) cc_final: 0.7585 (t0) REVERT: C 178 GLU cc_start: 0.8915 (mp0) cc_final: 0.8599 (mp0) REVERT: D 56 GLU cc_start: 0.8649 (pm20) cc_final: 0.8370 (pp20) REVERT: D 116 ASN cc_start: 0.8748 (m-40) cc_final: 0.8389 (m-40) REVERT: D 123 GLN cc_start: 0.8578 (pt0) cc_final: 0.8253 (pt0) REVERT: D 163 VAL cc_start: 0.8815 (m) cc_final: 0.8575 (p) REVERT: D 165 GLU cc_start: 0.8695 (mt-10) cc_final: 0.7987 (mt-10) REVERT: D 169 ASP cc_start: 0.8722 (t0) cc_final: 0.8093 (t0) REVERT: E 56 GLU cc_start: 0.8559 (pm20) cc_final: 0.8274 (pp20) REVERT: E 123 GLN cc_start: 0.8438 (pt0) cc_final: 0.8013 (pt0) REVERT: E 151 LYS cc_start: 0.8834 (ttmt) cc_final: 0.8246 (ttmm) REVERT: E 152 VAL cc_start: 0.9090 (t) cc_final: 0.8700 (p) REVERT: E 155 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8118 (mp0) REVERT: E 163 VAL cc_start: 0.8649 (OUTLIER) cc_final: 0.8425 (p) REVERT: E 165 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8320 (mt-10) REVERT: E 169 ASP cc_start: 0.8496 (t70) cc_final: 0.7650 (t0) REVERT: F 57 LYS cc_start: 0.9129 (mmtt) cc_final: 0.8908 (mmmt) REVERT: F 155 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8276 (mp0) REVERT: F 163 VAL cc_start: 0.8687 (OUTLIER) cc_final: 0.8482 (p) REVERT: G 56 GLU cc_start: 0.8696 (pm20) cc_final: 0.8440 (pp20) REVERT: G 78 ASP cc_start: 0.8557 (m-30) cc_final: 0.8090 (m-30) REVERT: G 118 GLU cc_start: 0.8859 (pt0) cc_final: 0.8280 (pt0) REVERT: G 165 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8810 (tm-30) REVERT: G 169 ASP cc_start: 0.8349 (t70) cc_final: 0.7874 (t0) REVERT: H 94 MET cc_start: 0.8737 (tpp) cc_final: 0.8455 (tpp) REVERT: H 162 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8521 (tp30) REVERT: H 165 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8359 (tt0) REVERT: I 94 MET cc_start: 0.8629 (tpp) cc_final: 0.8323 (tpp) REVERT: K 155 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7929 (mp0) REVERT: L 56 GLU cc_start: 0.7885 (pm20) cc_final: 0.7492 (pm20) REVERT: M 54 ASP cc_start: 0.8755 (m-30) cc_final: 0.8432 (m-30) REVERT: M 56 GLU cc_start: 0.7754 (pm20) cc_final: 0.7497 (mp0) REVERT: M 165 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8175 (tm-30) REVERT: N 25 LYS cc_start: 0.8843 (tppt) cc_final: 0.8562 (tttt) REVERT: N 165 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8415 (tt0) outliers start: 45 outliers final: 39 residues processed: 517 average time/residue: 0.2814 time to fit residues: 227.4119 Evaluate side-chains 514 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 472 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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 178 GLU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 79 THR 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 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 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 65 SER Chi-restraints excluded: chain G residue 170 ARG Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain J residue 60 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 L residue 65 SER Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 185 ILE Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 70 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 153 optimal weight: 10.0000 chunk 82 optimal weight: 0.5980 chunk 7 optimal weight: 7.9990 chunk 19 optimal weight: 0.1980 chunk 23 optimal weight: 0.0980 chunk 179 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 chunk 9 optimal weight: 0.3980 chunk 100 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 HIS ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.105593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.090496 restraints weight = 124817.917| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 4.88 r_work: 0.3097 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.7771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18860 Z= 0.107 Angle : 0.679 25.853 25328 Z= 0.342 Chirality : 0.089 1.709 2954 Planarity : 0.003 0.034 3290 Dihedral : 5.829 74.280 2647 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.75 % Favored : 93.12 % Rotamer: Outliers : 0.88 % Allowed : 23.73 % Favored : 75.39 % 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: -1.81 (0.17), residues: 2310 helix: -0.31 (0.17), residues: 1078 sheet: -2.55 (0.28), residues: 266 loop : -1.72 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 141 TYR 0.010 0.001 TYR J 77 PHE 0.014 0.001 PHE I 101 HIS 0.001 0.000 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00257 (18818) covalent geometry : angle 0.67903 (25328) hydrogen bonds : bond 0.03268 ( 431) hydrogen bonds : angle 4.44083 ( 1251) Misc. bond : bond 0.00182 ( 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 542 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 525 time to evaluate : 0.894 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: A 78 ASP cc_start: 0.8475 (m-30) cc_final: 0.7965 (m-30) REVERT: A 116 ASN cc_start: 0.8674 (m-40) cc_final: 0.8374 (m110) REVERT: A 118 GLU cc_start: 0.8568 (pt0) cc_final: 0.8325 (pt0) REVERT: A 163 VAL cc_start: 0.8599 (OUTLIER) cc_final: 0.8383 (p) REVERT: A 169 ASP cc_start: 0.8110 (t70) cc_final: 0.7786 (t70) REVERT: B 116 ASN cc_start: 0.8629 (m-40) cc_final: 0.8200 (m-40) REVERT: C 78 ASP cc_start: 0.8585 (m-30) cc_final: 0.8215 (m-30) REVERT: C 81 GLN cc_start: 0.8617 (tm-30) cc_final: 0.8394 (tm-30) REVERT: C 165 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8786 (tm-30) REVERT: C 169 ASP cc_start: 0.7957 (t0) cc_final: 0.7634 (t0) REVERT: C 178 GLU cc_start: 0.8945 (mp0) cc_final: 0.8622 (mp0) REVERT: D 56 GLU cc_start: 0.8640 (pm20) cc_final: 0.8398 (pp20) REVERT: D 116 ASN cc_start: 0.8772 (m-40) cc_final: 0.8418 (m-40) REVERT: D 123 GLN cc_start: 0.8623 (pt0) cc_final: 0.8296 (pt0) REVERT: D 163 VAL cc_start: 0.8782 (m) cc_final: 0.8563 (p) REVERT: D 169 ASP cc_start: 0.8716 (t0) cc_final: 0.8119 (t0) REVERT: E 56 GLU cc_start: 0.8563 (pm20) cc_final: 0.8262 (pp20) REVERT: E 123 GLN cc_start: 0.8461 (pt0) cc_final: 0.8008 (pt0) REVERT: E 151 LYS cc_start: 0.8842 (ttmt) cc_final: 0.8258 (ttmm) REVERT: E 152 VAL cc_start: 0.8991 (t) cc_final: 0.8645 (p) REVERT: E 155 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7980 (mp0) REVERT: E 163 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8413 (p) REVERT: E 165 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8413 (mt-10) REVERT: E 169 ASP cc_start: 0.8447 (t70) cc_final: 0.7637 (t0) REVERT: F 57 LYS cc_start: 0.9102 (mmtt) cc_final: 0.8862 (mmmt) REVERT: F 163 VAL cc_start: 0.8683 (OUTLIER) cc_final: 0.8470 (p) REVERT: G 56 GLU cc_start: 0.8712 (pm20) cc_final: 0.8432 (pp20) REVERT: G 78 ASP cc_start: 0.8551 (m-30) cc_final: 0.8044 (m-30) REVERT: G 118 GLU cc_start: 0.8725 (pt0) cc_final: 0.8164 (pt0) REVERT: G 165 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8761 (tm-30) REVERT: G 169 ASP cc_start: 0.8265 (t70) cc_final: 0.7743 (t0) REVERT: H 94 MET cc_start: 0.8812 (tpp) cc_final: 0.8501 (tpp) REVERT: H 159 GLN cc_start: 0.8528 (mm-40) cc_final: 0.7806 (mp10) REVERT: H 182 TYR cc_start: 0.7496 (m-80) cc_final: 0.7177 (m-80) REVERT: I 81 GLN cc_start: 0.9034 (mt0) cc_final: 0.8629 (mt0) REVERT: I 159 GLN cc_start: 0.8448 (mm-40) cc_final: 0.7783 (mp10) REVERT: K 155 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7905 (mp0) REVERT: L 56 GLU cc_start: 0.8021 (pm20) cc_final: 0.7727 (mp0) REVERT: M 56 GLU cc_start: 0.7748 (pm20) cc_final: 0.7514 (mp0) REVERT: M 155 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7837 (mp0) REVERT: M 165 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8194 (tm-30) REVERT: N 23 LEU cc_start: 0.9278 (mt) cc_final: 0.9072 (mt) REVERT: N 25 LYS cc_start: 0.8713 (tppt) cc_final: 0.8468 (tttt) REVERT: N 159 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8031 (mp10) REVERT: N 165 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8407 (tt0) outliers start: 17 outliers final: 12 residues processed: 533 average time/residue: 0.2793 time to fit residues: 233.1275 Evaluate side-chains 518 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 503 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 178 GLU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain L residue 97 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 115 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 172 optimal weight: 2.9990 chunk 206 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.102783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.087652 restraints weight = 126765.108| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 4.85 r_work: 0.3052 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.7890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18860 Z= 0.180 Angle : 0.713 26.182 25328 Z= 0.366 Chirality : 0.091 1.742 2954 Planarity : 0.004 0.031 3290 Dihedral : 6.500 80.730 2647 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.35 % Favored : 89.52 % Rotamer: Outliers : 0.94 % Allowed : 23.99 % Favored : 75.08 % 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: -1.99 (0.17), residues: 2310 helix: -0.63 (0.16), residues: 1134 sheet: -2.63 (0.28), residues: 266 loop : -1.62 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 141 TYR 0.006 0.001 TYR C 77 PHE 0.016 0.001 PHE I 101 HIS 0.003 0.000 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00391 (18818) covalent geometry : angle 0.71273 (25328) hydrogen bonds : bond 0.04102 ( 431) hydrogen bonds : angle 5.01647 ( 1251) Misc. bond : bond 0.00195 ( 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 493 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 475 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8488 (m-30) cc_final: 0.8074 (m-30) REVERT: A 116 ASN cc_start: 0.8685 (m-40) cc_final: 0.8410 (m-40) REVERT: A 163 VAL cc_start: 0.8672 (OUTLIER) cc_final: 0.8462 (p) REVERT: A 169 ASP cc_start: 0.8253 (t70) cc_final: 0.7988 (t70) REVERT: B 116 ASN cc_start: 0.8634 (m-40) cc_final: 0.8191 (m-40) REVERT: C 78 ASP cc_start: 0.8553 (m-30) cc_final: 0.8102 (m-30) REVERT: C 165 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8822 (tm-30) REVERT: C 169 ASP cc_start: 0.8076 (t0) cc_final: 0.7661 (t0) REVERT: C 170 ARG cc_start: 0.7789 (ptm-80) cc_final: 0.7459 (ptm160) REVERT: C 178 GLU cc_start: 0.8996 (mp0) cc_final: 0.8672 (mp0) REVERT: D 56 GLU cc_start: 0.8643 (pm20) cc_final: 0.8400 (pp20) REVERT: D 116 ASN cc_start: 0.8776 (m-40) cc_final: 0.8403 (m-40) REVERT: D 123 GLN cc_start: 0.8610 (pt0) cc_final: 0.8330 (pt0) REVERT: D 163 VAL cc_start: 0.8812 (m) cc_final: 0.8575 (p) REVERT: D 165 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8008 (mt-10) REVERT: D 169 ASP cc_start: 0.8841 (t0) cc_final: 0.8206 (t0) REVERT: E 56 GLU cc_start: 0.8589 (pm20) cc_final: 0.8322 (pp20) REVERT: E 123 GLN cc_start: 0.8398 (pt0) cc_final: 0.7990 (pt0) REVERT: E 151 LYS cc_start: 0.8866 (ttmt) cc_final: 0.8276 (ttmm) REVERT: E 152 VAL cc_start: 0.9092 (t) cc_final: 0.8715 (p) REVERT: E 155 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8032 (mp0) REVERT: E 163 VAL cc_start: 0.8708 (OUTLIER) cc_final: 0.8495 (p) REVERT: E 169 ASP cc_start: 0.8479 (t70) cc_final: 0.7650 (t0) REVERT: F 57 LYS cc_start: 0.9105 (mmtt) cc_final: 0.8883 (mmmt) REVERT: G 56 GLU cc_start: 0.8686 (pm20) cc_final: 0.8439 (pp20) REVERT: G 78 ASP cc_start: 0.8542 (m-30) cc_final: 0.8095 (m-30) REVERT: G 118 GLU cc_start: 0.8894 (pt0) cc_final: 0.8368 (pt0) REVERT: G 169 ASP cc_start: 0.8328 (t70) cc_final: 0.7797 (t0) REVERT: H 94 MET cc_start: 0.8819 (tpp) cc_final: 0.8516 (tpp) REVERT: L 56 GLU cc_start: 0.7983 (pm20) cc_final: 0.7545 (pm20) REVERT: M 54 ASP cc_start: 0.8799 (m-30) cc_final: 0.8437 (m-30) REVERT: M 56 GLU cc_start: 0.7730 (pm20) cc_final: 0.7485 (mp0) REVERT: M 165 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8257 (tm-30) REVERT: N 25 LYS cc_start: 0.8852 (tppt) cc_final: 0.8591 (tttt) REVERT: N 165 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8419 (tt0) outliers start: 18 outliers final: 13 residues processed: 485 average time/residue: 0.2792 time to fit residues: 212.2295 Evaluate side-chains 483 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 468 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 26 ASP 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 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 163 VAL 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 K residue 97 SER Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain M residue 107 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 195 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 181 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 173 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.105365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.090275 restraints weight = 123836.866| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 4.87 r_work: 0.3087 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.7984 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= 0.105 Angle : 0.679 25.941 25328 Z= 0.342 Chirality : 0.090 1.711 2954 Planarity : 0.003 0.034 3290 Dihedral : 5.761 81.224 2647 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.80 % Favored : 93.12 % Rotamer: Outliers : 0.83 % Allowed : 24.40 % Favored : 74.77 % 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: -1.44 (0.18), residues: 2310 helix: -0.06 (0.17), residues: 1078 sheet: -2.46 (0.29), residues: 266 loop : -1.42 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 141 TYR 0.007 0.000 TYR G 77 PHE 0.015 0.001 PHE I 101 HIS 0.001 0.000 HIS J 122 Details of bonding type rmsd covalent geometry : bond 0.00251 (18818) covalent geometry : angle 0.67891 (25328) hydrogen bonds : bond 0.03272 ( 431) hydrogen bonds : angle 4.48769 ( 1251) Misc. bond : bond 0.00180 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7459.43 seconds wall clock time: 126 minutes 51.91 seconds (7611.91 seconds total)