Starting phenix.real_space_refine on Wed Aug 27 02:24:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uti_20880/08_2025/6uti_20880.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uti_20880/08_2025/6uti_20880.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 { model { file = "/net/cci-nas-00/data/ceres_data/6uti_20880/08_2025/6uti_20880.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uti_20880/08_2025/6uti_20880.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uti_20880/08_2025/6uti_20880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uti_20880/08_2025/6uti_20880.map" } 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= 0.001 sd= 0.255 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 196 5.16 5 C 29407 2.51 5 N 7840 2.21 5 O 8953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.06s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 46396 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1748 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain: "B" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1748 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain: "C" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1748 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain: "D" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1748 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain: "E" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1748 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain: "F" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1748 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain: "G" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1748 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain: "O" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1766 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "P" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1766 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "Q" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1766 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "R" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1766 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "S" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1766 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "T" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1766 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "U" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1766 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "H" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1557 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "I" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1557 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "J" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1557 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "K" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1557 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "L" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1557 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "M" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1557 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "N" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1557 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "V" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1557 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "W" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1557 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "X" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1557 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "Y" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1557 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "Z" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1557 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "a" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1557 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "b" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1557 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Residues with excluded nonbonded symmetry interactions: 57 residue: pdb=" N VAL O 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 77 " occ=0.50 residue: pdb=" N VAL P 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL P 77 " occ=0.50 residue: pdb=" N VAL Q 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL Q 77 " occ=0.50 residue: pdb=" N VAL R 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL R 77 " occ=0.50 residue: pdb=" N VAL S 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL S 77 " occ=0.50 residue: pdb=" N ASN H 24 " occ=0.50 ... (6 atoms not shown) pdb=" ND2 ASN H 24 " occ=0.50 residue: pdb=" N TYR H 58 " occ=0.50 ... (10 atoms not shown) pdb=" OH TYR H 58 " occ=0.50 residue: pdb=" N GLN H 89 " occ=0.50 ... (7 atoms not shown) pdb=" NE2 GLN H 89 " occ=0.50 residue: pdb=" N MET H 96 " occ=0.50 ... (6 atoms not shown) pdb=" CE MET H 96 " occ=0.50 residue: pdb=" N ASN I 24 " occ=0.50 ... (6 atoms not shown) pdb=" ND2 ASN I 24 " occ=0.50 residue: pdb=" N TYR I 58 " occ=0.50 ... (10 atoms not shown) pdb=" OH TYR I 58 " occ=0.50 residue: pdb=" N MET I 96 " occ=0.50 ... (6 atoms not shown) pdb=" CE MET I 96 " occ=0.50 ... (remaining 45 not shown) Time building chain proxies: 10.84, per 1000 atoms: 0.23 Number of scatterers: 46396 At special positions: 0 Unit cell: (135, 136.08, 176.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 196 16.00 O 8953 8.00 N 7840 7.00 C 29407 6.00 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=0, symmetry=0 Time building additional restraints: 4.23 Conformation dependent library (CDL) restraints added in 2.0 seconds Enol-peptide restraints added in 1.2 microseconds 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11060 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 56 sheets defined 40.8% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 21 through 32 Processing helix chain 'A' and resid 81 through 104 Processing helix chain 'A' and resid 108 through 126 removed outlier: 3.887A pdb=" N LEU A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR A 123 " --> pdb=" O GLN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 180 Processing helix chain 'A' and resid 185 through 202 removed outlier: 3.570A pdb=" N SER A 200 " --> pdb=" O ALA A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 removed outlier: 3.784A pdb=" N VAL A 229 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS A 230 " --> pdb=" O GLN A 226 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 32 Processing helix chain 'B' and resid 81 through 104 Processing helix chain 'B' and resid 108 through 126 removed outlier: 3.924A pdb=" N LEU B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 180 Processing helix chain 'B' and resid 185 through 202 removed outlier: 3.607A pdb=" N SER B 200 " --> pdb=" O ALA B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 233 removed outlier: 3.806A pdb=" N VAL B 229 " --> pdb=" O ASP B 225 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS B 230 " --> pdb=" O GLN B 226 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 32 Processing helix chain 'C' and resid 81 through 104 Processing helix chain 'C' and resid 108 through 126 removed outlier: 3.929A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR C 123 " --> pdb=" O GLN C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 180 Processing helix chain 'C' and resid 185 through 202 removed outlier: 3.581A pdb=" N SER C 200 " --> pdb=" O ALA C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 233 removed outlier: 3.806A pdb=" N VAL C 229 " --> pdb=" O ASP C 225 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS C 230 " --> pdb=" O GLN C 226 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 32 Processing helix chain 'D' and resid 81 through 104 Processing helix chain 'D' and resid 108 through 126 removed outlier: 3.895A pdb=" N LEU D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR D 123 " --> pdb=" O GLN D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 180 Processing helix chain 'D' and resid 185 through 202 removed outlier: 3.569A pdb=" N SER D 200 " --> pdb=" O ALA D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 233 removed outlier: 3.778A pdb=" N VAL D 229 " --> pdb=" O ASP D 225 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS D 230 " --> pdb=" O GLN D 226 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 32 Processing helix chain 'E' and resid 81 through 104 Processing helix chain 'E' and resid 108 through 126 removed outlier: 3.922A pdb=" N LEU E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR E 123 " --> pdb=" O GLN E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 180 Processing helix chain 'E' and resid 185 through 202 removed outlier: 3.576A pdb=" N SER E 200 " --> pdb=" O ALA E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 233 removed outlier: 3.792A pdb=" N VAL E 229 " --> pdb=" O ASP E 225 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS E 230 " --> pdb=" O GLN E 226 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 32 Processing helix chain 'F' and resid 81 through 103 Processing helix chain 'F' and resid 108 through 126 removed outlier: 3.880A pdb=" N LEU F 112 " --> pdb=" O ASN F 108 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL F 116 " --> pdb=" O LEU F 112 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR F 123 " --> pdb=" O GLN F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 180 Processing helix chain 'F' and resid 185 through 202 removed outlier: 3.573A pdb=" N SER F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 233 removed outlier: 3.790A pdb=" N VAL F 229 " --> pdb=" O ASP F 225 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS F 230 " --> pdb=" O GLN F 226 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 32 Processing helix chain 'G' and resid 81 through 104 Processing helix chain 'G' and resid 108 through 126 removed outlier: 3.885A pdb=" N LEU G 112 " --> pdb=" O ASN G 108 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL G 116 " --> pdb=" O LEU G 112 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR G 123 " --> pdb=" O GLN G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 180 Processing helix chain 'G' and resid 185 through 202 removed outlier: 3.567A pdb=" N SER G 200 " --> pdb=" O ALA G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 233 removed outlier: 3.788A pdb=" N VAL G 229 " --> pdb=" O ASP G 225 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS G 230 " --> pdb=" O GLN G 226 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS G 231 " --> pdb=" O GLU G 227 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 32 removed outlier: 3.547A pdb=" N LYS O 32 " --> pdb=" O LEU O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 60 through 64 removed outlier: 3.739A pdb=" N ILE O 64 " --> pdb=" O GLN O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 104 Processing helix chain 'O' and resid 108 through 123 removed outlier: 4.297A pdb=" N LEU O 112 " --> pdb=" O ASN O 108 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR O 123 " --> pdb=" O GLN O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 168 through 180 removed outlier: 3.559A pdb=" N ARG O 178 " --> pdb=" O SER O 174 " (cutoff:3.500A) Processing helix chain 'O' and resid 185 through 199 Processing helix chain 'O' and resid 225 through 231 removed outlier: 3.619A pdb=" N LYS O 231 " --> pdb=" O GLU O 227 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 32 removed outlier: 3.601A pdb=" N LYS P 32 " --> pdb=" O LEU P 28 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 64 removed outlier: 3.751A pdb=" N ILE P 64 " --> pdb=" O GLN P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 104 Processing helix chain 'P' and resid 108 through 123 removed outlier: 4.260A pdb=" N LEU P 112 " --> pdb=" O ASN P 108 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR P 123 " --> pdb=" O GLN P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 168 through 180 removed outlier: 3.558A pdb=" N ARG P 178 " --> pdb=" O SER P 174 " (cutoff:3.500A) Processing helix chain 'P' and resid 185 through 199 Processing helix chain 'P' and resid 225 through 231 removed outlier: 3.629A pdb=" N LYS P 231 " --> pdb=" O GLU P 227 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 32 removed outlier: 3.556A pdb=" N LYS Q 32 " --> pdb=" O LEU Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 64 removed outlier: 3.710A pdb=" N ILE Q 64 " --> pdb=" O GLN Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 104 Processing helix chain 'Q' and resid 108 through 123 removed outlier: 4.283A pdb=" N LEU Q 112 " --> pdb=" O ASN Q 108 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR Q 123 " --> pdb=" O GLN Q 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 168 through 180 removed outlier: 3.551A pdb=" N ARG Q 178 " --> pdb=" O SER Q 174 " (cutoff:3.500A) Processing helix chain 'Q' and resid 185 through 199 Processing helix chain 'Q' and resid 225 through 231 removed outlier: 3.615A pdb=" N LYS Q 231 " --> pdb=" O GLU Q 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 32 removed outlier: 3.568A pdb=" N LYS R 32 " --> pdb=" O LEU R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 64 removed outlier: 3.755A pdb=" N ILE R 64 " --> pdb=" O GLN R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 104 Processing helix chain 'R' and resid 108 through 123 removed outlier: 4.272A pdb=" N LEU R 112 " --> pdb=" O ASN R 108 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR R 123 " --> pdb=" O GLN R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 180 removed outlier: 3.570A pdb=" N ARG R 178 " --> pdb=" O SER R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 199 Processing helix chain 'R' and resid 225 through 231 removed outlier: 3.623A pdb=" N LYS R 231 " --> pdb=" O GLU R 227 " (cutoff:3.500A) Processing helix chain 'S' and resid 21 through 32 Processing helix chain 'S' and resid 60 through 64 removed outlier: 3.718A pdb=" N ILE S 64 " --> pdb=" O GLN S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 104 Processing helix chain 'S' and resid 108 through 123 removed outlier: 4.296A pdb=" N LEU S 112 " --> pdb=" O ASN S 108 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR S 123 " --> pdb=" O GLN S 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 168 through 180 removed outlier: 3.559A pdb=" N ARG S 178 " --> pdb=" O SER S 174 " (cutoff:3.500A) Processing helix chain 'S' and resid 185 through 199 Processing helix chain 'S' and resid 225 through 230 Processing helix chain 'S' and resid 231 through 233 No H-bonds generated for 'chain 'S' and resid 231 through 233' Processing helix chain 'T' and resid 21 through 32 Processing helix chain 'T' and resid 60 through 64 removed outlier: 3.738A pdb=" N ILE T 64 " --> pdb=" O GLN T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 81 through 104 Processing helix chain 'T' and resid 108 through 123 removed outlier: 4.236A pdb=" N LEU T 112 " --> pdb=" O ASN T 108 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYR T 123 " --> pdb=" O GLN T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 180 removed outlier: 3.575A pdb=" N ARG T 178 " --> pdb=" O SER T 174 " (cutoff:3.500A) Processing helix chain 'T' and resid 185 through 199 Processing helix chain 'T' and resid 225 through 231 removed outlier: 3.611A pdb=" N LYS T 231 " --> pdb=" O GLU T 227 " (cutoff:3.500A) Processing helix chain 'U' and resid 21 through 32 Processing helix chain 'U' and resid 60 through 64 removed outlier: 3.740A pdb=" N ILE U 64 " --> pdb=" O GLN U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 81 through 104 Processing helix chain 'U' and resid 108 through 123 removed outlier: 4.262A pdb=" N LEU U 112 " --> pdb=" O ASN U 108 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR U 123 " --> pdb=" O GLN U 119 " (cutoff:3.500A) Processing helix chain 'U' and resid 168 through 180 removed outlier: 3.575A pdb=" N ARG U 178 " --> pdb=" O SER U 174 " (cutoff:3.500A) Processing helix chain 'U' and resid 185 through 199 Processing helix chain 'U' and resid 225 through 231 removed outlier: 3.623A pdb=" N LYS U 231 " --> pdb=" O GLU U 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 71 Processing helix chain 'H' and resid 75 through 89 Processing helix chain 'H' and resid 130 through 142 removed outlier: 4.017A pdb=" N SER H 140 " --> pdb=" O GLY H 136 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR H 142 " --> pdb=" O LEU H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 163 Processing helix chain 'H' and resid 188 through 200 Processing helix chain 'I' and resid 48 through 71 Processing helix chain 'I' and resid 75 through 89 Processing helix chain 'I' and resid 130 through 142 removed outlier: 4.017A pdb=" N SER I 140 " --> pdb=" O GLY I 136 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR I 142 " --> pdb=" O LEU I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 163 Processing helix chain 'I' and resid 188 through 200 Processing helix chain 'J' and resid 48 through 71 Processing helix chain 'J' and resid 75 through 89 Processing helix chain 'J' and resid 130 through 142 removed outlier: 4.017A pdb=" N SER J 140 " --> pdb=" O GLY J 136 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR J 142 " --> pdb=" O LEU J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 163 Processing helix chain 'J' and resid 188 through 200 Processing helix chain 'K' and resid 48 through 71 Processing helix chain 'K' and resid 75 through 89 Processing helix chain 'K' and resid 130 through 142 removed outlier: 4.017A pdb=" N SER K 140 " --> pdb=" O GLY K 136 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR K 142 " --> pdb=" O LEU K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 163 Processing helix chain 'K' and resid 188 through 200 Processing helix chain 'L' and resid 48 through 71 Processing helix chain 'L' and resid 75 through 89 Processing helix chain 'L' and resid 130 through 142 removed outlier: 4.017A pdb=" N SER L 140 " --> pdb=" O GLY L 136 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR L 142 " --> pdb=" O LEU L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 163 Processing helix chain 'L' and resid 188 through 200 Processing helix chain 'M' and resid 48 through 71 Processing helix chain 'M' and resid 75 through 89 Processing helix chain 'M' and resid 130 through 142 removed outlier: 4.017A pdb=" N SER M 140 " --> pdb=" O GLY M 136 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR M 142 " --> pdb=" O LEU M 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 163 Processing helix chain 'M' and resid 188 through 200 Processing helix chain 'N' and resid 48 through 71 Processing helix chain 'N' and resid 75 through 89 Processing helix chain 'N' and resid 130 through 142 removed outlier: 4.017A pdb=" N SER N 140 " --> pdb=" O GLY N 136 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR N 142 " --> pdb=" O LEU N 138 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 163 Processing helix chain 'N' and resid 188 through 200 Processing helix chain 'V' and resid 48 through 71 Processing helix chain 'V' and resid 75 through 89 Processing helix chain 'V' and resid 130 through 142 removed outlier: 4.017A pdb=" N SER V 140 " --> pdb=" O GLY V 136 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR V 142 " --> pdb=" O LEU V 138 " (cutoff:3.500A) Processing helix chain 'V' and resid 147 through 163 Processing helix chain 'V' and resid 188 through 200 Processing helix chain 'W' and resid 48 through 71 Processing helix chain 'W' and resid 75 through 89 Processing helix chain 'W' and resid 130 through 142 removed outlier: 4.018A pdb=" N SER W 140 " --> pdb=" O GLY W 136 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR W 142 " --> pdb=" O LEU W 138 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 163 Processing helix chain 'W' and resid 188 through 200 Processing helix chain 'X' and resid 48 through 71 Processing helix chain 'X' and resid 75 through 89 Processing helix chain 'X' and resid 130 through 142 removed outlier: 4.018A pdb=" N SER X 140 " --> pdb=" O GLY X 136 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR X 142 " --> pdb=" O LEU X 138 " (cutoff:3.500A) Processing helix chain 'X' and resid 147 through 163 Processing helix chain 'X' and resid 188 through 200 Processing helix chain 'Y' and resid 48 through 71 Processing helix chain 'Y' and resid 75 through 89 Processing helix chain 'Y' and resid 130 through 142 removed outlier: 4.017A pdb=" N SER Y 140 " --> pdb=" O GLY Y 136 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR Y 142 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) Processing helix chain 'Y' and resid 147 through 163 Processing helix chain 'Y' and resid 188 through 200 Processing helix chain 'Z' and resid 48 through 71 Processing helix chain 'Z' and resid 75 through 89 Processing helix chain 'Z' and resid 130 through 142 removed outlier: 4.018A pdb=" N SER Z 140 " --> pdb=" O GLY Z 136 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR Z 142 " --> pdb=" O LEU Z 138 " (cutoff:3.500A) Processing helix chain 'Z' and resid 147 through 163 Processing helix chain 'Z' and resid 188 through 200 Processing helix chain 'a' and resid 48 through 71 Processing helix chain 'a' and resid 75 through 89 Processing helix chain 'a' and resid 130 through 142 removed outlier: 4.018A pdb=" N SER a 140 " --> pdb=" O GLY a 136 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR a 142 " --> pdb=" O LEU a 138 " (cutoff:3.500A) Processing helix chain 'a' and resid 147 through 163 Processing helix chain 'a' and resid 188 through 200 Processing helix chain 'b' and resid 48 through 71 Processing helix chain 'b' and resid 75 through 89 Processing helix chain 'b' and resid 130 through 142 removed outlier: 4.017A pdb=" N SER b 140 " --> pdb=" O GLY b 136 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR b 142 " --> pdb=" O LEU b 138 " (cutoff:3.500A) Processing helix chain 'b' and resid 147 through 163 Processing helix chain 'b' and resid 188 through 200 Processing sheet with id=AA1, first strand: chain 'A' and resid 162 through 165 removed outlier: 3.646A pdb=" N GLY A 45 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 222 " --> pdb=" O SER A 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 71 removed outlier: 6.287A pdb=" N VAL A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 136 " --> pdb=" O CYS A 151 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE A 138 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN A 158 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 162 through 165 removed outlier: 3.510A pdb=" N ARG B 222 " --> pdb=" O SER B 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 67 through 71 removed outlier: 6.274A pdb=" N VAL B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 162 through 165 removed outlier: 3.643A pdb=" N GLY C 45 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG C 222 " --> pdb=" O SER C 214 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 67 through 71 removed outlier: 6.267A pdb=" N VAL C 74 " --> pdb=" O ILE C 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 162 through 165 removed outlier: 3.632A pdb=" N GLY D 45 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG D 222 " --> pdb=" O SER D 214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 67 through 71 removed outlier: 6.295A pdb=" N VAL D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 162 through 165 removed outlier: 3.629A pdb=" N GLY E 45 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG E 222 " --> pdb=" O SER E 214 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 67 through 71 removed outlier: 6.287A pdb=" N VAL E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 162 through 165 removed outlier: 3.650A pdb=" N GLY F 45 " --> pdb=" O PHE F 42 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 67 through 71 removed outlier: 6.270A pdb=" N VAL F 74 " --> pdb=" O ILE F 70 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU F 136 " --> pdb=" O CYS F 151 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE F 138 " --> pdb=" O PHE F 149 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN F 158 " --> pdb=" O ASP F 150 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 162 through 165 removed outlier: 3.631A pdb=" N GLY G 45 " --> pdb=" O PHE G 42 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG G 222 " --> pdb=" O SER G 214 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 67 through 71 removed outlier: 6.278A pdb=" N VAL G 74 " --> pdb=" O ILE G 70 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU G 136 " --> pdb=" O CYS G 151 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE G 138 " --> pdb=" O PHE G 149 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN G 158 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 162 through 165 removed outlier: 3.513A pdb=" N GLY O 45 " --> pdb=" O PHE O 42 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ILE O 212 " --> pdb=" O TYR O 224 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'O' and resid 67 through 69 removed outlier: 3.567A pdb=" N ASN O 158 " --> pdb=" O ASP O 150 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 162 through 165 removed outlier: 3.509A pdb=" N GLY P 45 " --> pdb=" O PHE P 42 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ILE P 212 " --> pdb=" O TYR P 224 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 67 through 69 removed outlier: 3.553A pdb=" N ASN P 158 " --> pdb=" O ASP P 150 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Q' and resid 162 through 165 removed outlier: 3.507A pdb=" N GLY Q 45 " --> pdb=" O PHE Q 42 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE Q 212 " --> pdb=" O TYR Q 224 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Q' and resid 67 through 69 removed outlier: 3.561A pdb=" N ASN Q 158 " --> pdb=" O ASP Q 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'R' and resid 162 through 165 removed outlier: 3.510A pdb=" N GLY R 45 " --> pdb=" O PHE R 42 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ILE R 212 " --> pdb=" O TYR R 224 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'R' and resid 67 through 69 removed outlier: 3.545A pdb=" N ASN R 158 " --> pdb=" O ASP R 150 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'S' and resid 162 through 165 removed outlier: 3.521A pdb=" N GLY S 45 " --> pdb=" O PHE S 42 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE S 212 " --> pdb=" O TYR S 224 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'S' and resid 67 through 69 removed outlier: 3.556A pdb=" N ASN S 158 " --> pdb=" O ASP S 150 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'T' and resid 162 through 165 removed outlier: 3.547A pdb=" N GLY T 45 " --> pdb=" O PHE T 42 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ILE T 212 " --> pdb=" O TYR T 224 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'T' and resid 67 through 69 removed outlier: 3.548A pdb=" N ASN T 158 " --> pdb=" O ASP T 150 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'U' and resid 162 through 165 removed outlier: 3.505A pdb=" N GLY U 45 " --> pdb=" O PHE U 42 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE U 212 " --> pdb=" O TYR U 224 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'U' and resid 67 through 69 removed outlier: 3.566A pdb=" N ASN U 158 " --> pdb=" O ASP U 150 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 8 removed outlier: 4.062A pdb=" N ALA H 11 " --> pdb=" O LEU H 8 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 34 through 38 removed outlier: 6.673A pdb=" N THR H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 3 through 8 removed outlier: 4.063A pdb=" N ALA I 11 " --> pdb=" O LEU I 8 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.673A pdb=" N THR I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 3 through 8 removed outlier: 4.062A pdb=" N ALA J 11 " --> pdb=" O LEU J 8 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 34 through 38 removed outlier: 6.674A pdb=" N THR J 41 " --> pdb=" O ILE J 37 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 3 through 8 removed outlier: 4.062A pdb=" N ALA K 11 " --> pdb=" O LEU K 8 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 34 through 38 removed outlier: 6.673A pdb=" N THR K 41 " --> pdb=" O ILE K 37 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 3 through 8 removed outlier: 4.063A pdb=" N ALA L 11 " --> pdb=" O LEU L 8 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 34 through 38 removed outlier: 6.672A pdb=" N THR L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 3 through 8 removed outlier: 4.062A pdb=" N ALA M 11 " --> pdb=" O LEU M 8 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 34 through 38 removed outlier: 6.673A pdb=" N THR M 41 " --> pdb=" O ILE M 37 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 3 through 8 removed outlier: 4.062A pdb=" N ALA N 11 " --> pdb=" O LEU N 8 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 34 through 38 removed outlier: 6.673A pdb=" N THR N 41 " --> pdb=" O ILE N 37 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'V' and resid 3 through 8 removed outlier: 4.063A pdb=" N ALA V 11 " --> pdb=" O LEU V 8 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'V' and resid 34 through 38 removed outlier: 6.673A pdb=" N THR V 41 " --> pdb=" O ILE V 37 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'W' and resid 3 through 8 removed outlier: 4.062A pdb=" N ALA W 11 " --> pdb=" O LEU W 8 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.673A pdb=" N THR W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'X' and resid 3 through 8 removed outlier: 4.063A pdb=" N ALA X 11 " --> pdb=" O LEU X 8 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'X' and resid 34 through 38 removed outlier: 6.674A pdb=" N THR X 41 " --> pdb=" O ILE X 37 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Y' and resid 3 through 8 removed outlier: 4.062A pdb=" N ALA Y 11 " --> pdb=" O LEU Y 8 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Y' and resid 34 through 38 removed outlier: 6.673A pdb=" N THR Y 41 " --> pdb=" O ILE Y 37 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Z' and resid 3 through 8 removed outlier: 4.062A pdb=" N ALA Z 11 " --> pdb=" O LEU Z 8 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Z' and resid 34 through 38 removed outlier: 6.673A pdb=" N THR Z 41 " --> pdb=" O ILE Z 37 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'a' and resid 3 through 8 removed outlier: 4.063A pdb=" N ALA a 11 " --> pdb=" O LEU a 8 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'a' and resid 34 through 38 removed outlier: 6.673A pdb=" N THR a 41 " --> pdb=" O ILE a 37 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'b' and resid 3 through 8 removed outlier: 4.062A pdb=" N ALA b 11 " --> pdb=" O LEU b 8 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'b' and resid 34 through 38 removed outlier: 6.673A pdb=" N THR b 41 " --> pdb=" O ILE b 37 " (cutoff:3.500A) 2538 hydrogen bonds defined for protein. 7401 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: 11.67 Time building geometry restraints manager: 5.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14685 1.34 - 1.46: 6286 1.46 - 1.57: 25635 1.57 - 1.69: 7 1.69 - 1.81: 378 Bond restraints: 46991 Sorted by residual: bond pdb=" CA LYS B 53 " pdb=" CB LYS B 53 " ideal model delta sigma weight residual 1.525 1.593 -0.068 1.47e-02 4.63e+03 2.15e+01 bond pdb=" CA LYS E 53 " pdb=" CB LYS E 53 " ideal model delta sigma weight residual 1.525 1.591 -0.066 1.47e-02 4.63e+03 2.02e+01 bond pdb=" CA LYS C 53 " pdb=" CB LYS C 53 " ideal model delta sigma weight residual 1.525 1.591 -0.066 1.47e-02 4.63e+03 2.02e+01 bond pdb=" CA LYS D 53 " pdb=" CB LYS D 53 " ideal model delta sigma weight residual 1.525 1.590 -0.065 1.47e-02 4.63e+03 1.97e+01 bond pdb=" CA LYS A 53 " pdb=" CB LYS A 53 " ideal model delta sigma weight residual 1.525 1.590 -0.065 1.47e-02 4.63e+03 1.95e+01 ... (remaining 46986 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 61942 3.07 - 6.14: 1320 6.14 - 9.21: 144 9.21 - 12.28: 21 12.28 - 15.35: 7 Bond angle restraints: 63434 Sorted by residual: angle pdb=" C LEU A 207 " pdb=" N LYS A 208 " pdb=" CA LYS A 208 " ideal model delta sigma weight residual 121.54 136.89 -15.35 1.91e+00 2.74e-01 6.46e+01 angle pdb=" C LEU F 207 " pdb=" N LYS F 208 " pdb=" CA LYS F 208 " ideal model delta sigma weight residual 121.54 136.85 -15.31 1.91e+00 2.74e-01 6.42e+01 angle pdb=" C LEU C 207 " pdb=" N LYS C 208 " pdb=" CA LYS C 208 " ideal model delta sigma weight residual 121.54 136.83 -15.29 1.91e+00 2.74e-01 6.41e+01 angle pdb=" C LEU B 207 " pdb=" N LYS B 208 " pdb=" CA LYS B 208 " ideal model delta sigma weight residual 121.54 136.82 -15.28 1.91e+00 2.74e-01 6.40e+01 angle pdb=" C LEU D 207 " pdb=" N LYS D 208 " pdb=" CA LYS D 208 " ideal model delta sigma weight residual 121.54 136.82 -15.28 1.91e+00 2.74e-01 6.40e+01 ... (remaining 63429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 27480 16.18 - 32.36: 939 32.36 - 48.54: 261 48.54 - 64.72: 27 64.72 - 80.90: 49 Dihedral angle restraints: 28756 sinusoidal: 11445 harmonic: 17311 Sorted by residual: dihedral pdb=" CA LEU B 207 " pdb=" C LEU B 207 " pdb=" N LYS B 208 " pdb=" CA LYS B 208 " ideal model delta harmonic sigma weight residual 180.00 144.54 35.46 0 5.00e+00 4.00e-02 5.03e+01 dihedral pdb=" CA LEU D 207 " pdb=" C LEU D 207 " pdb=" N LYS D 208 " pdb=" CA LYS D 208 " ideal model delta harmonic sigma weight residual 180.00 144.65 35.35 0 5.00e+00 4.00e-02 5.00e+01 dihedral pdb=" CA LEU C 207 " pdb=" C LEU C 207 " pdb=" N LYS C 208 " pdb=" CA LYS C 208 " ideal model delta harmonic sigma weight residual 180.00 144.67 35.33 0 5.00e+00 4.00e-02 4.99e+01 ... (remaining 28753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 6616 0.095 - 0.190: 778 0.190 - 0.285: 40 0.285 - 0.380: 0 0.380 - 0.475: 7 Chirality restraints: 7441 Sorted by residual: chirality pdb=" CB ILE G 212 " pdb=" CA ILE G 212 " pdb=" CG1 ILE G 212 " pdb=" CG2 ILE G 212 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" CB ILE A 212 " pdb=" CA ILE A 212 " pdb=" CG1 ILE A 212 " pdb=" CG2 ILE A 212 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.42e+00 chirality pdb=" CB ILE F 212 " pdb=" CA ILE F 212 " pdb=" CG1 ILE F 212 " pdb=" CG2 ILE F 212 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.38e+00 ... (remaining 7438 not shown) Planarity restraints: 8134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 49 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C ILE F 49 " 0.056 2.00e-02 2.50e+03 pdb=" O ILE F 49 " -0.021 2.00e-02 2.50e+03 pdb=" N SER F 50 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 49 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C ILE G 49 " 0.056 2.00e-02 2.50e+03 pdb=" O ILE G 49 " -0.021 2.00e-02 2.50e+03 pdb=" N SER G 50 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 152 " 0.053 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO G 153 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO G 153 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO G 153 " 0.044 5.00e-02 4.00e+02 ... (remaining 8131 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 7315 2.77 - 3.30: 40567 3.30 - 3.83: 72554 3.83 - 4.37: 84541 4.37 - 4.90: 152161 Nonbonded interactions: 357138 Sorted by model distance: nonbonded pdb=" O LYS Q 41 " pdb=" OH TYR Q 180 " model vdw 2.232 3.040 nonbonded pdb=" O LYS O 41 " pdb=" OH TYR O 180 " model vdw 2.233 3.040 nonbonded pdb=" O LYS P 41 " pdb=" OH TYR P 180 " model vdw 2.233 3.040 nonbonded pdb=" O LYS R 41 " pdb=" OH TYR R 180 " model vdw 2.238 3.040 nonbonded pdb=" O LYS S 41 " pdb=" OH TYR S 180 " model vdw 2.244 3.040 ... (remaining 357133 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' 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=0.50 max=1.00 mean=0.99 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: 3.390 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: 0.030 Extract box with map and model: 0.670 Check model and map are aligned: 0.150 Set scattering table: 0.120 Process input model: 45.340 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.210 Set refine NCS operators: 0.010 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:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 0.007 0.091 46991 Z= 0.308 Angle : 1.115 15.346 63434 Z= 0.651 Chirality : 0.060 0.475 7441 Planarity : 0.007 0.080 8134 Dihedral : 10.054 80.902 17696 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.09 % Favored : 94.79 % Rotamer: Outliers : 0.22 % Allowed : 3.88 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.89 (0.09), residues: 5950 helix: -1.19 (0.09), residues: 2247 sheet: -1.36 (0.14), residues: 1274 loop : -2.86 (0.10), residues: 2429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG U 147 TYR 0.027 0.003 TYR J 135 PHE 0.029 0.003 PHE A 42 HIS 0.006 0.003 HIS J 109 Details of bonding type rmsd covalent geometry : bond 0.00685 (46991) covalent geometry : angle 1.11528 (63434) hydrogen bonds : bond 0.19614 ( 2538) hydrogen bonds : angle 7.45081 ( 7401) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1257 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 1246 time to evaluate : 2.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9173 (mtp) cc_final: 0.8934 (mtm) REVERT: C 40 MET cc_start: 0.8698 (ptp) cc_final: 0.8348 (ptp) REVERT: D 40 MET cc_start: 0.8836 (ptp) cc_final: 0.8605 (ptp) REVERT: E 173 VAL cc_start: 0.8324 (t) cc_final: 0.8043 (t) REVERT: F 120 MET cc_start: 0.9042 (mtp) cc_final: 0.8747 (mtp) REVERT: G 40 MET cc_start: 0.8947 (ptp) cc_final: 0.8682 (ptp) REVERT: G 120 MET cc_start: 0.9041 (mtp) cc_final: 0.8823 (mtp) REVERT: O 135 SER cc_start: 0.8923 (m) cc_final: 0.8614 (t) REVERT: P 12 ILE cc_start: 0.8530 (tp) cc_final: 0.8165 (tp) REVERT: P 40 MET cc_start: 0.7595 (pmt) cc_final: 0.7283 (ptp) REVERT: P 67 ILE cc_start: 0.8035 (tt) cc_final: 0.7785 (mt) REVERT: Q 67 ILE cc_start: 0.7815 (tt) cc_final: 0.7536 (mt) REVERT: Q 105 SER cc_start: 0.8836 (p) cc_final: 0.8633 (m) REVERT: R 67 ILE cc_start: 0.7958 (tt) cc_final: 0.7644 (mt) REVERT: S 40 MET cc_start: 0.7758 (pmt) cc_final: 0.7468 (ptp) REVERT: S 67 ILE cc_start: 0.8014 (tt) cc_final: 0.7461 (mt) REVERT: U 12 ILE cc_start: 0.8487 (tp) cc_final: 0.8020 (tp) REVERT: U 67 ILE cc_start: 0.8102 (tt) cc_final: 0.7632 (mt) REVERT: H 172 MET cc_start: 0.7531 (tpt) cc_final: 0.7272 (tpt) REVERT: I 105 ASP cc_start: 0.8497 (p0) cc_final: 0.8257 (p0) REVERT: I 172 MET cc_start: 0.7510 (tpt) cc_final: 0.7190 (tpt) REVERT: J 195 ARG cc_start: 0.7175 (mmt180) cc_final: 0.6922 (mmt180) REVERT: Y 67 ARG cc_start: 0.7684 (tmm-80) cc_final: 0.7169 (ttm170) REVERT: Z 18 ARG cc_start: 0.8200 (ptp-170) cc_final: 0.7999 (ptm160) REVERT: b 67 ARG cc_start: 0.7742 (tmm-80) cc_final: 0.7404 (ttp80) outliers start: 11 outliers final: 2 residues processed: 1250 average time/residue: 0.2986 time to fit residues: 587.5289 Evaluate side-chains 718 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 716 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain G residue 212 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 394 optimal weight: 0.6980 chunk 430 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 265 optimal weight: 2.9990 chunk 523 optimal weight: 0.8980 chunk 497 optimal weight: 0.9980 chunk 414 optimal weight: 0.9990 chunk 310 optimal weight: 1.9990 chunk 488 optimal weight: 2.9990 chunk 366 optimal weight: 0.7980 chunk 223 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN B 121 GLN C 23 GLN C 121 GLN D 23 GLN D 121 GLN E 23 GLN E 121 GLN F 121 GLN F 122 GLN G 121 GLN O 68 GLN P 68 GLN Q 68 GLN S 68 GLN U 68 GLN I 30 ASN I 88 ASN J 30 ASN K 30 ASN K 88 ASN L 30 ASN M 30 ASN M 88 ASN V 30 ASN W 30 ASN X 30 ASN Y 30 ASN Z 30 ASN Z 88 ASN a 30 ASN a 89 GLN b 30 ASN b 89 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.157441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.127632 restraints weight = 51992.861| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.17 r_work: 0.3264 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 46991 Z= 0.122 Angle : 0.582 9.134 63434 Z= 0.317 Chirality : 0.044 0.162 7441 Planarity : 0.005 0.057 8134 Dihedral : 5.130 42.683 6584 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.61 % Favored : 97.28 % Rotamer: Outliers : 2.30 % Allowed : 8.44 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.10), residues: 5950 helix: 0.89 (0.10), residues: 2282 sheet: -0.70 (0.14), residues: 1281 loop : -2.48 (0.10), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG W 67 TYR 0.016 0.001 TYR F 221 PHE 0.013 0.002 PHE E 42 HIS 0.003 0.001 HIS Z 109 Details of bonding type rmsd covalent geometry : bond 0.00281 (46991) covalent geometry : angle 0.58204 (63434) hydrogen bonds : bond 0.04093 ( 2538) hydrogen bonds : angle 4.61109 ( 7401) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 849 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 GLN cc_start: 0.7720 (tt0) cc_final: 0.7495 (mt0) REVERT: B 120 MET cc_start: 0.8981 (mtp) cc_final: 0.8693 (mtp) REVERT: C 48 LEU cc_start: 0.8812 (mt) cc_final: 0.8582 (mp) REVERT: E 70 ILE cc_start: 0.9190 (mm) cc_final: 0.8886 (mt) REVERT: G 18 ASP cc_start: 0.8508 (p0) cc_final: 0.7795 (t0) REVERT: O 20 ARG cc_start: 0.8762 (mtp180) cc_final: 0.8522 (mtm180) REVERT: O 70 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8693 (mt) REVERT: O 122 GLN cc_start: 0.8726 (tt0) cc_final: 0.8494 (tt0) REVERT: O 231 LYS cc_start: 0.7647 (mtpm) cc_final: 0.7305 (mmtm) REVERT: P 67 ILE cc_start: 0.8011 (tt) cc_final: 0.7562 (mt) REVERT: P 231 LYS cc_start: 0.7814 (mtpm) cc_final: 0.7404 (mmtm) REVERT: Q 67 ILE cc_start: 0.7812 (tt) cc_final: 0.7383 (mt) REVERT: Q 70 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8668 (mt) REVERT: Q 143 GLN cc_start: 0.8528 (tp40) cc_final: 0.7900 (pt0) REVERT: R 40 MET cc_start: 0.8098 (ptp) cc_final: 0.7863 (ptp) REVERT: R 70 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8698 (mt) REVERT: R 224 TYR cc_start: 0.8502 (m-10) cc_final: 0.8052 (m-10) REVERT: S 20 ARG cc_start: 0.8632 (mtp180) cc_final: 0.8305 (mtp180) REVERT: S 70 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8805 (mt) REVERT: S 106 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8393 (tp) REVERT: S 230 LYS cc_start: 0.6954 (ttmt) cc_final: 0.6687 (mtmt) REVERT: T 20 ARG cc_start: 0.8434 (mtp180) cc_final: 0.8013 (mtm180) REVERT: T 70 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8670 (mt) REVERT: U 67 ILE cc_start: 0.8049 (tt) cc_final: 0.7461 (mt) REVERT: U 70 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8697 (mt) REVERT: U 99 GLU cc_start: 0.7859 (tp30) cc_final: 0.6782 (mm-30) REVERT: H 62 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7389 (mt-10) REVERT: H 172 MET cc_start: 0.8438 (tpt) cc_final: 0.8162 (tpt) REVERT: I 64 GLU cc_start: 0.8126 (tt0) cc_final: 0.7827 (tt0) REVERT: K 14 MET cc_start: 0.9053 (mtm) cc_final: 0.8826 (mtp) REVERT: K 18 ARG cc_start: 0.8332 (ptp-170) cc_final: 0.8043 (ptm160) REVERT: K 25 PHE cc_start: 0.9005 (t80) cc_final: 0.8584 (t80) REVERT: K 64 GLU cc_start: 0.7991 (tt0) cc_final: 0.7723 (tt0) REVERT: M 45 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8979 (pp) REVERT: M 62 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7376 (mt-10) REVERT: M 89 GLN cc_start: 0.8348 (mt0) cc_final: 0.8056 (mm-40) REVERT: N 66 TYR cc_start: 0.8542 (t80) cc_final: 0.8341 (t80) REVERT: V 30 ASN cc_start: 0.8726 (OUTLIER) cc_final: 0.8485 (m110) REVERT: V 71 ARG cc_start: 0.7924 (mtt90) cc_final: 0.7569 (mtm110) REVERT: V 88 ASN cc_start: 0.9100 (t0) cc_final: 0.8860 (t0) REVERT: V 146 MET cc_start: 0.9013 (mtp) cc_final: 0.8695 (mtm) REVERT: W 18 ARG cc_start: 0.8400 (ptp-170) cc_final: 0.8166 (ptm160) REVERT: W 67 ARG cc_start: 0.7468 (ttp80) cc_final: 0.7217 (ttp-170) REVERT: X 88 ASN cc_start: 0.9020 (t0) cc_final: 0.8768 (t0) REVERT: Y 67 ARG cc_start: 0.7798 (tmm-80) cc_final: 0.7351 (ttp80) REVERT: a 18 ARG cc_start: 0.8440 (ptm160) cc_final: 0.8148 (mtm180) REVERT: a 70 ARG cc_start: 0.6663 (OUTLIER) cc_final: 0.4477 (mpt180) REVERT: a 88 ASN cc_start: 0.8917 (t0) cc_final: 0.8705 (t0) REVERT: b 67 ARG cc_start: 0.7944 (tmm-80) cc_final: 0.7526 (ttp80) outliers start: 115 outliers final: 55 residues processed: 914 average time/residue: 0.2708 time to fit residues: 402.2871 Evaluate side-chains 780 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 713 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 194 ILE Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 173 VAL Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain R residue 70 ILE Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain T residue 173 VAL Chi-restraints excluded: chain U residue 70 ILE Chi-restraints excluded: chain U residue 173 VAL Chi-restraints excluded: chain U residue 194 ILE Chi-restraints excluded: chain U residue 212 ILE Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 196 ILE Chi-restraints excluded: chain K residue 196 ILE Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 62 GLU Chi-restraints excluded: chain M residue 196 ILE Chi-restraints excluded: chain N residue 30 ASN Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain V residue 30 ASN Chi-restraints excluded: chain W residue 27 MET Chi-restraints excluded: chain Y residue 30 ASN Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain a residue 30 ASN Chi-restraints excluded: chain a residue 70 ARG Chi-restraints excluded: chain b residue 30 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 407 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 386 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 313 optimal weight: 3.9990 chunk 261 optimal weight: 0.2980 chunk 7 optimal weight: 6.9990 chunk 374 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 264 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN E 111 ASN F 108 ASN F 111 ASN G 108 ASN G 111 ASN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 GLN H 30 ASN J 141 GLN K 30 ASN M 30 ASN N 30 ASN ** V 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 30 ASN a 89 GLN a 141 GLN b 89 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.142470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.112905 restraints weight = 52688.002| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.22 r_work: 0.3008 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 46991 Z= 0.141 Angle : 0.579 10.241 63434 Z= 0.312 Chirality : 0.044 0.159 7441 Planarity : 0.004 0.057 8134 Dihedral : 4.893 40.999 6582 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.92 % Favored : 96.96 % Rotamer: Outliers : 3.00 % Allowed : 10.66 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.11), residues: 5950 helix: 1.73 (0.11), residues: 2289 sheet: -0.23 (0.14), residues: 1309 loop : -2.16 (0.11), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 18 TYR 0.015 0.001 TYR R 8 PHE 0.016 0.002 PHE T 15 HIS 0.004 0.002 HIS Z 109 Details of bonding type rmsd covalent geometry : bond 0.00336 (46991) covalent geometry : angle 0.57860 (63434) hydrogen bonds : bond 0.05057 ( 2538) hydrogen bonds : angle 4.42130 ( 7401) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 731 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8961 (mtp) cc_final: 0.8483 (mtm) REVERT: B 18 ASP cc_start: 0.8278 (p0) cc_final: 0.7855 (t0) REVERT: D 18 ASP cc_start: 0.8839 (t0) cc_final: 0.8602 (t0) REVERT: E 70 ILE cc_start: 0.9267 (mm) cc_final: 0.8947 (mt) REVERT: O 20 ARG cc_start: 0.9059 (mtp180) cc_final: 0.8780 (mtp180) REVERT: O 70 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8732 (mt) REVERT: O 122 GLN cc_start: 0.8779 (tt0) cc_final: 0.8465 (tt0) REVERT: O 143 GLN cc_start: 0.8667 (tp40) cc_final: 0.7979 (pt0) REVERT: P 143 GLN cc_start: 0.8476 (tp40) cc_final: 0.7672 (pt0) REVERT: P 181 LYS cc_start: 0.7357 (mtmt) cc_final: 0.7013 (ptmm) REVERT: P 223 ILE cc_start: 0.8249 (mp) cc_final: 0.8028 (mp) REVERT: Q 70 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8718 (mt) REVERT: Q 99 GLU cc_start: 0.8392 (tp30) cc_final: 0.8183 (tt0) REVERT: Q 143 GLN cc_start: 0.8586 (tp40) cc_final: 0.7766 (pt0) REVERT: Q 160 TYR cc_start: 0.8731 (m-10) cc_final: 0.8148 (m-10) REVERT: R 40 MET cc_start: 0.8600 (ptp) cc_final: 0.8348 (ptp) REVERT: R 70 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8730 (mt) REVERT: R 99 GLU cc_start: 0.8524 (tp30) cc_final: 0.8272 (tt0) REVERT: S 70 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8845 (mt) REVERT: S 99 GLU cc_start: 0.8413 (tp30) cc_final: 0.8157 (tt0) REVERT: S 181 LYS cc_start: 0.7565 (mtmt) cc_final: 0.7170 (ptmm) REVERT: T 70 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8865 (mt) REVERT: U 40 MET cc_start: 0.8390 (ptp) cc_final: 0.8176 (ptt) REVERT: U 70 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8699 (mt) REVERT: U 143 GLN cc_start: 0.8488 (tp40) cc_final: 0.7521 (pt0) REVERT: U 182 GLU cc_start: 0.8503 (pm20) cc_final: 0.8212 (pm20) REVERT: H 62 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: H 172 MET cc_start: 0.8592 (tpt) cc_final: 0.8339 (tpt) REVERT: I 64 GLU cc_start: 0.8314 (tt0) cc_final: 0.8026 (tt0) REVERT: J 62 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7671 (mt-10) REVERT: K 14 MET cc_start: 0.9182 (mtm) cc_final: 0.8943 (mtp) REVERT: K 64 GLU cc_start: 0.8290 (tt0) cc_final: 0.8003 (tt0) REVERT: L 30 ASN cc_start: 0.8807 (t0) cc_final: 0.8556 (t0) REVERT: M 27 MET cc_start: 0.8570 (tpt) cc_final: 0.7026 (mtt) REVERT: M 45 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.9030 (pp) REVERT: M 62 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7657 (mm-30) REVERT: M 89 GLN cc_start: 0.8641 (mt0) cc_final: 0.8218 (mm110) REVERT: V 71 ARG cc_start: 0.8214 (mtt90) cc_final: 0.7886 (mtm-85) REVERT: V 88 ASN cc_start: 0.9114 (t0) cc_final: 0.8880 (t0) REVERT: V 146 MET cc_start: 0.9109 (mtp) cc_final: 0.8763 (mtp) REVERT: V 195 ARG cc_start: 0.6661 (mmt-90) cc_final: 0.6177 (mmt180) REVERT: W 18 ARG cc_start: 0.8717 (ptp-170) cc_final: 0.8506 (ptm160) REVERT: X 88 ASN cc_start: 0.9048 (t0) cc_final: 0.8842 (t0) REVERT: X 99 LEU cc_start: 0.8938 (pp) cc_final: 0.8652 (pt) REVERT: X 146 MET cc_start: 0.9305 (mtm) cc_final: 0.9092 (mtm) REVERT: Y 67 ARG cc_start: 0.8149 (tmm-80) cc_final: 0.7930 (ttp80) REVERT: Y 98 GLN cc_start: 0.8723 (tt0) cc_final: 0.8044 (pt0) REVERT: Y 99 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8578 (pt) REVERT: Z 62 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7736 (mt-10) REVERT: Z 96 MET cc_start: 0.8348 (mmt) cc_final: 0.7972 (mmt) REVERT: a 18 ARG cc_start: 0.8625 (ptm160) cc_final: 0.8262 (mtm180) REVERT: a 70 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.5009 (mpt180) REVERT: a 88 ASN cc_start: 0.8906 (t0) cc_final: 0.8670 (t0) REVERT: a 98 GLN cc_start: 0.8763 (tt0) cc_final: 0.8113 (pt0) REVERT: b 67 ARG cc_start: 0.8210 (tmm-80) cc_final: 0.7670 (ttp80) outliers start: 150 outliers final: 74 residues processed: 837 average time/residue: 0.2739 time to fit residues: 373.0092 Evaluate side-chains 755 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 668 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 108 ASN Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 108 ASN Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 194 ILE Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 229 VAL Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 173 VAL Chi-restraints excluded: chain P residue 194 ILE Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain Q residue 12 ILE Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain Q residue 229 VAL Chi-restraints excluded: chain R residue 70 ILE Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 229 VAL Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 173 VAL Chi-restraints excluded: chain U residue 70 ILE Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain U residue 173 VAL Chi-restraints excluded: chain U residue 212 ILE Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain M residue 30 ASN Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 62 GLU Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 30 ASN Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Z residue 62 GLU Chi-restraints excluded: chain a residue 70 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 57 optimal weight: 0.4980 chunk 63 optimal weight: 9.9990 chunk 166 optimal weight: 0.8980 chunk 216 optimal weight: 7.9990 chunk 523 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 310 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 chunk 129 optimal weight: 6.9990 chunk 244 optimal weight: 0.8980 chunk 300 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN E 111 ASN F 108 ASN F 111 ASN G 108 ASN G 111 ASN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN I 30 ASN K 30 ASN N 30 ASN ** V 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 30 ASN Y 89 GLN b 69 GLN b 89 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.144119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.114905 restraints weight = 52171.928| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.22 r_work: 0.3017 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 46991 Z= 0.109 Angle : 0.513 8.948 63434 Z= 0.278 Chirality : 0.043 0.148 7441 Planarity : 0.004 0.042 8134 Dihedral : 4.571 37.250 6580 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.59 % Favored : 97.29 % Rotamer: Outliers : 2.48 % Allowed : 12.38 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.11), residues: 5950 helix: 2.09 (0.11), residues: 2289 sheet: -0.03 (0.14), residues: 1309 loop : -1.91 (0.11), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 70 TYR 0.011 0.001 TYR R 8 PHE 0.014 0.001 PHE U 175 HIS 0.005 0.001 HIS M 28 Details of bonding type rmsd covalent geometry : bond 0.00254 (46991) covalent geometry : angle 0.51276 (63434) hydrogen bonds : bond 0.03892 ( 2538) hydrogen bonds : angle 4.16291 ( 7401) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 712 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.7744 (tt0) cc_final: 0.7401 (mt0) REVERT: A 120 MET cc_start: 0.8933 (mtp) cc_final: 0.8457 (mtm) REVERT: B 120 MET cc_start: 0.8806 (mtp) cc_final: 0.8317 (mtp) REVERT: C 48 LEU cc_start: 0.8974 (mt) cc_final: 0.8728 (mp) REVERT: D 18 ASP cc_start: 0.8884 (t0) cc_final: 0.8567 (t0) REVERT: F 18 ASP cc_start: 0.8434 (p0) cc_final: 0.7999 (t70) REVERT: F 98 GLN cc_start: 0.7791 (tt0) cc_final: 0.7569 (tt0) REVERT: G 44 ASN cc_start: 0.8514 (t0) cc_final: 0.8282 (t0) REVERT: G 98 GLN cc_start: 0.8004 (tt0) cc_final: 0.7591 (mt0) REVERT: O 20 ARG cc_start: 0.9068 (mtp180) cc_final: 0.8800 (mtp180) REVERT: O 70 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8691 (mt) REVERT: O 122 GLN cc_start: 0.8648 (tt0) cc_final: 0.8374 (tt0) REVERT: O 143 GLN cc_start: 0.8599 (tp40) cc_final: 0.7901 (pt0) REVERT: P 143 GLN cc_start: 0.8510 (tp40) cc_final: 0.7702 (pt0) REVERT: P 181 LYS cc_start: 0.7317 (mtmt) cc_final: 0.6957 (ptmm) REVERT: Q 70 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8716 (mt) REVERT: Q 143 GLN cc_start: 0.8508 (tp40) cc_final: 0.7725 (pt0) REVERT: Q 160 TYR cc_start: 0.8734 (m-10) cc_final: 0.8320 (m-10) REVERT: R 67 ILE cc_start: 0.8373 (tt) cc_final: 0.7815 (mt) REVERT: R 70 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8709 (mt) REVERT: R 99 GLU cc_start: 0.8478 (tp30) cc_final: 0.8234 (tt0) REVERT: S 70 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8765 (mt) REVERT: S 99 GLU cc_start: 0.8401 (tp30) cc_final: 0.8128 (tt0) REVERT: S 181 LYS cc_start: 0.7597 (mtmt) cc_final: 0.7103 (ptmm) REVERT: S 230 LYS cc_start: 0.7632 (ttmt) cc_final: 0.7163 (mmmt) REVERT: T 70 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8917 (mp) REVERT: U 40 MET cc_start: 0.8379 (ptp) cc_final: 0.8159 (ptt) REVERT: U 70 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8647 (mp) REVERT: U 143 GLN cc_start: 0.8493 (tp40) cc_final: 0.7554 (pt0) REVERT: H 62 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7646 (mt-10) REVERT: I 64 GLU cc_start: 0.8287 (tt0) cc_final: 0.7991 (tt0) REVERT: J 145 LYS cc_start: 0.9147 (mmmt) cc_final: 0.8929 (mmtm) REVERT: K 14 MET cc_start: 0.9171 (mtm) cc_final: 0.8948 (mtp) REVERT: K 64 GLU cc_start: 0.8240 (tt0) cc_final: 0.7938 (tt0) REVERT: K 192 ILE cc_start: 0.7430 (mm) cc_final: 0.7184 (mt) REVERT: L 14 MET cc_start: 0.9070 (mtm) cc_final: 0.8802 (mtt) REVERT: L 98 GLN cc_start: 0.9006 (mt0) cc_final: 0.8531 (pt0) REVERT: M 45 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8886 (pp) REVERT: M 89 GLN cc_start: 0.8601 (mt0) cc_final: 0.8082 (mm110) REVERT: V 88 ASN cc_start: 0.9092 (t0) cc_final: 0.8860 (t0) REVERT: V 98 GLN cc_start: 0.8575 (tt0) cc_final: 0.8045 (pt0) REVERT: V 146 MET cc_start: 0.9102 (mtp) cc_final: 0.8711 (mtp) REVERT: V 195 ARG cc_start: 0.6682 (mmt-90) cc_final: 0.6347 (mmt-90) REVERT: W 18 ARG cc_start: 0.8769 (ptp-170) cc_final: 0.8551 (ptm160) REVERT: W 98 GLN cc_start: 0.8636 (tt0) cc_final: 0.7986 (pt0) REVERT: W 146 MET cc_start: 0.9263 (mtm) cc_final: 0.9010 (ptp) REVERT: X 98 GLN cc_start: 0.8460 (tt0) cc_final: 0.8117 (pt0) REVERT: Y 98 GLN cc_start: 0.8619 (tt0) cc_final: 0.8117 (pt0) REVERT: Y 146 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8669 (mtp) REVERT: Y 198 LYS cc_start: 0.7886 (tttm) cc_final: 0.7567 (ttpt) REVERT: Z 62 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7751 (mm-30) REVERT: Z 96 MET cc_start: 0.8372 (mmt) cc_final: 0.8039 (mmt) REVERT: Z 98 GLN cc_start: 0.8640 (tt0) cc_final: 0.8080 (pt0) REVERT: Z 141 GLN cc_start: 0.8812 (mt0) cc_final: 0.8530 (mt0) REVERT: Z 144 GLU cc_start: 0.7983 (tp30) cc_final: 0.7781 (tp30) REVERT: a 70 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.5068 (mpt180) REVERT: a 88 ASN cc_start: 0.8886 (t0) cc_final: 0.8646 (t0) REVERT: a 98 GLN cc_start: 0.8634 (tt0) cc_final: 0.8038 (pt0) REVERT: b 67 ARG cc_start: 0.8159 (tmm-80) cc_final: 0.7633 (ttp80) REVERT: b 98 GLN cc_start: 0.8545 (tt0) cc_final: 0.8170 (pt0) outliers start: 124 outliers final: 78 residues processed: 787 average time/residue: 0.2595 time to fit residues: 329.9627 Evaluate side-chains 765 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 676 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 108 ASN Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 108 ASN Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 212 ILE Chi-restraints excluded: chain O residue 229 VAL Chi-restraints excluded: chain P residue 12 ILE Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 173 VAL Chi-restraints excluded: chain P residue 194 ILE Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain R residue 70 ILE Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 122 GLN Chi-restraints excluded: chain S residue 173 VAL Chi-restraints excluded: chain S residue 212 ILE Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain U residue 70 ILE Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 107 VAL Chi-restraints excluded: chain U residue 173 VAL Chi-restraints excluded: chain U residue 194 ILE Chi-restraints excluded: chain U residue 206 GLU Chi-restraints excluded: chain U residue 212 ILE Chi-restraints excluded: chain H residue 30 ASN Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain L residue 141 GLN Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 98 GLN Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain W residue 27 MET Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain X residue 30 ASN Chi-restraints excluded: chain Y residue 68 LEU Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 146 MET Chi-restraints excluded: chain Z residue 62 GLU Chi-restraints excluded: chain Z residue 146 MET Chi-restraints excluded: chain a residue 70 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 449 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 437 optimal weight: 2.9990 chunk 577 optimal weight: 2.9990 chunk 469 optimal weight: 2.9990 chunk 372 optimal weight: 7.9990 chunk 519 optimal weight: 4.9990 chunk 582 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 508 optimal weight: 4.9990 chunk 409 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN F 108 ASN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN J 30 ASN K 30 ASN L 30 ASN N 30 ASN N 88 ASN N 141 GLN ** V 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 30 ASN Y 73 ASN ** Y 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 GLN Y 141 GLN b 69 GLN b 88 ASN b 89 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.133391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.104726 restraints weight = 52748.726| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.21 r_work: 0.2876 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 46991 Z= 0.219 Angle : 0.644 10.890 63434 Z= 0.343 Chirality : 0.046 0.138 7441 Planarity : 0.004 0.049 8134 Dihedral : 5.159 48.516 6580 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.31 % Favored : 96.57 % Rotamer: Outliers : 3.36 % Allowed : 12.51 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.11), residues: 5950 helix: 1.86 (0.11), residues: 2275 sheet: 0.11 (0.14), residues: 1267 loop : -1.97 (0.10), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Y 67 TYR 0.020 0.002 TYR R 8 PHE 0.025 0.002 PHE T 175 HIS 0.008 0.002 HIS H 28 Details of bonding type rmsd covalent geometry : bond 0.00557 (46991) covalent geometry : angle 0.64376 (63434) hydrogen bonds : bond 0.06492 ( 2538) hydrogen bonds : angle 4.53489 ( 7401) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 664 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.7691 (tt0) cc_final: 0.7353 (mt0) REVERT: A 120 MET cc_start: 0.8935 (mtp) cc_final: 0.8575 (mtm) REVERT: A 221 TYR cc_start: 0.9364 (OUTLIER) cc_final: 0.7795 (m-80) REVERT: B 18 ASP cc_start: 0.9018 (t0) cc_final: 0.8815 (t0) REVERT: B 49 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8633 (mt) REVERT: C 221 TYR cc_start: 0.9375 (OUTLIER) cc_final: 0.7972 (m-80) REVERT: D 18 ASP cc_start: 0.8925 (t0) cc_final: 0.8650 (t0) REVERT: D 98 GLN cc_start: 0.8268 (tt0) cc_final: 0.7983 (tt0) REVERT: D 232 PHE cc_start: 0.7892 (m-80) cc_final: 0.7548 (m-80) REVERT: E 49 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8596 (mt) REVERT: E 221 TYR cc_start: 0.9406 (OUTLIER) cc_final: 0.8511 (m-80) REVERT: F 98 GLN cc_start: 0.7969 (tt0) cc_final: 0.7569 (mt0) REVERT: G 18 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8018 (t0) REVERT: G 44 ASN cc_start: 0.8759 (t0) cc_final: 0.8430 (t0) REVERT: G 98 GLN cc_start: 0.8046 (tt0) cc_final: 0.7667 (mt0) REVERT: O 10 ARG cc_start: 0.8938 (mpt-90) cc_final: 0.8729 (mmt-90) REVERT: O 20 ARG cc_start: 0.9134 (mtp180) cc_final: 0.8870 (mtp180) REVERT: O 70 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8860 (mt) REVERT: O 122 GLN cc_start: 0.8705 (tt0) cc_final: 0.8424 (tt0) REVERT: O 143 GLN cc_start: 0.8549 (tp40) cc_final: 0.7779 (pt0) REVERT: P 143 GLN cc_start: 0.8480 (tp40) cc_final: 0.7710 (pt0) REVERT: P 181 LYS cc_start: 0.7801 (mtmt) cc_final: 0.7372 (ptmm) REVERT: Q 20 ARG cc_start: 0.9156 (mtm180) cc_final: 0.8828 (mtm180) REVERT: Q 70 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.8878 (mt) REVERT: R 70 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8736 (mt) REVERT: R 99 GLU cc_start: 0.8472 (tp30) cc_final: 0.8216 (tt0) REVERT: R 181 LYS cc_start: 0.7991 (mtmt) cc_final: 0.7543 (ptmm) REVERT: R 230 LYS cc_start: 0.7868 (ttmt) cc_final: 0.7571 (mmmt) REVERT: S 70 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.8922 (mt) REVERT: S 106 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8705 (tp) REVERT: S 114 LYS cc_start: 0.8221 (tppt) cc_final: 0.7247 (tttp) REVERT: S 177 GLU cc_start: 0.8466 (tp30) cc_final: 0.8252 (tp30) REVERT: S 181 LYS cc_start: 0.7989 (mtmt) cc_final: 0.7503 (ptmm) REVERT: S 230 LYS cc_start: 0.7907 (ttmt) cc_final: 0.7385 (mmmt) REVERT: T 40 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8717 (ptm) REVERT: T 70 ILE cc_start: 0.9277 (OUTLIER) cc_final: 0.8998 (mp) REVERT: T 181 LYS cc_start: 0.8014 (mtmt) cc_final: 0.7537 (ttpp) REVERT: U 40 MET cc_start: 0.8774 (ptp) cc_final: 0.8534 (ptp) REVERT: U 70 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.8837 (mt) REVERT: U 143 GLN cc_start: 0.8505 (tp40) cc_final: 0.7645 (pt0) REVERT: H 62 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: H 195 ARG cc_start: 0.6558 (mmt180) cc_final: 0.6086 (mtt-85) REVERT: J 64 GLU cc_start: 0.8397 (tt0) cc_final: 0.8052 (tt0) REVERT: M 45 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8824 (pp) REVERT: M 89 GLN cc_start: 0.8863 (mt0) cc_final: 0.8505 (mm-40) REVERT: M 145 LYS cc_start: 0.9188 (mmmt) cc_final: 0.8883 (mppt) REVERT: M 195 ARG cc_start: 0.6399 (mmt180) cc_final: 0.5877 (mtt-85) REVERT: V 64 GLU cc_start: 0.8317 (tt0) cc_final: 0.8069 (tt0) REVERT: V 88 ASN cc_start: 0.9186 (t0) cc_final: 0.8884 (t0) REVERT: V 146 MET cc_start: 0.9184 (mtp) cc_final: 0.8873 (mtp) REVERT: Y 98 GLN cc_start: 0.8796 (tt0) cc_final: 0.8081 (pt0) REVERT: Y 141 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8729 (mt0) REVERT: Y 198 LYS cc_start: 0.7968 (tttm) cc_final: 0.7651 (ttpt) REVERT: Z 43 MET cc_start: 0.9506 (ttt) cc_final: 0.9291 (ttt) REVERT: a 70 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.5740 (mpt180) REVERT: a 88 ASN cc_start: 0.8982 (t0) cc_final: 0.8706 (t0) REVERT: a 98 GLN cc_start: 0.8787 (tt0) cc_final: 0.8446 (tt0) REVERT: b 67 ARG cc_start: 0.8463 (tmm-80) cc_final: 0.8067 (ttp80) outliers start: 168 outliers final: 108 residues processed: 775 average time/residue: 0.2436 time to fit residues: 305.4085 Evaluate side-chains 728 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 602 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 108 ASN Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 212 ILE Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 173 VAL Chi-restraints excluded: chain P residue 194 ILE Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 70 ILE Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 122 GLN Chi-restraints excluded: chain S residue 173 VAL Chi-restraints excluded: chain S residue 212 ILE Chi-restraints excluded: chain T residue 20 ARG Chi-restraints excluded: chain T residue 40 MET Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 173 VAL Chi-restraints excluded: chain T residue 222 ARG Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 70 ILE Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 107 VAL Chi-restraints excluded: chain U residue 173 VAL Chi-restraints excluded: chain U residue 174 SER Chi-restraints excluded: chain U residue 182 GLU Chi-restraints excluded: chain U residue 206 GLU Chi-restraints excluded: chain U residue 212 ILE Chi-restraints excluded: chain H residue 30 ASN Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 30 ASN Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 98 GLN Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain W residue 27 MET Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 141 GLN Chi-restraints excluded: chain Z residue 146 MET Chi-restraints excluded: chain a residue 70 ARG Chi-restraints excluded: chain b residue 157 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 466 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 217 optimal weight: 10.0000 chunk 308 optimal weight: 0.9990 chunk 468 optimal weight: 0.7980 chunk 533 optimal weight: 0.7980 chunk 433 optimal weight: 0.6980 chunk 325 optimal weight: 1.9990 chunk 252 optimal weight: 5.9990 chunk 226 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 98 GLN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN J 30 ASN K 30 ASN L 30 ASN M 30 ASN V 69 GLN ** Y 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 69 GLN a 89 GLN b 69 GLN b 88 ASN b 89 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.136097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.106942 restraints weight = 53289.279| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.29 r_work: 0.3086 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 46991 Z= 0.106 Angle : 0.513 9.516 63434 Z= 0.278 Chirality : 0.043 0.142 7441 Planarity : 0.003 0.041 8134 Dihedral : 4.634 43.756 6580 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.79 % Favored : 97.09 % Rotamer: Outliers : 2.74 % Allowed : 14.07 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.11), residues: 5950 helix: 2.20 (0.11), residues: 2289 sheet: -0.17 (0.14), residues: 1400 loop : -1.85 (0.11), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 178 TYR 0.010 0.001 TYR R 8 PHE 0.025 0.001 PHE R 175 HIS 0.003 0.001 HIS a 109 Details of bonding type rmsd covalent geometry : bond 0.00247 (46991) covalent geometry : angle 0.51318 (63434) hydrogen bonds : bond 0.03909 ( 2538) hydrogen bonds : angle 4.16366 ( 7401) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 670 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.7595 (tt0) cc_final: 0.7183 (tt0) REVERT: B 49 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8555 (mt) REVERT: B 120 MET cc_start: 0.8733 (mtp) cc_final: 0.8346 (mtp) REVERT: C 18 ASP cc_start: 0.8419 (p0) cc_final: 0.8110 (t70) REVERT: C 98 GLN cc_start: 0.7991 (tt0) cc_final: 0.7485 (tt0) REVERT: C 221 TYR cc_start: 0.9159 (OUTLIER) cc_final: 0.7573 (m-80) REVERT: D 18 ASP cc_start: 0.8964 (t0) cc_final: 0.8707 (t0) REVERT: D 98 GLN cc_start: 0.8119 (tt0) cc_final: 0.7818 (tt0) REVERT: E 49 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8526 (mt) REVERT: E 178 ARG cc_start: 0.7766 (ttp80) cc_final: 0.7560 (ttm170) REVERT: E 221 TYR cc_start: 0.9149 (OUTLIER) cc_final: 0.8097 (m-80) REVERT: F 18 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8006 (t70) REVERT: F 98 GLN cc_start: 0.7670 (tt0) cc_final: 0.7357 (mt0) REVERT: G 18 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.8000 (t0) REVERT: G 98 GLN cc_start: 0.7885 (tt0) cc_final: 0.7496 (mt0) REVERT: O 20 ARG cc_start: 0.9054 (mtp180) cc_final: 0.8804 (mtp180) REVERT: O 70 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8662 (mt) REVERT: O 122 GLN cc_start: 0.8648 (tt0) cc_final: 0.8334 (tt0) REVERT: O 143 GLN cc_start: 0.8507 (tp40) cc_final: 0.7752 (pt0) REVERT: O 160 TYR cc_start: 0.9134 (m-80) cc_final: 0.8877 (m-80) REVERT: P 143 GLN cc_start: 0.8459 (tp40) cc_final: 0.7709 (pt0) REVERT: P 181 LYS cc_start: 0.7544 (mtmt) cc_final: 0.7047 (ptmm) REVERT: Q 70 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8709 (mt) REVERT: Q 72 ASP cc_start: 0.8830 (OUTLIER) cc_final: 0.8596 (t0) REVERT: R 70 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8580 (mt) REVERT: R 99 GLU cc_start: 0.8406 (tp30) cc_final: 0.8198 (tt0) REVERT: R 230 LYS cc_start: 0.7888 (ttmt) cc_final: 0.7556 (mmmt) REVERT: S 70 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8718 (mt) REVERT: S 143 GLN cc_start: 0.8488 (tp40) cc_final: 0.7764 (pt0) REVERT: S 181 LYS cc_start: 0.7707 (mtmt) cc_final: 0.7075 (ptmm) REVERT: S 230 LYS cc_start: 0.7905 (ttmt) cc_final: 0.7361 (mmmt) REVERT: T 40 MET cc_start: 0.8891 (ptp) cc_final: 0.8552 (ptm) REVERT: T 67 ILE cc_start: 0.8495 (tt) cc_final: 0.8187 (mt) REVERT: T 70 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8816 (mp) REVERT: U 70 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8619 (mp) REVERT: U 143 GLN cc_start: 0.8506 (tp40) cc_final: 0.7530 (pt0) REVERT: H 62 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7536 (mt-10) REVERT: I 139 GLU cc_start: 0.8681 (tp30) cc_final: 0.8218 (tp30) REVERT: K 14 MET cc_start: 0.9152 (mtm) cc_final: 0.8866 (mtp) REVERT: M 45 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8806 (pp) REVERT: M 89 GLN cc_start: 0.8644 (mt0) cc_final: 0.8010 (mm110) REVERT: V 88 ASN cc_start: 0.9061 (t0) cc_final: 0.8807 (t0) REVERT: V 98 GLN cc_start: 0.8508 (tt0) cc_final: 0.7975 (pt0) REVERT: V 146 MET cc_start: 0.9055 (mtp) cc_final: 0.8699 (mtp) REVERT: V 195 ARG cc_start: 0.6694 (mmt-90) cc_final: 0.6364 (mmt-90) REVERT: W 98 GLN cc_start: 0.8612 (tt0) cc_final: 0.8025 (pt0) REVERT: W 146 MET cc_start: 0.9205 (mtm) cc_final: 0.8997 (ptp) REVERT: X 98 GLN cc_start: 0.8421 (tt0) cc_final: 0.8130 (pt0) REVERT: X 99 LEU cc_start: 0.8959 (pp) cc_final: 0.8704 (pt) REVERT: Y 98 GLN cc_start: 0.8633 (tt0) cc_final: 0.8064 (pt0) REVERT: Y 146 MET cc_start: 0.9191 (mtm) cc_final: 0.8831 (mtp) REVERT: Y 198 LYS cc_start: 0.7882 (tttm) cc_final: 0.7545 (ttpt) REVERT: Z 43 MET cc_start: 0.9458 (ttt) cc_final: 0.9223 (ttt) REVERT: Z 62 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7558 (mt-10) REVERT: Z 141 GLN cc_start: 0.8788 (mt0) cc_final: 0.8466 (mt0) REVERT: a 88 ASN cc_start: 0.8864 (t0) cc_final: 0.8635 (t0) REVERT: a 98 GLN cc_start: 0.8665 (tt0) cc_final: 0.8067 (pt0) REVERT: a 198 LYS cc_start: 0.8231 (ttmm) cc_final: 0.7883 (ttpt) REVERT: b 67 ARG cc_start: 0.8299 (tmm-80) cc_final: 0.7858 (ttp80) REVERT: b 98 GLN cc_start: 0.8515 (tt0) cc_final: 0.8204 (pt0) outliers start: 137 outliers final: 90 residues processed: 757 average time/residue: 0.2596 time to fit residues: 318.3904 Evaluate side-chains 754 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 648 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 212 ILE Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 194 ILE Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain Q residue 194 ILE Chi-restraints excluded: chain Q residue 206 GLU Chi-restraints excluded: chain R residue 70 ILE Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 122 GLN Chi-restraints excluded: chain S residue 212 ILE Chi-restraints excluded: chain T residue 20 ARG Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 173 VAL Chi-restraints excluded: chain T residue 222 ARG Chi-restraints excluded: chain U residue 70 ILE Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 174 SER Chi-restraints excluded: chain U residue 182 GLU Chi-restraints excluded: chain U residue 212 ILE Chi-restraints excluded: chain H residue 30 ASN Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain L residue 141 GLN Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 98 GLN Chi-restraints excluded: chain W residue 27 MET Chi-restraints excluded: chain X residue 30 ASN Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Z residue 62 GLU Chi-restraints excluded: chain Z residue 146 MET Chi-restraints excluded: chain b residue 44 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 463 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 548 optimal weight: 4.9990 chunk 460 optimal weight: 0.8980 chunk 418 optimal weight: 1.9990 chunk 272 optimal weight: 3.9990 chunk 394 optimal weight: 0.5980 chunk 139 optimal weight: 4.9990 chunk 576 optimal weight: 0.8980 chunk 316 optimal weight: 3.9990 chunk 501 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN E 98 GLN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 GLN T 23 GLN H 30 ASN J 30 ASN K 30 ASN M 30 ASN N 30 ASN W 69 GLN X 69 GLN ** Y 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 69 GLN a 89 GLN b 89 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.142592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.114633 restraints weight = 51996.690| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.14 r_work: 0.3000 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 46991 Z= 0.103 Angle : 0.506 11.164 63434 Z= 0.272 Chirality : 0.042 0.138 7441 Planarity : 0.003 0.039 8134 Dihedral : 4.434 35.385 6580 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.50 % Favored : 97.38 % Rotamer: Outliers : 2.52 % Allowed : 14.41 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.11), residues: 5950 helix: 2.34 (0.11), residues: 2289 sheet: -0.16 (0.14), residues: 1421 loop : -1.72 (0.11), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 178 TYR 0.008 0.001 TYR R 8 PHE 0.026 0.001 PHE U 175 HIS 0.003 0.001 HIS H 28 Details of bonding type rmsd covalent geometry : bond 0.00238 (46991) covalent geometry : angle 0.50612 (63434) hydrogen bonds : bond 0.03834 ( 2538) hydrogen bonds : angle 4.07628 ( 7401) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 665 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.7781 (tt0) cc_final: 0.7442 (tt0) REVERT: A 221 TYR cc_start: 0.9126 (OUTLIER) cc_final: 0.8722 (m-80) REVERT: B 49 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8670 (mt) REVERT: C 18 ASP cc_start: 0.8354 (p0) cc_final: 0.8147 (t70) REVERT: C 98 GLN cc_start: 0.8159 (tt0) cc_final: 0.7634 (tt0) REVERT: D 18 ASP cc_start: 0.8998 (t0) cc_final: 0.8731 (t0) REVERT: D 98 GLN cc_start: 0.8306 (tt0) cc_final: 0.8098 (tt0) REVERT: D 221 TYR cc_start: 0.9423 (OUTLIER) cc_final: 0.8773 (m-80) REVERT: E 49 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8615 (mt) REVERT: E 221 TYR cc_start: 0.9138 (OUTLIER) cc_final: 0.8104 (m-80) REVERT: F 98 GLN cc_start: 0.7910 (tt0) cc_final: 0.7676 (tt0) REVERT: F 178 ARG cc_start: 0.7925 (ttp80) cc_final: 0.7377 (ttm170) REVERT: G 44 ASN cc_start: 0.8509 (t0) cc_final: 0.8256 (t0) REVERT: G 98 GLN cc_start: 0.8028 (tt0) cc_final: 0.7653 (tt0) REVERT: O 18 ASP cc_start: 0.8710 (m-30) cc_final: 0.8273 (m-30) REVERT: O 20 ARG cc_start: 0.9091 (mtp180) cc_final: 0.8886 (mtp180) REVERT: O 70 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8719 (mt) REVERT: O 122 GLN cc_start: 0.8651 (tt0) cc_final: 0.8345 (tt0) REVERT: O 143 GLN cc_start: 0.8461 (tp40) cc_final: 0.7684 (pt0) REVERT: O 160 TYR cc_start: 0.9182 (m-80) cc_final: 0.8895 (m-80) REVERT: P 143 GLN cc_start: 0.8464 (tp40) cc_final: 0.7748 (pt0) REVERT: P 181 LYS cc_start: 0.7722 (mtmt) cc_final: 0.7253 (ptmm) REVERT: P 212 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8535 (mt) REVERT: Q 70 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8723 (mt) REVERT: Q 72 ASP cc_start: 0.8817 (OUTLIER) cc_final: 0.8572 (t0) REVERT: R 70 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8706 (mt) REVERT: R 99 GLU cc_start: 0.8470 (tp30) cc_final: 0.8264 (tt0) REVERT: R 230 LYS cc_start: 0.7954 (ttmt) cc_final: 0.7633 (mmmt) REVERT: S 70 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8707 (mt) REVERT: S 143 GLN cc_start: 0.8461 (tp40) cc_final: 0.7780 (pt0) REVERT: S 181 LYS cc_start: 0.7748 (mtmt) cc_final: 0.7532 (mtpp) REVERT: S 230 LYS cc_start: 0.7982 (ttmt) cc_final: 0.7440 (mmmt) REVERT: T 40 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8505 (ptm) REVERT: T 67 ILE cc_start: 0.8536 (tt) cc_final: 0.8218 (mt) REVERT: T 70 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8892 (mp) REVERT: U 70 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8619 (mp) REVERT: U 143 GLN cc_start: 0.8401 (tp40) cc_final: 0.7619 (pt0) REVERT: U 212 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8146 (mt) REVERT: H 62 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7739 (mt-10) REVERT: I 64 GLU cc_start: 0.8128 (tt0) cc_final: 0.7730 (tt0) REVERT: I 139 GLU cc_start: 0.8703 (tp30) cc_final: 0.8286 (tp30) REVERT: J 145 LYS cc_start: 0.9222 (mmmt) cc_final: 0.8954 (mmtm) REVERT: K 14 MET cc_start: 0.9098 (mtm) cc_final: 0.8879 (mtp) REVERT: K 98 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8559 (pt0) REVERT: M 27 MET cc_start: 0.8505 (tpt) cc_final: 0.7069 (mtt) REVERT: M 45 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8825 (pp) REVERT: M 89 GLN cc_start: 0.8659 (mt0) cc_final: 0.7985 (mm110) REVERT: V 88 ASN cc_start: 0.9109 (t0) cc_final: 0.8846 (t0) REVERT: V 98 GLN cc_start: 0.8530 (tt0) cc_final: 0.8083 (pt0) REVERT: V 146 MET cc_start: 0.9064 (mtp) cc_final: 0.8690 (mtp) REVERT: V 195 ARG cc_start: 0.6781 (mmt-90) cc_final: 0.6425 (mmt180) REVERT: W 98 GLN cc_start: 0.8642 (tt0) cc_final: 0.8131 (pt0) REVERT: W 146 MET cc_start: 0.9262 (mtm) cc_final: 0.9042 (ptp) REVERT: X 98 GLN cc_start: 0.8637 (tt0) cc_final: 0.8269 (pt0) REVERT: Y 98 GLN cc_start: 0.8574 (tt0) cc_final: 0.8135 (pt0) REVERT: Y 99 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8601 (pt) REVERT: Y 198 LYS cc_start: 0.7916 (tttm) cc_final: 0.7610 (ttpt) REVERT: Z 43 MET cc_start: 0.9470 (ttt) cc_final: 0.9269 (ttt) REVERT: Z 98 GLN cc_start: 0.8723 (tt0) cc_final: 0.8202 (pt0) REVERT: Z 141 GLN cc_start: 0.8758 (mt0) cc_final: 0.8449 (mt0) REVERT: a 88 ASN cc_start: 0.8896 (t0) cc_final: 0.8650 (t0) REVERT: a 98 GLN cc_start: 0.8603 (tt0) cc_final: 0.8109 (pt0) REVERT: a 198 LYS cc_start: 0.8257 (ttmm) cc_final: 0.7950 (ttpt) REVERT: b 67 ARG cc_start: 0.8349 (tmm-80) cc_final: 0.8123 (ttp80) REVERT: b 98 GLN cc_start: 0.8510 (tt0) cc_final: 0.8230 (pt0) outliers start: 126 outliers final: 92 residues processed: 743 average time/residue: 0.2274 time to fit residues: 274.6028 Evaluate side-chains 766 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 655 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 212 ILE Chi-restraints excluded: chain P residue 72 ASP Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 194 ILE Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain Q residue 206 GLU Chi-restraints excluded: chain R residue 70 ILE Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 122 GLN Chi-restraints excluded: chain S residue 212 ILE Chi-restraints excluded: chain T residue 20 ARG Chi-restraints excluded: chain T residue 40 MET Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain U residue 70 ILE Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 174 SER Chi-restraints excluded: chain U residue 182 GLU Chi-restraints excluded: chain U residue 212 ILE Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 141 GLN Chi-restraints excluded: chain M residue 30 ASN Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain N residue 30 ASN Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 98 GLN Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain W residue 27 MET Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain X residue 30 ASN Chi-restraints excluded: chain X residue 69 GLN Chi-restraints excluded: chain Y residue 22 MET Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Z residue 69 GLN Chi-restraints excluded: chain Z residue 146 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 248 optimal weight: 0.4980 chunk 513 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 296 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 540 optimal weight: 6.9990 chunk 267 optimal weight: 5.9990 chunk 298 optimal weight: 3.9990 chunk 568 optimal weight: 4.9990 chunk 236 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 98 GLN P 23 GLN Q 122 GLN H 30 ASN J 30 ASN K 30 ASN M 30 ASN M 141 GLN N 30 ASN ** V 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 88 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.133144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.105175 restraints weight = 52833.208| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.20 r_work: 0.2844 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 46991 Z= 0.211 Angle : 0.623 10.957 63434 Z= 0.331 Chirality : 0.046 0.143 7441 Planarity : 0.004 0.041 8134 Dihedral : 4.912 35.372 6580 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.65 % Favored : 96.24 % Rotamer: Outliers : 3.22 % Allowed : 14.09 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.11), residues: 5950 helix: 2.02 (0.11), residues: 2275 sheet: -0.12 (0.14), residues: 1386 loop : -1.84 (0.11), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 178 TYR 0.017 0.002 TYR U 103 PHE 0.027 0.002 PHE U 175 HIS 0.006 0.002 HIS I 109 Details of bonding type rmsd covalent geometry : bond 0.00536 (46991) covalent geometry : angle 0.62349 (63434) hydrogen bonds : bond 0.06087 ( 2538) hydrogen bonds : angle 4.39787 ( 7401) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 636 time to evaluate : 1.828 Fit side-chains revert: symmetry clash REVERT: A 98 GLN cc_start: 0.7655 (tt0) cc_final: 0.7249 (tt0) REVERT: A 221 TYR cc_start: 0.9354 (OUTLIER) cc_final: 0.8878 (m-80) REVERT: B 49 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8609 (mt) REVERT: C 98 GLN cc_start: 0.8164 (tt0) cc_final: 0.7708 (tt0) REVERT: C 221 TYR cc_start: 0.9306 (OUTLIER) cc_final: 0.7887 (m-80) REVERT: D 18 ASP cc_start: 0.9013 (t0) cc_final: 0.8686 (t0) REVERT: D 71 ASP cc_start: 0.8854 (t70) cc_final: 0.8647 (t0) REVERT: D 98 GLN cc_start: 0.8322 (tt0) cc_final: 0.8016 (tt0) REVERT: D 221 TYR cc_start: 0.9494 (OUTLIER) cc_final: 0.8884 (m-80) REVERT: E 49 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8598 (mt) REVERT: E 120 MET cc_start: 0.9060 (mtp) cc_final: 0.8859 (mtm) REVERT: E 221 TYR cc_start: 0.9360 (OUTLIER) cc_final: 0.8274 (m-80) REVERT: F 98 GLN cc_start: 0.8095 (tt0) cc_final: 0.7843 (tt0) REVERT: G 44 ASN cc_start: 0.8625 (t0) cc_final: 0.8394 (t0) REVERT: G 98 GLN cc_start: 0.8056 (tt0) cc_final: 0.7650 (tt0) REVERT: O 20 ARG cc_start: 0.9119 (mtp180) cc_final: 0.8866 (mtp180) REVERT: O 70 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8816 (mt) REVERT: O 122 GLN cc_start: 0.8694 (tt0) cc_final: 0.8410 (tt0) REVERT: O 143 GLN cc_start: 0.8419 (tp40) cc_final: 0.7608 (pt0) REVERT: P 143 GLN cc_start: 0.8445 (tp40) cc_final: 0.7708 (pt0) REVERT: P 181 LYS cc_start: 0.7862 (mtmt) cc_final: 0.7365 (ptmm) REVERT: Q 20 ARG cc_start: 0.9064 (mtm180) cc_final: 0.8825 (mtp180) REVERT: Q 70 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.8842 (mt) REVERT: Q 72 ASP cc_start: 0.8838 (OUTLIER) cc_final: 0.8576 (t0) REVERT: R 70 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8735 (mt) REVERT: R 99 GLU cc_start: 0.8473 (tp30) cc_final: 0.8189 (tt0) REVERT: R 181 LYS cc_start: 0.7990 (mtmt) cc_final: 0.7490 (ptmm) REVERT: R 230 LYS cc_start: 0.7985 (ttmt) cc_final: 0.7666 (mmmt) REVERT: S 70 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.8841 (mt) REVERT: S 143 GLN cc_start: 0.8495 (tp40) cc_final: 0.7745 (pt0) REVERT: S 181 LYS cc_start: 0.7947 (mtmt) cc_final: 0.7731 (mtpp) REVERT: S 230 LYS cc_start: 0.7994 (ttmt) cc_final: 0.7494 (mmmt) REVERT: T 40 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8711 (ptm) REVERT: T 70 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.8997 (mp) REVERT: U 20 ARG cc_start: 0.9161 (mtp180) cc_final: 0.8691 (mtp180) REVERT: U 70 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8816 (mt) REVERT: U 143 GLN cc_start: 0.8417 (tp40) cc_final: 0.7500 (pt0) REVERT: H 62 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: H 195 ARG cc_start: 0.6584 (mmt180) cc_final: 0.6162 (mtt-85) REVERT: I 64 GLU cc_start: 0.8361 (tt0) cc_final: 0.7979 (tt0) REVERT: J 64 GLU cc_start: 0.8393 (tt0) cc_final: 0.8003 (tt0) REVERT: M 45 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8830 (pp) REVERT: M 89 GLN cc_start: 0.8797 (mt0) cc_final: 0.8422 (mm-40) REVERT: M 195 ARG cc_start: 0.6361 (mmt180) cc_final: 0.5995 (mtt-85) REVERT: V 64 GLU cc_start: 0.8254 (tt0) cc_final: 0.8014 (tt0) REVERT: V 88 ASN cc_start: 0.9162 (t0) cc_final: 0.8832 (t0) REVERT: V 146 MET cc_start: 0.9148 (mtp) cc_final: 0.8816 (mtp) REVERT: W 146 MET cc_start: 0.9326 (mtm) cc_final: 0.9054 (ptp) REVERT: X 98 GLN cc_start: 0.8631 (tt0) cc_final: 0.8336 (pt0) REVERT: Y 98 GLN cc_start: 0.8753 (tt0) cc_final: 0.8147 (pt0) REVERT: Y 146 MET cc_start: 0.9307 (mtm) cc_final: 0.9007 (mtp) REVERT: Y 198 LYS cc_start: 0.7990 (tttm) cc_final: 0.7655 (ttpt) REVERT: Z 139 GLU cc_start: 0.8499 (tp30) cc_final: 0.8008 (tp30) REVERT: a 70 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.5639 (mpt180) REVERT: a 88 ASN cc_start: 0.8996 (t0) cc_final: 0.8700 (t0) REVERT: a 98 GLN cc_start: 0.8750 (tt0) cc_final: 0.8219 (pt0) REVERT: a 198 LYS cc_start: 0.8370 (ttmm) cc_final: 0.7998 (ttpt) REVERT: b 67 ARG cc_start: 0.8526 (tmm-80) cc_final: 0.8159 (ttp80) REVERT: b 98 GLN cc_start: 0.8565 (tt0) cc_final: 0.8299 (pt0) outliers start: 161 outliers final: 115 residues processed: 749 average time/residue: 0.1826 time to fit residues: 223.3836 Evaluate side-chains 756 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 624 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 212 ILE Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 173 VAL Chi-restraints excluded: chain P residue 194 ILE Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain R residue 70 ILE Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain S residue 50 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 122 GLN Chi-restraints excluded: chain S residue 134 VAL Chi-restraints excluded: chain S residue 173 VAL Chi-restraints excluded: chain S residue 212 ILE Chi-restraints excluded: chain T residue 20 ARG Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 40 MET Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 107 VAL Chi-restraints excluded: chain T residue 173 VAL Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 70 ILE Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 107 VAL Chi-restraints excluded: chain U residue 173 VAL Chi-restraints excluded: chain U residue 174 SER Chi-restraints excluded: chain U residue 182 GLU Chi-restraints excluded: chain U residue 212 ILE Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain M residue 30 ASN Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 30 ASN Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 98 GLN Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain V residue 194 SER Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain X residue 69 GLN Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 194 SER Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 146 MET Chi-restraints excluded: chain Z residue 194 SER Chi-restraints excluded: chain a residue 70 ARG Chi-restraints excluded: chain b residue 194 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 171 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 578 optimal weight: 0.6980 chunk 176 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 316 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 234 optimal weight: 1.9990 chunk 144 optimal weight: 0.5980 chunk 164 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 98 GLN O 23 GLN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 23 GLN J 30 ASN K 30 ASN M 30 ASN N 30 ASN ** Y 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 69 GLN a 89 GLN b 69 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.140954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.113069 restraints weight = 52114.788| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.16 r_work: 0.2980 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.5255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 46991 Z= 0.103 Angle : 0.512 10.321 63434 Z= 0.276 Chirality : 0.043 0.142 7441 Planarity : 0.003 0.039 8134 Dihedral : 4.492 29.932 6580 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.89 % Favored : 96.99 % Rotamer: Outliers : 2.30 % Allowed : 15.19 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.11), residues: 5950 helix: 2.33 (0.11), residues: 2282 sheet: -0.18 (0.14), residues: 1421 loop : -1.74 (0.11), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 178 TYR 0.013 0.001 TYR U 103 PHE 0.022 0.001 PHE U 175 HIS 0.003 0.001 HIS Z 109 Details of bonding type rmsd covalent geometry : bond 0.00237 (46991) covalent geometry : angle 0.51226 (63434) hydrogen bonds : bond 0.03820 ( 2538) hydrogen bonds : angle 4.09564 ( 7401) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 662 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: A 98 GLN cc_start: 0.7724 (tt0) cc_final: 0.7432 (tt0) REVERT: A 221 TYR cc_start: 0.9186 (OUTLIER) cc_final: 0.8796 (m-80) REVERT: B 49 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8616 (mt) REVERT: C 18 ASP cc_start: 0.8323 (p0) cc_final: 0.8095 (t70) REVERT: C 98 GLN cc_start: 0.8114 (tt0) cc_final: 0.7677 (tt0) REVERT: C 221 TYR cc_start: 0.9111 (OUTLIER) cc_final: 0.7464 (m-80) REVERT: D 18 ASP cc_start: 0.9007 (t0) cc_final: 0.8738 (t0) REVERT: D 221 TYR cc_start: 0.9398 (OUTLIER) cc_final: 0.8747 (m-80) REVERT: E 49 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8612 (mt) REVERT: E 178 ARG cc_start: 0.7935 (ttp80) cc_final: 0.7704 (ttm170) REVERT: E 221 TYR cc_start: 0.9171 (OUTLIER) cc_final: 0.8011 (m-80) REVERT: F 98 GLN cc_start: 0.7862 (tt0) cc_final: 0.7607 (tt0) REVERT: F 178 ARG cc_start: 0.7895 (ttp80) cc_final: 0.7505 (ttm170) REVERT: G 44 ASN cc_start: 0.8422 (t0) cc_final: 0.8152 (t0) REVERT: G 98 GLN cc_start: 0.8039 (tt0) cc_final: 0.7640 (tt0) REVERT: O 18 ASP cc_start: 0.8751 (m-30) cc_final: 0.8329 (m-30) REVERT: O 70 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8728 (mt) REVERT: O 122 GLN cc_start: 0.8643 (tt0) cc_final: 0.8347 (tt0) REVERT: P 143 GLN cc_start: 0.8458 (tp40) cc_final: 0.7741 (pt0) REVERT: P 181 LYS cc_start: 0.7766 (mtmt) cc_final: 0.7298 (ptmm) REVERT: Q 20 ARG cc_start: 0.9006 (mtm180) cc_final: 0.8708 (mtp180) REVERT: Q 70 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8725 (mt) REVERT: Q 72 ASP cc_start: 0.8799 (OUTLIER) cc_final: 0.8551 (t0) REVERT: R 70 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8709 (mt) REVERT: R 230 LYS cc_start: 0.7999 (ttmt) cc_final: 0.7709 (mmmt) REVERT: S 70 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8687 (mt) REVERT: S 143 GLN cc_start: 0.8478 (tp40) cc_final: 0.7782 (pt0) REVERT: S 230 LYS cc_start: 0.8063 (ttmt) cc_final: 0.7575 (mmmt) REVERT: T 40 MET cc_start: 0.8907 (ptp) cc_final: 0.8587 (ptm) REVERT: T 67 ILE cc_start: 0.8573 (tt) cc_final: 0.8284 (mt) REVERT: T 70 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8875 (mp) REVERT: U 70 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8667 (mp) REVERT: U 103 TYR cc_start: 0.8288 (m-80) cc_final: 0.8026 (m-80) REVERT: U 143 GLN cc_start: 0.8382 (tp40) cc_final: 0.7505 (pt0) REVERT: H 62 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7661 (mt-10) REVERT: I 64 GLU cc_start: 0.8181 (tt0) cc_final: 0.7791 (tt0) REVERT: I 139 GLU cc_start: 0.8775 (tp30) cc_final: 0.8248 (tp30) REVERT: J 62 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7639 (mm-30) REVERT: K 14 MET cc_start: 0.9115 (mtm) cc_final: 0.8856 (mtp) REVERT: M 45 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8790 (pp) REVERT: M 89 GLN cc_start: 0.8728 (mt0) cc_final: 0.8024 (mm110) REVERT: V 88 ASN cc_start: 0.9076 (t0) cc_final: 0.8794 (t0) REVERT: V 146 MET cc_start: 0.9011 (mtp) cc_final: 0.8615 (mtp) REVERT: V 195 ARG cc_start: 0.6850 (mmt-90) cc_final: 0.6477 (mmt180) REVERT: W 98 GLN cc_start: 0.8623 (tt0) cc_final: 0.8002 (pt0) REVERT: W 146 MET cc_start: 0.9228 (mtm) cc_final: 0.9009 (ptp) REVERT: X 98 GLN cc_start: 0.8557 (tt0) cc_final: 0.8232 (pt0) REVERT: X 99 LEU cc_start: 0.8943 (pp) cc_final: 0.8720 (pt) REVERT: Y 98 GLN cc_start: 0.8589 (tt0) cc_final: 0.8118 (pt0) REVERT: Y 99 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8638 (pt) REVERT: Y 198 LYS cc_start: 0.7932 (tttm) cc_final: 0.7608 (ttpt) REVERT: Z 98 GLN cc_start: 0.8739 (tt0) cc_final: 0.8149 (pt0) REVERT: Z 139 GLU cc_start: 0.8359 (tp30) cc_final: 0.7908 (tp30) REVERT: Z 141 GLN cc_start: 0.8799 (mt0) cc_final: 0.8494 (mt0) REVERT: a 88 ASN cc_start: 0.8876 (t0) cc_final: 0.8623 (t0) REVERT: a 98 GLN cc_start: 0.8653 (tt0) cc_final: 0.8198 (pt0) REVERT: a 139 GLU cc_start: 0.8381 (tp30) cc_final: 0.8054 (tp30) REVERT: a 198 LYS cc_start: 0.8281 (ttmm) cc_final: 0.7958 (ttpt) REVERT: b 67 ARG cc_start: 0.8353 (tmm-80) cc_final: 0.8127 (ttp80) REVERT: b 98 GLN cc_start: 0.8531 (tt0) cc_final: 0.8284 (pt0) outliers start: 115 outliers final: 83 residues processed: 740 average time/residue: 0.1897 time to fit residues: 230.1343 Evaluate side-chains 750 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 650 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 212 ILE Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 194 ILE Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 206 GLU Chi-restraints excluded: chain R residue 70 ILE Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 122 GLN Chi-restraints excluded: chain S residue 212 ILE Chi-restraints excluded: chain T residue 20 ARG Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 107 VAL Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 70 ILE Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 174 SER Chi-restraints excluded: chain U residue 182 GLU Chi-restraints excluded: chain U residue 212 ILE Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain K residue 30 ASN Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 98 GLN Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 30 ASN Chi-restraints excluded: chain N residue 98 GLN Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Z residue 146 MET Chi-restraints excluded: chain a residue 69 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 480 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 442 optimal weight: 0.0770 chunk 82 optimal weight: 3.9990 chunk 565 optimal weight: 3.9990 chunk 305 optimal weight: 0.3980 chunk 271 optimal weight: 4.9990 chunk 346 optimal weight: 3.9990 chunk 454 optimal weight: 3.9990 chunk 339 optimal weight: 4.9990 chunk 451 optimal weight: 0.8980 overall best weight: 1.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 219 ASN J 30 ASN K 30 ASN M 30 ASN N 30 ASN ** Y 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 89 GLN b 69 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.113007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.087764 restraints weight = 54928.481| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.84 r_work: 0.3058 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 46991 Z= 0.178 Angle : 0.585 10.478 63434 Z= 0.312 Chirality : 0.045 0.157 7441 Planarity : 0.004 0.038 8134 Dihedral : 4.721 29.836 6580 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.21 % Favored : 96.67 % Rotamer: Outliers : 2.40 % Allowed : 15.17 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.11), residues: 5950 helix: 2.15 (0.11), residues: 2275 sheet: -0.12 (0.14), residues: 1365 loop : -1.81 (0.11), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 178 TYR 0.014 0.001 TYR T 160 PHE 0.024 0.002 PHE U 175 HIS 0.005 0.002 HIS I 109 Details of bonding type rmsd covalent geometry : bond 0.00449 (46991) covalent geometry : angle 0.58542 (63434) hydrogen bonds : bond 0.05440 ( 2538) hydrogen bonds : angle 4.29535 ( 7401) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 637 time to evaluate : 1.082 Fit side-chains REVERT: A 98 GLN cc_start: 0.7733 (tt0) cc_final: 0.7361 (tt0) REVERT: A 221 TYR cc_start: 0.9321 (OUTLIER) cc_final: 0.8746 (m-80) REVERT: B 49 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8626 (mt) REVERT: C 98 GLN cc_start: 0.8094 (tt0) cc_final: 0.7673 (tt0) REVERT: C 221 TYR cc_start: 0.9262 (OUTLIER) cc_final: 0.7708 (m-80) REVERT: D 18 ASP cc_start: 0.9009 (t0) cc_final: 0.8669 (t0) REVERT: D 221 TYR cc_start: 0.9466 (OUTLIER) cc_final: 0.8788 (m-80) REVERT: E 49 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8632 (mt) REVERT: E 221 TYR cc_start: 0.9299 (OUTLIER) cc_final: 0.8104 (m-80) REVERT: F 98 GLN cc_start: 0.7972 (tt0) cc_final: 0.7720 (tt0) REVERT: F 178 ARG cc_start: 0.7882 (ttp80) cc_final: 0.7496 (ttm170) REVERT: G 98 GLN cc_start: 0.7994 (tt0) cc_final: 0.7592 (tt0) REVERT: O 70 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8792 (mt) REVERT: O 122 GLN cc_start: 0.8647 (tt0) cc_final: 0.8368 (tt0) REVERT: P 143 GLN cc_start: 0.8416 (tp40) cc_final: 0.7730 (pt0) REVERT: P 181 LYS cc_start: 0.7854 (mtmt) cc_final: 0.7383 (ptmm) REVERT: Q 70 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8810 (mt) REVERT: Q 72 ASP cc_start: 0.8794 (OUTLIER) cc_final: 0.8527 (t0) REVERT: R 70 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8743 (mt) REVERT: R 181 LYS cc_start: 0.7976 (mtmt) cc_final: 0.7443 (ptmm) REVERT: R 230 LYS cc_start: 0.8132 (ttmt) cc_final: 0.7802 (mmmt) REVERT: S 70 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8769 (mt) REVERT: S 143 GLN cc_start: 0.8445 (tp40) cc_final: 0.7769 (pt0) REVERT: S 230 LYS cc_start: 0.8115 (ttmt) cc_final: 0.7653 (mmmt) REVERT: T 40 MET cc_start: 0.9013 (ptp) cc_final: 0.8692 (ptm) REVERT: T 70 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8937 (mp) REVERT: T 230 LYS cc_start: 0.8194 (mttt) cc_final: 0.7795 (mmmt) REVERT: U 20 ARG cc_start: 0.9140 (mtp180) cc_final: 0.8728 (mtp180) REVERT: U 70 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8752 (mt) REVERT: U 143 GLN cc_start: 0.8447 (tp40) cc_final: 0.7553 (pt0) REVERT: H 62 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7585 (mt-10) REVERT: H 195 ARG cc_start: 0.6637 (mmt180) cc_final: 0.6188 (mtt-85) REVERT: I 64 GLU cc_start: 0.8204 (tt0) cc_final: 0.7805 (tt0) REVERT: J 62 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7573 (mm-30) REVERT: J 64 GLU cc_start: 0.8316 (tt0) cc_final: 0.7931 (tt0) REVERT: M 45 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8832 (pp) REVERT: M 89 GLN cc_start: 0.8780 (mt0) cc_final: 0.8243 (mm-40) REVERT: M 195 ARG cc_start: 0.6307 (mmt180) cc_final: 0.5991 (mtt-85) REVERT: N 1 THR cc_start: 0.8285 (p) cc_final: 0.7901 (t) REVERT: V 14 MET cc_start: 0.9383 (mtp) cc_final: 0.9147 (mtt) REVERT: V 88 ASN cc_start: 0.9128 (t0) cc_final: 0.8825 (t0) REVERT: V 146 MET cc_start: 0.9085 (mtp) cc_final: 0.8705 (mtp) REVERT: W 98 GLN cc_start: 0.8611 (tt0) cc_final: 0.8007 (pt0) REVERT: W 146 MET cc_start: 0.9315 (mtm) cc_final: 0.9056 (ptp) REVERT: X 98 GLN cc_start: 0.8531 (tt0) cc_final: 0.8314 (pt0) REVERT: Y 98 GLN cc_start: 0.8673 (tt0) cc_final: 0.8172 (pt0) REVERT: Y 198 LYS cc_start: 0.8049 (tttm) cc_final: 0.7710 (ttpt) REVERT: Z 139 GLU cc_start: 0.8364 (tp30) cc_final: 0.7971 (tp30) REVERT: a 88 ASN cc_start: 0.8958 (t0) cc_final: 0.8664 (t0) REVERT: a 98 GLN cc_start: 0.8697 (tt0) cc_final: 0.8239 (pt0) REVERT: a 198 LYS cc_start: 0.8404 (ttmm) cc_final: 0.8039 (ttpt) REVERT: b 67 ARG cc_start: 0.8529 (tmm-80) cc_final: 0.8317 (ttp80) REVERT: b 98 GLN cc_start: 0.8516 (tt0) cc_final: 0.8298 (pt0) outliers start: 120 outliers final: 96 residues processed: 723 average time/residue: 0.1861 time to fit residues: 219.7527 Evaluate side-chains 738 residues out of total 4998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 626 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 212 ILE Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 72 ASP Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 194 ILE Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain R residue 70 ILE Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 50 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 122 GLN Chi-restraints excluded: chain S residue 173 VAL Chi-restraints excluded: chain S residue 212 ILE Chi-restraints excluded: chain T residue 20 ARG Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 107 VAL Chi-restraints excluded: chain T residue 173 VAL Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 70 ILE Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 107 VAL Chi-restraints excluded: chain U residue 173 VAL Chi-restraints excluded: chain U residue 174 SER Chi-restraints excluded: chain U residue 182 GLU Chi-restraints excluded: chain U residue 212 ILE Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 98 GLN Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 98 GLN Chi-restraints excluded: chain M residue 30 ASN Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 98 GLN Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain W residue 99 LEU Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain Y residue 194 SER Chi-restraints excluded: chain Z residue 146 MET Chi-restraints excluded: chain a residue 194 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 548 optimal weight: 3.9990 chunk 411 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 369 optimal weight: 0.0870 chunk 472 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 494 optimal weight: 2.9990 chunk 322 optimal weight: 1.9990 chunk 101 optimal weight: 0.0870 chunk 506 optimal weight: 1.9990 overall best weight: 1.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 23 GLN H 30 ASN J 30 ASN K 30 ASN M 30 ASN N 30 ASN ** Y 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 GLN a 69 GLN a 89 GLN b 69 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.134579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.106288 restraints weight = 53312.119| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.22 r_work: 0.2893 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 46991 Z= 0.132 Angle : 0.538 10.062 63434 Z= 0.289 Chirality : 0.043 0.155 7441 Planarity : 0.004 0.040 8134 Dihedral : 4.544 28.627 6580 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.09 % Favored : 96.79 % Rotamer: Outliers : 2.66 % Allowed : 14.89 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.11), residues: 5950 helix: 2.27 (0.11), residues: 2275 sheet: -0.07 (0.14), residues: 1365 loop : -1.80 (0.11), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 178 TYR 0.013 0.001 TYR T 160 PHE 0.022 0.001 PHE U 175 HIS 0.004 0.001 HIS M 28 Details of bonding type rmsd covalent geometry : bond 0.00322 (46991) covalent geometry : angle 0.53825 (63434) hydrogen bonds : bond 0.04461 ( 2538) hydrogen bonds : angle 4.16061 ( 7401) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9880.90 seconds wall clock time: 169 minutes 35.07 seconds (10175.07 seconds total)