Starting phenix.real_space_refine on Sun Feb 8 09:58:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zsg_60414/02_2026/8zsg_60414.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zsg_60414/02_2026/8zsg_60414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zsg_60414/02_2026/8zsg_60414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zsg_60414/02_2026/8zsg_60414.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zsg_60414/02_2026/8zsg_60414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zsg_60414/02_2026/8zsg_60414.map" } resolution = 3.66 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= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 28188 2.51 5 N 7164 2.21 5 O 8184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 124 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43668 Number of models: 1 Model: "" Number of chains: 24 Chain: "R" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2166 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "T" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2166 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "V" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1473 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "X" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1473 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "Z" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1473 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "d" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1473 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "b" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2166 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "f" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2166 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "A" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2166 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "C" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2166 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "E" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1473 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "G" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1473 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "I" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1473 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "M" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1473 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "K" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2166 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "O" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2166 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "B" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2166 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "D" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2166 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "F" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1473 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "H" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1473 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "J" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1473 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "N" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1473 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "L" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2166 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "P" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2166 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 253} Time building chain proxies: 9.94, per 1000 atoms: 0.23 Number of scatterers: 43668 At special positions: 0 Unit cell: (186.56, 183.38, 183.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 8184 8.00 N 7164 7.00 C 28188 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: 3.95 Conformation dependent library (CDL) restraints added in 1.9 seconds 10656 Ramachandran restraints generated. 5328 Oldfield, 0 Emsley, 5328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10032 Finding SS restraints... Secondary structure from input PDB file: 258 helices and 33 sheets defined 50.2% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'R' and resid 1 through 11 Processing helix chain 'R' and resid 19 through 23 removed outlier: 3.963A pdb=" N MET R 23 " --> pdb=" O GLY R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 41 Processing helix chain 'R' and resid 44 through 50 Processing helix chain 'R' and resid 55 through 65 Processing helix chain 'R' and resid 68 through 80 removed outlier: 3.666A pdb=" N HIS R 80 " --> pdb=" O ASP R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 88 removed outlier: 3.719A pdb=" N LYS R 88 " --> pdb=" O ASP R 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 85 through 88' Processing helix chain 'R' and resid 89 through 98 Processing helix chain 'R' and resid 110 through 119 removed outlier: 3.522A pdb=" N TYR R 119 " --> pdb=" O ALA R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 135 removed outlier: 3.722A pdb=" N ASP R 131 " --> pdb=" O SER R 128 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE R 132 " --> pdb=" O VAL R 129 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA R 133 " --> pdb=" O SER R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 164 Processing helix chain 'R' and resid 170 through 181 removed outlier: 3.522A pdb=" N ILE R 174 " --> pdb=" O THR R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 194 through 211 removed outlier: 4.016A pdb=" N ARG R 198 " --> pdb=" O ASP R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 228 through 236 Processing helix chain 'R' and resid 249 through 259 Processing helix chain 'R' and resid 260 through 262 No H-bonds generated for 'chain 'R' and resid 260 through 262' Processing helix chain 'T' and resid 2 through 10 removed outlier: 3.529A pdb=" N LYS T 10 " --> pdb=" O ALA T 6 " (cutoff:3.500A) Processing helix chain 'T' and resid 21 through 26 removed outlier: 3.602A pdb=" N ASN T 24 " --> pdb=" O VAL T 21 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU T 25 " --> pdb=" O SER T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 29 through 41 Processing helix chain 'T' and resid 54 through 66 Processing helix chain 'T' and resid 68 through 79 Processing helix chain 'T' and resid 89 through 98 removed outlier: 3.525A pdb=" N GLU T 93 " --> pdb=" O SER T 89 " (cutoff:3.500A) Processing helix chain 'T' and resid 110 through 119 Processing helix chain 'T' and resid 128 through 135 removed outlier: 3.745A pdb=" N ILE T 132 " --> pdb=" O VAL T 129 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA T 133 " --> pdb=" O SER T 130 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE T 135 " --> pdb=" O ILE T 132 " (cutoff:3.500A) Processing helix chain 'T' and resid 158 through 168 removed outlier: 3.751A pdb=" N PHE T 168 " --> pdb=" O GLN T 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 170 through 181 removed outlier: 3.502A pdb=" N ILE T 174 " --> pdb=" O THR T 170 " (cutoff:3.500A) Processing helix chain 'T' and resid 195 through 211 removed outlier: 3.535A pdb=" N GLN T 211 " --> pdb=" O LEU T 207 " (cutoff:3.500A) Processing helix chain 'T' and resid 228 through 237 removed outlier: 3.828A pdb=" N GLN T 237 " --> pdb=" O GLU T 233 " (cutoff:3.500A) Processing helix chain 'T' and resid 249 through 263 removed outlier: 4.181A pdb=" N ASN T 260 " --> pdb=" O GLU T 256 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N PHE T 261 " --> pdb=" O PHE T 257 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL T 262 " --> pdb=" O LEU T 258 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU T 263 " --> pdb=" O LYS T 259 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 20 removed outlier: 3.804A pdb=" N ILE V 13 " --> pdb=" O ASN V 9 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS V 14 " --> pdb=" O ARG V 10 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN V 17 " --> pdb=" O ILE V 13 " (cutoff:3.500A) Processing helix chain 'V' and resid 41 through 57 Processing helix chain 'V' and resid 80 through 98 removed outlier: 8.023A pdb=" N ALA V 90 " --> pdb=" O ASP V 86 " (cutoff:3.500A) removed outlier: 9.347A pdb=" N ASP V 91 " --> pdb=" O LYS V 87 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYS V 92 " --> pdb=" O LEU V 88 " (cutoff:3.500A) Processing helix chain 'V' and resid 154 through 159 removed outlier: 3.587A pdb=" N GLY V 159 " --> pdb=" O PHE V 155 " (cutoff:3.500A) Processing helix chain 'V' and resid 160 through 165 removed outlier: 4.282A pdb=" N ASN V 163 " --> pdb=" O ASP V 160 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU V 164 " --> pdb=" O ARG V 161 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE V 165 " --> pdb=" O LYS V 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 160 through 165' Processing helix chain 'V' and resid 166 through 181 removed outlier: 3.706A pdb=" N GLU V 181 " --> pdb=" O GLU V 177 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 20 removed outlier: 4.576A pdb=" N LYS X 14 " --> pdb=" O ARG X 10 " (cutoff:3.500A) Processing helix chain 'X' and resid 41 through 57 Processing helix chain 'X' and resid 80 through 89 Processing helix chain 'X' and resid 89 through 98 Processing helix chain 'X' and resid 140 through 144 removed outlier: 3.523A pdb=" N ASP X 143 " --> pdb=" O PHE X 140 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N CYS X 144 " --> pdb=" O GLN X 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 140 through 144' Processing helix chain 'X' and resid 160 through 166 Processing helix chain 'X' and resid 166 through 180 Processing helix chain 'Z' and resid 9 through 20 removed outlier: 3.759A pdb=" N ILE Z 13 " --> pdb=" O ASN Z 9 " (cutoff:3.500A) Processing helix chain 'Z' and resid 41 through 58 Processing helix chain 'Z' and resid 80 through 89 Processing helix chain 'Z' and resid 89 through 98 Processing helix chain 'Z' and resid 140 through 144 removed outlier: 4.275A pdb=" N CYS Z 144 " --> pdb=" O GLN Z 141 " (cutoff:3.500A) Processing helix chain 'Z' and resid 154 through 159 removed outlier: 3.695A pdb=" N GLY Z 159 " --> pdb=" O PHE Z 155 " (cutoff:3.500A) Processing helix chain 'Z' and resid 161 through 166 removed outlier: 3.701A pdb=" N ILE Z 165 " --> pdb=" O ARG Z 161 " (cutoff:3.500A) Processing helix chain 'Z' and resid 166 through 181 removed outlier: 3.538A pdb=" N GLU Z 181 " --> pdb=" O GLU Z 177 " (cutoff:3.500A) Processing helix chain 'd' and resid 11 through 20 removed outlier: 4.027A pdb=" N GLU d 15 " --> pdb=" O HIS d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 57 Processing helix chain 'd' and resid 80 through 98 removed outlier: 7.947A pdb=" N ALA d 90 " --> pdb=" O ASP d 86 " (cutoff:3.500A) removed outlier: 9.537A pdb=" N ASP d 91 " --> pdb=" O LYS d 87 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS d 92 " --> pdb=" O LEU d 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 140 through 144 removed outlier: 4.502A pdb=" N CYS d 144 " --> pdb=" O GLN d 141 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 159 removed outlier: 3.729A pdb=" N MET d 158 " --> pdb=" O THR d 154 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY d 159 " --> pdb=" O PHE d 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 154 through 159' Processing helix chain 'd' and resid 160 through 165 removed outlier: 3.602A pdb=" N GLU d 164 " --> pdb=" O ARG d 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 166 through 181 Processing helix chain 'b' and resid 2 through 11 Processing helix chain 'b' and resid 29 through 36 Processing helix chain 'b' and resid 47 through 52 removed outlier: 4.121A pdb=" N GLY b 52 " --> pdb=" O ARG b 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 54 through 65 Processing helix chain 'b' and resid 68 through 80 removed outlier: 3.619A pdb=" N HIS b 80 " --> pdb=" O ASP b 76 " (cutoff:3.500A) Processing helix chain 'b' and resid 89 through 98 removed outlier: 3.676A pdb=" N GLU b 93 " --> pdb=" O SER b 89 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA b 98 " --> pdb=" O TYR b 94 " (cutoff:3.500A) Processing helix chain 'b' and resid 110 through 119 Processing helix chain 'b' and resid 128 through 133 removed outlier: 4.360A pdb=" N ALA b 133 " --> pdb=" O VAL b 129 " (cutoff:3.500A) Processing helix chain 'b' and resid 158 through 165 Processing helix chain 'b' and resid 170 through 181 removed outlier: 3.532A pdb=" N ILE b 174 " --> pdb=" O THR b 170 " (cutoff:3.500A) Processing helix chain 'b' and resid 194 through 211 removed outlier: 3.726A pdb=" N ARG b 198 " --> pdb=" O ASP b 194 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU b 207 " --> pdb=" O LYS b 203 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TRP b 208 " --> pdb=" O LEU b 204 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS b 209 " --> pdb=" O SER b 205 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN b 211 " --> pdb=" O LEU b 207 " (cutoff:3.500A) Processing helix chain 'b' and resid 228 through 237 removed outlier: 3.661A pdb=" N GLU b 232 " --> pdb=" O ASN b 228 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLN b 237 " --> pdb=" O GLU b 233 " (cutoff:3.500A) Processing helix chain 'b' and resid 249 through 260 Processing helix chain 'f' and resid 2 through 11 removed outlier: 3.574A pdb=" N LYS f 10 " --> pdb=" O ALA f 6 " (cutoff:3.500A) Processing helix chain 'f' and resid 18 through 23 removed outlier: 4.114A pdb=" N SER f 22 " --> pdb=" O GLY f 18 " (cutoff:3.500A) Processing helix chain 'f' and resid 29 through 42 Processing helix chain 'f' and resid 54 through 66 Processing helix chain 'f' and resid 68 through 79 Processing helix chain 'f' and resid 85 through 88 removed outlier: 3.727A pdb=" N LYS f 88 " --> pdb=" O ASP f 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 85 through 88' Processing helix chain 'f' and resid 89 through 98 removed outlier: 3.579A pdb=" N ALA f 98 " --> pdb=" O TYR f 94 " (cutoff:3.500A) Processing helix chain 'f' and resid 110 through 119 Processing helix chain 'f' and resid 158 through 166 Processing helix chain 'f' and resid 170 through 181 Processing helix chain 'f' and resid 194 through 211 removed outlier: 3.686A pdb=" N ARG f 198 " --> pdb=" O ASP f 194 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU f 207 " --> pdb=" O LYS f 203 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TRP f 208 " --> pdb=" O LEU f 204 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN f 211 " --> pdb=" O LEU f 207 " (cutoff:3.500A) Processing helix chain 'f' and resid 228 through 239 Processing helix chain 'f' and resid 249 through 263 removed outlier: 4.285A pdb=" N ASN f 260 " --> pdb=" O GLU f 256 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE f 261 " --> pdb=" O PHE f 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU f 263 " --> pdb=" O LYS f 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 19 through 24 removed outlier: 4.038A pdb=" N MET A 23 " --> pdb=" O GLY A 20 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN A 24 " --> pdb=" O VAL A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 41 Processing helix chain 'A' and resid 44 through 51 removed outlier: 3.791A pdb=" N PHE A 51 " --> pdb=" O ILE A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 65 removed outlier: 3.640A pdb=" N GLU A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 79 Processing helix chain 'A' and resid 89 through 98 removed outlier: 3.510A pdb=" N GLU A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 119 Processing helix chain 'A' and resid 128 through 135 removed outlier: 3.573A pdb=" N ASP A 131 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 132 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A 133 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 135 " --> pdb=" O ILE A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 181 removed outlier: 3.550A pdb=" N ILE A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 211 removed outlier: 3.844A pdb=" N ARG A 198 " --> pdb=" O ASP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 237 removed outlier: 3.907A pdb=" N GLN A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 263 removed outlier: 4.265A pdb=" N ASN A 260 " --> pdb=" O GLU A 256 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N PHE A 261 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 10 Processing helix chain 'C' and resid 18 through 23 removed outlier: 4.165A pdb=" N SER C 22 " --> pdb=" O GLY C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 30 through 41 removed outlier: 4.097A pdb=" N HIS C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 Processing helix chain 'C' and resid 68 through 79 Processing helix chain 'C' and resid 89 through 98 Processing helix chain 'C' and resid 110 through 119 Processing helix chain 'C' and resid 128 through 135 removed outlier: 3.569A pdb=" N ILE C 132 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA C 133 " --> pdb=" O SER C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 167 Processing helix chain 'C' and resid 170 through 181 Processing helix chain 'C' and resid 194 through 211 removed outlier: 4.193A pdb=" N ARG C 198 " --> pdb=" O ASP C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 237 removed outlier: 3.788A pdb=" N GLN C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 259 Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'E' and resid 9 through 20 removed outlier: 4.281A pdb=" N ILE E 13 " --> pdb=" O ASN E 9 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LYS E 14 " --> pdb=" O ARG E 10 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASN E 17 " --> pdb=" O ILE E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 57 removed outlier: 3.520A pdb=" N LEU E 45 " --> pdb=" O ASN E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 79 No H-bonds generated for 'chain 'E' and resid 77 through 79' Processing helix chain 'E' and resid 80 through 97 removed outlier: 8.109A pdb=" N ALA E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N ASP E 91 " --> pdb=" O LYS E 87 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS E 92 " --> pdb=" O LEU E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 165 removed outlier: 4.263A pdb=" N GLY E 159 " --> pdb=" O ALA E 156 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASP E 160 " --> pdb=" O GLU E 157 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS E 162 " --> pdb=" O GLY E 159 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASN E 163 " --> pdb=" O ASP E 160 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE E 165 " --> pdb=" O LYS E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 181 removed outlier: 3.553A pdb=" N GLU E 181 " --> pdb=" O GLU E 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 20 removed outlier: 4.250A pdb=" N ILE G 13 " --> pdb=" O ASN G 9 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS G 14 " --> pdb=" O ARG G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 57 Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 89 through 98 Processing helix chain 'G' and resid 140 through 144 removed outlier: 3.722A pdb=" N ASP G 143 " --> pdb=" O PHE G 140 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N CYS G 144 " --> pdb=" O GLN G 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 140 through 144' Processing helix chain 'G' and resid 161 through 166 Processing helix chain 'G' and resid 166 through 181 Processing helix chain 'I' and resid 9 through 20 Processing helix chain 'I' and resid 41 through 57 Processing helix chain 'I' and resid 80 through 89 Processing helix chain 'I' and resid 89 through 98 Processing helix chain 'I' and resid 140 through 144 removed outlier: 4.277A pdb=" N CYS I 144 " --> pdb=" O GLN I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 159 removed outlier: 4.207A pdb=" N MET I 158 " --> pdb=" O THR I 154 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY I 159 " --> pdb=" O PHE I 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 154 through 159' Processing helix chain 'I' and resid 159 through 166 Processing helix chain 'I' and resid 166 through 180 Processing helix chain 'M' and resid 11 through 20 removed outlier: 3.939A pdb=" N GLU M 15 " --> pdb=" O HIS M 11 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 58 Processing helix chain 'M' and resid 80 through 89 Processing helix chain 'M' and resid 89 through 98 Processing helix chain 'M' and resid 140 through 144 removed outlier: 4.541A pdb=" N CYS M 144 " --> pdb=" O GLN M 141 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 165 removed outlier: 4.111A pdb=" N ARG M 161 " --> pdb=" O MET M 158 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS M 162 " --> pdb=" O GLY M 159 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN M 163 " --> pdb=" O ASP M 160 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU M 164 " --> pdb=" O ARG M 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 166 through 180 Processing helix chain 'K' and resid 2 through 11 Processing helix chain 'K' and resid 22 through 26 removed outlier: 3.712A pdb=" N LEU K 25 " --> pdb=" O SER K 22 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY K 26 " --> pdb=" O MET K 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 22 through 26' Processing helix chain 'K' and resid 29 through 36 Processing helix chain 'K' and resid 48 through 52 removed outlier: 4.246A pdb=" N GLY K 52 " --> pdb=" O ARG K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 66 Processing helix chain 'K' and resid 68 through 80 Processing helix chain 'K' and resid 89 through 98 removed outlier: 3.730A pdb=" N GLU K 93 " --> pdb=" O SER K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 119 removed outlier: 3.527A pdb=" N TYR K 119 " --> pdb=" O ALA K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 133 removed outlier: 3.761A pdb=" N ALA K 133 " --> pdb=" O VAL K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 165 Processing helix chain 'K' and resid 170 through 181 removed outlier: 3.504A pdb=" N ILE K 174 " --> pdb=" O THR K 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 211 removed outlier: 3.696A pdb=" N LEU K 207 " --> pdb=" O LYS K 203 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP K 208 " --> pdb=" O LEU K 204 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS K 209 " --> pdb=" O SER K 205 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN K 211 " --> pdb=" O LEU K 207 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 236 removed outlier: 3.734A pdb=" N GLU K 232 " --> pdb=" O ASN K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 249 through 263 removed outlier: 4.065A pdb=" N ASN K 260 " --> pdb=" O GLU K 256 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE K 261 " --> pdb=" O PHE K 257 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU K 263 " --> pdb=" O LYS K 259 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 10 Processing helix chain 'O' and resid 18 through 23 removed outlier: 4.159A pdb=" N SER O 22 " --> pdb=" O GLY O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 24 through 26 No H-bonds generated for 'chain 'O' and resid 24 through 26' Processing helix chain 'O' and resid 29 through 41 Processing helix chain 'O' and resid 47 through 51 removed outlier: 4.182A pdb=" N THR O 50 " --> pdb=" O ILE O 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 54 through 66 Processing helix chain 'O' and resid 68 through 79 Processing helix chain 'O' and resid 89 through 98 Processing helix chain 'O' and resid 110 through 119 Processing helix chain 'O' and resid 128 through 135 removed outlier: 4.114A pdb=" N ALA O 133 " --> pdb=" O SER O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 158 through 166 removed outlier: 3.517A pdb=" N TYR O 162 " --> pdb=" O ASP O 158 " (cutoff:3.500A) Processing helix chain 'O' and resid 170 through 181 removed outlier: 3.544A pdb=" N ILE O 174 " --> pdb=" O THR O 170 " (cutoff:3.500A) Processing helix chain 'O' and resid 194 through 211 removed outlier: 3.516A pdb=" N PHE O 201 " --> pdb=" O ILE O 197 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU O 207 " --> pdb=" O LYS O 203 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TRP O 208 " --> pdb=" O LEU O 204 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS O 209 " --> pdb=" O SER O 205 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU O 210 " --> pdb=" O LYS O 206 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN O 211 " --> pdb=" O LEU O 207 " (cutoff:3.500A) Processing helix chain 'O' and resid 228 through 236 Processing helix chain 'O' and resid 252 through 263 removed outlier: 4.492A pdb=" N ASN O 260 " --> pdb=" O GLU O 256 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE O 261 " --> pdb=" O PHE O 257 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU O 263 " --> pdb=" O LYS O 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 19 through 24 removed outlier: 3.509A pdb=" N SER B 22 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET B 23 " --> pdb=" O GLY B 20 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASN B 24 " --> pdb=" O VAL B 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 19 through 24' Processing helix chain 'B' and resid 29 through 42 removed outlier: 3.710A pdb=" N LEU B 33 " --> pdb=" O SER B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 51 removed outlier: 4.631A pdb=" N PHE B 51 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 65 removed outlier: 3.506A pdb=" N GLU B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 80 Processing helix chain 'B' and resid 85 through 88 removed outlier: 3.979A pdb=" N LYS B 88 " --> pdb=" O ASP B 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 85 through 88' Processing helix chain 'B' and resid 89 through 97 Processing helix chain 'B' and resid 110 through 119 removed outlier: 3.530A pdb=" N TYR B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 135 removed outlier: 3.861A pdb=" N ILE B 135 " --> pdb=" O ILE B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 181 removed outlier: 3.552A pdb=" N ILE B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 211 removed outlier: 3.772A pdb=" N ARG B 198 " --> pdb=" O ASP B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 238 removed outlier: 3.962A pdb=" N GLN B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TRP B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 260 removed outlier: 4.075A pdb=" N ASN B 260 " --> pdb=" O GLU B 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 22 through 26 removed outlier: 3.686A pdb=" N LEU D 25 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY D 26 " --> pdb=" O MET D 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 22 through 26' Processing helix chain 'D' and resid 29 through 41 Processing helix chain 'D' and resid 46 through 51 removed outlier: 3.710A pdb=" N PHE D 51 " --> pdb=" O ILE D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 66 Processing helix chain 'D' and resid 68 through 80 removed outlier: 3.573A pdb=" N HIS D 80 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 98 removed outlier: 3.522A pdb=" N ALA D 98 " --> pdb=" O TYR D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 119 removed outlier: 3.517A pdb=" N TYR D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 135 removed outlier: 3.540A pdb=" N ILE D 132 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA D 133 " --> pdb=" O SER D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 168 removed outlier: 3.779A pdb=" N PHE D 168 " --> pdb=" O GLN D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 181 Processing helix chain 'D' and resid 195 through 211 Processing helix chain 'D' and resid 228 through 237 removed outlier: 3.819A pdb=" N GLN D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 263 removed outlier: 4.301A pdb=" N ASN D 260 " --> pdb=" O GLU D 256 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N PHE D 261 " --> pdb=" O PHE D 257 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL D 262 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 20 removed outlier: 3.513A pdb=" N LYS F 14 " --> pdb=" O ARG F 10 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASN F 17 " --> pdb=" O ILE F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 57 Processing helix chain 'F' and resid 80 through 89 Processing helix chain 'F' and resid 89 through 98 Processing helix chain 'F' and resid 154 through 159 removed outlier: 3.536A pdb=" N GLY F 159 " --> pdb=" O PHE F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 165 removed outlier: 4.238A pdb=" N ASN F 163 " --> pdb=" O ASP F 160 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU F 164 " --> pdb=" O ARG F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 180 Processing helix chain 'H' and resid 9 through 20 removed outlier: 3.692A pdb=" N ILE H 13 " --> pdb=" O ASN H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 57 Processing helix chain 'H' and resid 77 through 79 No H-bonds generated for 'chain 'H' and resid 77 through 79' Processing helix chain 'H' and resid 80 through 89 Processing helix chain 'H' and resid 89 through 98 Processing helix chain 'H' and resid 140 through 144 removed outlier: 4.151A pdb=" N ASP H 143 " --> pdb=" O PHE H 140 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N CYS H 144 " --> pdb=" O GLN H 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 140 through 144' Processing helix chain 'H' and resid 154 through 158 removed outlier: 3.686A pdb=" N MET H 158 " --> pdb=" O PHE H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 164 Processing helix chain 'H' and resid 166 through 180 Processing helix chain 'J' and resid 9 through 20 Processing helix chain 'J' and resid 41 through 57 Processing helix chain 'J' and resid 80 through 89 Processing helix chain 'J' and resid 89 through 98 Processing helix chain 'J' and resid 140 through 144 removed outlier: 4.287A pdb=" N CYS J 144 " --> pdb=" O GLN J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 154 through 159 Processing helix chain 'J' and resid 160 through 165 removed outlier: 3.773A pdb=" N GLU J 164 " --> pdb=" O ARG J 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 180 Processing helix chain 'N' and resid 11 through 20 removed outlier: 3.990A pdb=" N GLU N 15 " --> pdb=" O HIS N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 58 Processing helix chain 'N' and resid 80 through 89 removed outlier: 3.636A pdb=" N LYS N 87 " --> pdb=" O ILE N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 98 Processing helix chain 'N' and resid 140 through 144 removed outlier: 4.369A pdb=" N CYS N 144 " --> pdb=" O GLN N 141 " (cutoff:3.500A) Processing helix chain 'N' and resid 154 through 159 removed outlier: 3.577A pdb=" N MET N 158 " --> pdb=" O THR N 154 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY N 159 " --> pdb=" O PHE N 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 154 through 159' Processing helix chain 'N' and resid 160 through 165 removed outlier: 3.527A pdb=" N GLU N 164 " --> pdb=" O ARG N 161 " (cutoff:3.500A) Processing helix chain 'N' and resid 166 through 182 removed outlier: 3.971A pdb=" N GLY N 182 " --> pdb=" O TYR N 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 10 Processing helix chain 'L' and resid 21 through 26 removed outlier: 3.564A pdb=" N ASN L 24 " --> pdb=" O VAL L 21 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU L 25 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY L 26 " --> pdb=" O MET L 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 21 through 26' Processing helix chain 'L' and resid 29 through 36 removed outlier: 3.571A pdb=" N LEU L 33 " --> pdb=" O SER L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 51 Processing helix chain 'L' and resid 54 through 65 Processing helix chain 'L' and resid 68 through 78 Processing helix chain 'L' and resid 89 through 98 Processing helix chain 'L' and resid 110 through 119 Processing helix chain 'L' and resid 129 through 135 Processing helix chain 'L' and resid 158 through 166 Processing helix chain 'L' and resid 170 through 181 removed outlier: 3.567A pdb=" N ILE L 174 " --> pdb=" O THR L 170 " (cutoff:3.500A) Processing helix chain 'L' and resid 194 through 211 removed outlier: 3.523A pdb=" N ARG L 198 " --> pdb=" O ASP L 194 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU L 207 " --> pdb=" O LYS L 203 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TRP L 208 " --> pdb=" O LEU L 204 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS L 209 " --> pdb=" O SER L 205 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLN L 211 " --> pdb=" O LEU L 207 " (cutoff:3.500A) Processing helix chain 'L' and resid 228 through 237 removed outlier: 3.845A pdb=" N GLU L 232 " --> pdb=" O ASN L 228 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN L 237 " --> pdb=" O GLU L 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 249 through 259 Processing helix chain 'L' and resid 260 through 262 No H-bonds generated for 'chain 'L' and resid 260 through 262' Processing helix chain 'P' and resid 2 through 11 Processing helix chain 'P' and resid 18 through 26 removed outlier: 4.126A pdb=" N SER P 22 " --> pdb=" O GLY P 18 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN P 24 " --> pdb=" O GLY P 20 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU P 25 " --> pdb=" O VAL P 21 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY P 26 " --> pdb=" O SER P 22 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 41 Processing helix chain 'P' and resid 47 through 51 removed outlier: 3.789A pdb=" N THR P 50 " --> pdb=" O ILE P 47 " (cutoff:3.500A) Processing helix chain 'P' and resid 54 through 66 Processing helix chain 'P' and resid 68 through 79 Processing helix chain 'P' and resid 85 through 88 removed outlier: 3.635A pdb=" N LYS P 88 " --> pdb=" O ASP P 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 85 through 88' Processing helix chain 'P' and resid 89 through 98 Processing helix chain 'P' and resid 110 through 119 Processing helix chain 'P' and resid 130 through 135 removed outlier: 3.822A pdb=" N ALA P 133 " --> pdb=" O SER P 130 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE P 135 " --> pdb=" O ILE P 132 " (cutoff:3.500A) Processing helix chain 'P' and resid 158 through 166 Processing helix chain 'P' and resid 170 through 181 removed outlier: 3.591A pdb=" N ILE P 174 " --> pdb=" O THR P 170 " (cutoff:3.500A) Processing helix chain 'P' and resid 194 through 211 removed outlier: 4.121A pdb=" N LEU P 207 " --> pdb=" O LYS P 203 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TRP P 208 " --> pdb=" O LEU P 204 " (cutoff:3.500A) Processing helix chain 'P' and resid 228 through 236 removed outlier: 3.582A pdb=" N GLU P 232 " --> pdb=" O ASN P 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 249 through 263 removed outlier: 4.173A pdb=" N ASN P 260 " --> pdb=" O GLU P 256 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE P 261 " --> pdb=" O PHE P 257 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL P 262 " --> pdb=" O LEU P 258 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU P 263 " --> pdb=" O LYS P 259 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 123 through 126 removed outlier: 4.849A pdb=" N ILE R 102 " --> pdb=" O VAL R 13 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N SER R 220 " --> pdb=" O GLY R 241 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE R 243 " --> pdb=" O SER R 220 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE R 222 " --> pdb=" O ILE R 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'T' and resid 123 through 126 removed outlier: 7.249A pdb=" N VAL T 13 " --> pdb=" O ILE T 102 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N TYR T 104 " --> pdb=" O VAL T 13 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N LEU T 15 " --> pdb=" O TYR T 104 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE T 14 " --> pdb=" O LEU T 186 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE T 188 " --> pdb=" O ILE T 14 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N PHE T 16 " --> pdb=" O ILE T 188 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL T 185 " --> pdb=" O TYR T 221 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N PHE T 223 " --> pdb=" O VAL T 185 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N PHE T 187 " --> pdb=" O PHE T 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'V' and resid 26 through 30 removed outlier: 6.454A pdb=" N ILE V 3 " --> pdb=" O LEU V 28 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N SER V 30 " --> pdb=" O ILE V 3 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N PHE V 5 " --> pdb=" O SER V 30 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N PHE V 62 " --> pdb=" O ASN V 2 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ARG V 4 " --> pdb=" O PHE V 62 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N GLU V 64 " --> pdb=" O ARG V 4 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N ILE V 6 " --> pdb=" O GLU V 64 " (cutoff:3.500A) removed outlier: 10.941A pdb=" N THR V 66 " --> pdb=" O ILE V 6 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS V 65 " --> pdb=" O ILE V 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'X' and resid 26 through 28 removed outlier: 8.525A pdb=" N PHE X 62 " --> pdb=" O ASN X 2 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ARG X 4 " --> pdb=" O PHE X 62 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N GLU X 64 " --> pdb=" O ARG X 4 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Z' and resid 2 through 6 Processing sheet with id=AA6, first strand: chain 'Z' and resid 61 through 70 Processing sheet with id=AA7, first strand: chain 'Z' and resid 61 through 70 removed outlier: 3.801A pdb=" N ALA Z 107 " --> pdb=" O THR Z 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'd' and resid 26 through 30 removed outlier: 6.178A pdb=" N ILE d 3 " --> pdb=" O LEU d 28 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N SER d 30 " --> pdb=" O ILE d 3 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N PHE d 5 " --> pdb=" O SER d 30 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N PHE d 62 " --> pdb=" O ASN d 2 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ARG d 4 " --> pdb=" O PHE d 62 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N GLU d 64 " --> pdb=" O ARG d 4 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N ILE d 6 " --> pdb=" O GLU d 64 " (cutoff:3.500A) removed outlier: 11.129A pdb=" N THR d 66 " --> pdb=" O ILE d 6 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'd' and resid 26 through 30 removed outlier: 6.178A pdb=" N ILE d 3 " --> pdb=" O LEU d 28 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N SER d 30 " --> pdb=" O ILE d 3 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N PHE d 5 " --> pdb=" O SER d 30 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N PHE d 62 " --> pdb=" O ASN d 2 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ARG d 4 " --> pdb=" O PHE d 62 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N GLU d 64 " --> pdb=" O ARG d 4 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N ILE d 6 " --> pdb=" O GLU d 64 " (cutoff:3.500A) removed outlier: 11.129A pdb=" N THR d 66 " --> pdb=" O ILE d 6 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 141 through 144 removed outlier: 7.526A pdb=" N VAL b 13 " --> pdb=" O ILE b 102 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N TYR b 104 " --> pdb=" O VAL b 13 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU b 15 " --> pdb=" O TYR b 104 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL b 185 " --> pdb=" O TYR b 221 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N PHE b 223 " --> pdb=" O VAL b 185 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N PHE b 187 " --> pdb=" O PHE b 223 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N SER b 220 " --> pdb=" O GLY b 241 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ILE b 243 " --> pdb=" O SER b 220 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE b 222 " --> pdb=" O ILE b 243 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'f' and resid 123 through 126 removed outlier: 6.821A pdb=" N ILE f 103 " --> pdb=" O ILE f 143 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL f 13 " --> pdb=" O ILE f 102 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N TYR f 104 " --> pdb=" O VAL f 13 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LEU f 15 " --> pdb=" O TYR f 104 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE f 14 " --> pdb=" O LEU f 186 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ILE f 188 " --> pdb=" O ILE f 14 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE f 16 " --> pdb=" O ILE f 188 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N VAL f 185 " --> pdb=" O TYR f 221 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N PHE f 223 " --> pdb=" O VAL f 185 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N PHE f 187 " --> pdb=" O PHE f 223 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE f 222 " --> pdb=" O GLY f 241 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 123 through 126 removed outlier: 5.962A pdb=" N ILE A 124 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LYS A 144 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE A 126 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL A 13 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N TYR A 104 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU A 15 " --> pdb=" O TYR A 104 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL A 185 " --> pdb=" O TYR A 221 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N PHE A 223 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N PHE A 187 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER A 220 " --> pdb=" O GLY A 241 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE A 243 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE A 222 " --> pdb=" O ILE A 243 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 13 through 15 removed outlier: 6.041A pdb=" N ILE C 14 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL C 185 " --> pdb=" O TYR C 221 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N PHE C 223 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N PHE C 187 " --> pdb=" O PHE C 223 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 102 through 105 Processing sheet with id=AB6, first strand: chain 'E' and resid 26 through 30 removed outlier: 6.637A pdb=" N ILE E 3 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N SER E 30 " --> pdb=" O ILE E 3 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE E 5 " --> pdb=" O SER E 30 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N PHE E 62 " --> pdb=" O ASN E 2 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG E 4 " --> pdb=" O PHE E 62 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLU E 64 " --> pdb=" O ARG E 4 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N ILE E 6 " --> pdb=" O GLU E 64 " (cutoff:3.500A) removed outlier: 11.287A pdb=" N THR E 66 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA E 107 " --> pdb=" O THR E 126 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 26 through 30 removed outlier: 8.657A pdb=" N PHE G 62 " --> pdb=" O ASN G 2 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ARG G 4 " --> pdb=" O PHE G 62 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N GLU G 64 " --> pdb=" O ARG G 4 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N ILE G 6 " --> pdb=" O GLU G 64 " (cutoff:3.500A) removed outlier: 11.203A pdb=" N THR G 66 " --> pdb=" O ILE G 6 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR G 109 " --> pdb=" O GLY G 124 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 2 through 4 removed outlier: 6.149A pdb=" N ILE I 3 " --> pdb=" O LEU I 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'I' and resid 61 through 70 Processing sheet with id=AC1, first strand: chain 'M' and resid 26 through 30 removed outlier: 6.003A pdb=" N ILE M 3 " --> pdb=" O LEU M 28 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N SER M 30 " --> pdb=" O ILE M 3 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N PHE M 5 " --> pdb=" O SER M 30 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N PHE M 62 " --> pdb=" O ASN M 2 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG M 4 " --> pdb=" O PHE M 62 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N GLU M 64 " --> pdb=" O ARG M 4 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N ILE M 6 " --> pdb=" O GLU M 64 " (cutoff:3.500A) removed outlier: 11.360A pdb=" N THR M 66 " --> pdb=" O ILE M 6 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 26 through 30 removed outlier: 6.003A pdb=" N ILE M 3 " --> pdb=" O LEU M 28 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N SER M 30 " --> pdb=" O ILE M 3 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N PHE M 5 " --> pdb=" O SER M 30 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N PHE M 62 " --> pdb=" O ASN M 2 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG M 4 " --> pdb=" O PHE M 62 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N GLU M 64 " --> pdb=" O ARG M 4 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N ILE M 6 " --> pdb=" O GLU M 64 " (cutoff:3.500A) removed outlier: 11.360A pdb=" N THR M 66 " --> pdb=" O ILE M 6 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 141 through 144 removed outlier: 6.677A pdb=" N ILE K 103 " --> pdb=" O ILE K 143 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL K 13 " --> pdb=" O ILE K 102 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N TYR K 104 " --> pdb=" O VAL K 13 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU K 15 " --> pdb=" O TYR K 104 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE K 14 " --> pdb=" O LEU K 186 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ILE K 188 " --> pdb=" O ILE K 14 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N PHE K 16 " --> pdb=" O ILE K 188 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER K 220 " --> pdb=" O GLY K 241 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ILE K 243 " --> pdb=" O SER K 220 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE K 222 " --> pdb=" O ILE K 243 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'O' and resid 123 through 126 removed outlier: 7.073A pdb=" N VAL O 13 " --> pdb=" O ILE O 102 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N TYR O 104 " --> pdb=" O VAL O 13 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N LEU O 15 " --> pdb=" O TYR O 104 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE O 14 " --> pdb=" O LEU O 186 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ILE O 188 " --> pdb=" O ILE O 14 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE O 16 " --> pdb=" O ILE O 188 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL O 185 " --> pdb=" O TYR O 221 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N PHE O 223 " --> pdb=" O VAL O 185 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N PHE O 187 " --> pdb=" O PHE O 223 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY O 241 " --> pdb=" O SER O 220 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 123 through 126 removed outlier: 5.081A pdb=" N ILE B 102 " --> pdb=" O VAL B 13 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL B 185 " --> pdb=" O TYR B 221 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N PHE B 223 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N PHE B 187 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N SER B 220 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE B 243 " --> pdb=" O SER B 220 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE B 222 " --> pdb=" O ILE B 243 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 123 through 126 removed outlier: 6.018A pdb=" N ILE D 124 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LYS D 144 " --> pdb=" O ILE D 124 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE D 126 " --> pdb=" O LYS D 144 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE D 103 " --> pdb=" O ILE D 143 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL D 13 " --> pdb=" O ILE D 102 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N TYR D 104 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LEU D 15 " --> pdb=" O TYR D 104 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE D 14 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N VAL D 185 " --> pdb=" O TYR D 221 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N PHE D 223 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N PHE D 187 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N SER D 220 " --> pdb=" O GLY D 241 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE D 243 " --> pdb=" O SER D 220 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE D 222 " --> pdb=" O ILE D 243 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'F' and resid 2 through 3 Processing sheet with id=AC8, first strand: chain 'F' and resid 61 through 70 Processing sheet with id=AC9, first strand: chain 'H' and resid 26 through 30 removed outlier: 6.208A pdb=" N ILE H 3 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N SER H 30 " --> pdb=" O ILE H 3 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N PHE H 5 " --> pdb=" O SER H 30 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N PHE H 62 " --> pdb=" O ASN H 2 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ARG H 4 " --> pdb=" O PHE H 62 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N GLU H 64 " --> pdb=" O ARG H 4 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N ILE H 6 " --> pdb=" O GLU H 64 " (cutoff:3.500A) removed outlier: 12.234A pdb=" N THR H 66 " --> pdb=" O ILE H 6 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU H 105 " --> pdb=" O GLY H 128 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 26 through 30 removed outlier: 3.611A pdb=" N LEU J 28 " --> pdb=" O ILE J 3 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N PHE J 62 " --> pdb=" O ASN J 2 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG J 4 " --> pdb=" O PHE J 62 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N GLU J 64 " --> pdb=" O ARG J 4 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N ILE J 6 " --> pdb=" O GLU J 64 " (cutoff:3.500A) removed outlier: 11.297A pdb=" N THR J 66 " --> pdb=" O ILE J 6 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY J 112 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS J 65 " --> pdb=" O ILE J 110 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 26 through 30 removed outlier: 3.704A pdb=" N PHE N 5 " --> pdb=" O LEU N 28 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N PHE N 62 " --> pdb=" O ASN N 2 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ARG N 4 " --> pdb=" O PHE N 62 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N GLU N 64 " --> pdb=" O ARG N 4 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N ILE N 6 " --> pdb=" O GLU N 64 " (cutoff:3.500A) removed outlier: 11.377A pdb=" N THR N 66 " --> pdb=" O ILE N 6 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 26 through 30 removed outlier: 3.704A pdb=" N PHE N 5 " --> pdb=" O LEU N 28 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N PHE N 62 " --> pdb=" O ASN N 2 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ARG N 4 " --> pdb=" O PHE N 62 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N GLU N 64 " --> pdb=" O ARG N 4 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N ILE N 6 " --> pdb=" O GLU N 64 " (cutoff:3.500A) removed outlier: 11.377A pdb=" N THR N 66 " --> pdb=" O ILE N 6 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 141 through 144 removed outlier: 7.117A pdb=" N VAL L 13 " --> pdb=" O ILE L 102 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N TYR L 104 " --> pdb=" O VAL L 13 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU L 15 " --> pdb=" O TYR L 104 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER L 220 " --> pdb=" O GLY L 241 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ILE L 243 " --> pdb=" O SER L 220 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE L 222 " --> pdb=" O ILE L 243 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 123 through 126 removed outlier: 7.255A pdb=" N VAL P 13 " --> pdb=" O ILE P 102 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N TYR P 104 " --> pdb=" O VAL P 13 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU P 15 " --> pdb=" O TYR P 104 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE P 14 " --> pdb=" O LEU P 186 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 221 through 224 1896 hydrogen bonds defined for protein. 5469 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: 9.94 Time building geometry restraints manager: 5.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9952 1.33 - 1.45: 10484 1.45 - 1.58: 23964 1.58 - 1.70: 12 1.70 - 1.83: 240 Bond restraints: 44652 Sorted by residual: bond pdb=" CA GLN B 217 " pdb=" C GLN B 217 " ideal model delta sigma weight residual 1.524 1.448 0.076 1.26e-02 6.30e+03 3.64e+01 bond pdb=" CA TYR O 202 " pdb=" C TYR O 202 " ideal model delta sigma weight residual 1.523 1.447 0.076 1.34e-02 5.57e+03 3.26e+01 bond pdb=" C PHE I 76 " pdb=" N PRO I 77 " ideal model delta sigma weight residual 1.335 1.409 -0.074 1.36e-02 5.41e+03 2.96e+01 bond pdb=" CA TYR A 162 " pdb=" C TYR A 162 " ideal model delta sigma weight residual 1.523 1.450 0.073 1.34e-02 5.57e+03 2.95e+01 bond pdb=" CA GLN R 217 " pdb=" C GLN R 217 " ideal model delta sigma weight residual 1.524 1.456 0.068 1.26e-02 6.30e+03 2.94e+01 ... (remaining 44647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.30: 59934 6.30 - 12.60: 272 12.60 - 18.90: 18 18.90 - 25.20: 3 25.20 - 31.50: 1 Bond angle restraints: 60228 Sorted by residual: angle pdb=" N GLN B 217 " pdb=" CA GLN B 217 " pdb=" C GLN B 217 " ideal model delta sigma weight residual 109.81 89.76 20.05 2.21e+00 2.05e-01 8.23e+01 angle pdb=" CA LEU P 166 " pdb=" CB LEU P 166 " pdb=" CG LEU P 166 " ideal model delta sigma weight residual 116.30 147.80 -31.50 3.50e+00 8.16e-02 8.10e+01 angle pdb=" N LYS b 212 " pdb=" CA LYS b 212 " pdb=" C LYS b 212 " ideal model delta sigma weight residual 113.50 99.03 14.47 1.65e+00 3.67e-01 7.69e+01 angle pdb=" N TRP C 208 " pdb=" CA TRP C 208 " pdb=" C TRP C 208 " ideal model delta sigma weight residual 111.36 103.55 7.81 1.09e+00 8.42e-01 5.14e+01 angle pdb=" C HIS b 36 " pdb=" N ILE b 37 " pdb=" CA ILE b 37 " ideal model delta sigma weight residual 121.97 134.25 -12.28 1.80e+00 3.09e-01 4.65e+01 ... (remaining 60223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 23187 18.03 - 36.05: 2714 36.05 - 54.08: 753 54.08 - 72.11: 137 72.11 - 90.14: 41 Dihedral angle restraints: 26832 sinusoidal: 11232 harmonic: 15600 Sorted by residual: dihedral pdb=" CA PRO L 45 " pdb=" C PRO L 45 " pdb=" N ASP L 46 " pdb=" CA ASP L 46 " ideal model delta harmonic sigma weight residual 180.00 152.68 27.32 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA ILE L 37 " pdb=" C ILE L 37 " pdb=" N ALA L 38 " pdb=" CA ALA L 38 " ideal model delta harmonic sigma weight residual 180.00 155.10 24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA ILE b 37 " pdb=" C ILE b 37 " pdb=" N ALA b 38 " pdb=" CA ALA b 38 " ideal model delta harmonic sigma weight residual 180.00 156.56 23.44 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 26829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 6314 0.147 - 0.294: 185 0.294 - 0.442: 13 0.442 - 0.589: 2 0.589 - 0.736: 2 Chirality restraints: 6516 Sorted by residual: chirality pdb=" CB ILE E 6 " pdb=" CA ILE E 6 " pdb=" CG1 ILE E 6 " pdb=" CG2 ILE E 6 " both_signs ideal model delta sigma weight residual False 2.64 1.91 0.74 2.00e-01 2.50e+01 1.35e+01 chirality pdb=" CB ILE V 6 " pdb=" CA ILE V 6 " pdb=" CG1 ILE V 6 " pdb=" CG2 ILE V 6 " both_signs ideal model delta sigma weight residual False 2.64 2.02 0.62 2.00e-01 2.50e+01 9.71e+00 chirality pdb=" CG LEU O 57 " pdb=" CB LEU O 57 " pdb=" CD1 LEU O 57 " pdb=" CD2 LEU O 57 " both_signs ideal model delta sigma weight residual False -2.59 -2.07 -0.51 2.00e-01 2.50e+01 6.63e+00 ... (remaining 6513 not shown) Planarity restraints: 7668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE T 201 " -0.038 2.00e-02 2.50e+03 3.99e-02 2.78e+01 pdb=" CG PHE T 201 " 0.093 2.00e-02 2.50e+03 pdb=" CD1 PHE T 201 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE T 201 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE T 201 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE T 201 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE T 201 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP L 158 " 0.026 2.00e-02 2.50e+03 5.20e-02 2.70e+01 pdb=" CG ASP L 158 " -0.090 2.00e-02 2.50e+03 pdb=" OD1 ASP L 158 " 0.033 2.00e-02 2.50e+03 pdb=" OD2 ASP L 158 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU f 236 " -0.024 2.00e-02 2.50e+03 4.96e-02 2.46e+01 pdb=" C GLU f 236 " 0.086 2.00e-02 2.50e+03 pdb=" O GLU f 236 " -0.033 2.00e-02 2.50e+03 pdb=" N GLN f 237 " -0.029 2.00e-02 2.50e+03 ... (remaining 7665 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 9848 2.77 - 3.30: 39897 3.30 - 3.84: 78508 3.84 - 4.37: 87992 4.37 - 4.90: 148928 Nonbonded interactions: 365173 Sorted by model distance: nonbonded pdb=" OD1 ASP C 158 " pdb=" OG SER C 161 " model vdw 2.239 3.040 nonbonded pdb=" O PHE B 163 " pdb=" N ARG B 165 " model vdw 2.241 3.120 nonbonded pdb=" C PHE B 163 " pdb=" N ARG B 165 " model vdw 2.241 3.350 nonbonded pdb=" O ARG H 10 " pdb=" NZ LYS H 14 " model vdw 2.246 3.120 nonbonded pdb=" O LYS P 219 " pdb=" OG SER P 220 " model vdw 2.247 3.040 ... (remaining 365168 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'K' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'b' selection = chain 'f' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.680 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 41.460 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 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 0.097 44652 Z= 0.411 Angle : 1.183 31.502 60228 Z= 0.643 Chirality : 0.066 0.736 6516 Planarity : 0.008 0.091 7668 Dihedral : 16.800 90.135 16800 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 1.71 % Allowed : 6.57 % Favored : 91.72 % Rotamer: Outliers : 4.26 % Allowed : 21.72 % Favored : 74.02 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.10), residues: 5328 helix: -2.62 (0.08), residues: 2184 sheet: -0.82 (0.16), residues: 1098 loop : -1.69 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG J 8 TYR 0.085 0.003 TYR K 48 PHE 0.093 0.003 PHE T 201 TRP 0.057 0.002 TRP H 142 HIS 0.008 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00738 (44652) covalent geometry : angle 1.18281 (60228) hydrogen bonds : bond 0.18009 ( 1855) hydrogen bonds : angle 7.84674 ( 5469) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10656 Ramachandran restraints generated. 5328 Oldfield, 0 Emsley, 5328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10656 Ramachandran restraints generated. 5328 Oldfield, 0 Emsley, 5328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 4812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 397 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 217 GLN cc_start: 0.8314 (tp-100) cc_final: 0.7814 (pp30) REVERT: T 3 GLN cc_start: 0.7275 (pm20) cc_final: 0.7055 (tp40) REVERT: T 75 MET cc_start: 0.8716 (mtp) cc_final: 0.8368 (mtp) REVERT: Z 38 GLN cc_start: 0.8743 (mp10) cc_final: 0.8321 (pt0) REVERT: d 84 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7816 (t80) REVERT: b 141 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8022 (mt0) REVERT: b 196 ASN cc_start: 0.8337 (OUTLIER) cc_final: 0.7217 (p0) REVERT: f 237 GLN cc_start: 0.9200 (tp-100) cc_final: 0.8922 (tp-100) REVERT: A 206 LYS cc_start: 0.9516 (OUTLIER) cc_final: 0.9305 (mtmt) REVERT: A 217 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8059 (tt0) REVERT: E 48 ASP cc_start: 0.8961 (OUTLIER) cc_final: 0.8751 (p0) REVERT: E 158 MET cc_start: 0.6947 (mmp) cc_final: 0.5214 (mmt) REVERT: G 158 MET cc_start: 0.6598 (pmm) cc_final: 0.6104 (pmm) REVERT: K 59 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8437 (mm-30) REVERT: K 138 ASN cc_start: 0.8248 (OUTLIER) cc_final: 0.7823 (m-40) REVERT: O 203 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.8045 (tppt) REVERT: D 75 MET cc_start: 0.9109 (mmm) cc_final: 0.8894 (mmm) REVERT: F 7 THR cc_start: 0.7468 (p) cc_final: 0.7259 (p) REVERT: F 167 MET cc_start: 0.8159 (pmm) cc_final: 0.7754 (pmm) REVERT: N 158 MET cc_start: 0.7064 (mmm) cc_final: 0.6625 (mpp) REVERT: L 48 TYR cc_start: 0.7711 (OUTLIER) cc_final: 0.6541 (m-80) REVERT: L 124 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8833 (pt) REVERT: L 128 SER cc_start: 0.8356 (OUTLIER) cc_final: 0.7977 (p) REVERT: L 129 VAL cc_start: 0.9019 (OUTLIER) cc_final: 0.8737 (p) REVERT: L 169 GLU cc_start: 0.8258 (mp0) cc_final: 0.8044 (pm20) REVERT: L 206 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8017 (mmtm) outliers start: 205 outliers final: 71 residues processed: 559 average time/residue: 0.2658 time to fit residues: 245.2515 Evaluate side-chains 424 residues out of total 4812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 340 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 23 MET Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 205 SER Chi-restraints excluded: chain R residue 208 TRP Chi-restraints excluded: chain R residue 219 LYS Chi-restraints excluded: chain T residue 213 LEU Chi-restraints excluded: chain V residue 91 ASP Chi-restraints excluded: chain Z residue 72 SER Chi-restraints excluded: chain d residue 84 PHE Chi-restraints excluded: chain b residue 125 LYS Chi-restraints excluded: chain b residue 129 VAL Chi-restraints excluded: chain b residue 131 ASP Chi-restraints excluded: chain b residue 136 ASP Chi-restraints excluded: chain b residue 141 GLN Chi-restraints excluded: chain b residue 166 LEU Chi-restraints excluded: chain b residue 196 ASN Chi-restraints excluded: chain b residue 197 ILE Chi-restraints excluded: chain b residue 212 LYS Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain b residue 215 GLU Chi-restraints excluded: chain f residue 186 LEU Chi-restraints excluded: chain f residue 192 LEU Chi-restraints excluded: chain f residue 193 SER Chi-restraints excluded: chain f residue 206 LYS Chi-restraints excluded: chain f residue 210 GLU Chi-restraints excluded: chain f residue 211 GLN Chi-restraints excluded: chain f residue 212 LYS Chi-restraints excluded: chain f residue 215 GLU Chi-restraints excluded: chain f residue 240 ILE Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 134 LYS Chi-restraints excluded: chain K residue 138 ASN Chi-restraints excluded: chain K residue 196 ASN Chi-restraints excluded: chain K residue 197 ILE Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 217 GLN Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain O residue 196 ASN Chi-restraints excluded: chain O residue 197 ILE Chi-restraints excluded: chain O residue 199 LEU Chi-restraints excluded: chain O residue 203 LYS Chi-restraints excluded: chain O residue 210 GLU Chi-restraints excluded: chain O residue 212 LYS Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain O residue 220 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain D residue 30 TRP Chi-restraints excluded: chain F residue 8 ARG Chi-restraints excluded: chain F residue 10 ARG Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 127 SER Chi-restraints excluded: chain L residue 128 SER Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain L residue 136 ASP Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain L residue 196 ASN Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain L residue 206 LYS Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 214 GLU Chi-restraints excluded: chain L residue 215 GLU Chi-restraints excluded: chain P residue 138 ASN Chi-restraints excluded: chain P residue 139 LYS Chi-restraints excluded: chain P residue 191 SER Chi-restraints excluded: chain P residue 199 LEU Chi-restraints excluded: chain P residue 200 LEU Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 209 LYS Chi-restraints excluded: chain P residue 212 LYS Chi-restraints excluded: chain P residue 215 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 394 optimal weight: 0.9980 chunk 430 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 265 optimal weight: 6.9990 chunk 523 optimal weight: 6.9990 chunk 497 optimal weight: 9.9990 chunk 414 optimal weight: 20.0000 chunk 310 optimal weight: 4.9990 chunk 488 optimal weight: 7.9990 chunk 366 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 217 GLN R 228 ASN T 211 GLN T 237 GLN V 9 ASN V 32 HIS V 41 ASN ** V 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN X 89 GLN ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 163 ASN Z 17 ASN d 89 GLN b 92 HIS ** b 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 247 ASN f 228 ASN A 32 GLN A 211 GLN A 217 GLN A 228 ASN C 92 HIS E 11 HIS E 43 HIS G 17 ASN G 95 GLN G 141 GLN ** I 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 17 ASN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 GLN M 89 GLN M 102 ASN K 32 GLN K 87 ASN K 118 ASN K 231 GLN K 247 ASN O 32 GLN ** D 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** F 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 ASN H 95 GLN H 141 GLN J 32 HIS N 89 GLN ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 163 ASN ** L 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.065871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.045441 restraints weight = 192750.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.047025 restraints weight = 94379.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.048048 restraints weight = 60693.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.048673 restraints weight = 45930.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.049070 restraints weight = 38703.950| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 44652 Z= 0.201 Angle : 0.670 10.417 60228 Z= 0.351 Chirality : 0.047 0.263 6516 Planarity : 0.005 0.076 7668 Dihedral : 7.651 87.116 6003 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.84 % Favored : 94.89 % Rotamer: Outliers : 3.74 % Allowed : 20.24 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.11), residues: 5328 helix: -1.13 (0.10), residues: 2442 sheet: -0.50 (0.16), residues: 1092 loop : -1.00 (0.15), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 198 TYR 0.033 0.001 TYR K 48 PHE 0.036 0.002 PHE Z 76 TRP 0.018 0.002 TRP L 208 HIS 0.004 0.001 HIS V 65 Details of bonding type rmsd covalent geometry : bond 0.00438 (44652) covalent geometry : angle 0.66966 (60228) hydrogen bonds : bond 0.04398 ( 1855) hydrogen bonds : angle 5.38907 ( 5469) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10656 Ramachandran restraints generated. 5328 Oldfield, 0 Emsley, 5328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10656 Ramachandran restraints generated. 5328 Oldfield, 0 Emsley, 5328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 4812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 377 time to evaluate : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 59 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8499 (tp30) REVERT: R 228 ASN cc_start: 0.9172 (OUTLIER) cc_final: 0.8744 (t0) REVERT: T 179 ASP cc_start: 0.8402 (m-30) cc_final: 0.8125 (m-30) REVERT: V 117 MET cc_start: 0.8474 (tpp) cc_final: 0.8068 (tpp) REVERT: V 173 ASP cc_start: 0.8204 (m-30) cc_final: 0.7994 (m-30) REVERT: Z 158 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7472 (ptp) REVERT: Z 167 MET cc_start: 0.7512 (pmm) cc_final: 0.7156 (pmm) REVERT: d 41 ASN cc_start: 0.9018 (t0) cc_final: 0.8717 (t0) REVERT: d 82 GLN cc_start: 0.7982 (tp40) cc_final: 0.7249 (tp-100) REVERT: d 86 ASP cc_start: 0.8513 (p0) cc_final: 0.8203 (p0) REVERT: d 91 ASP cc_start: 0.9266 (m-30) cc_final: 0.9042 (m-30) REVERT: b 164 GLN cc_start: 0.8802 (tp40) cc_final: 0.8237 (tp-100) REVERT: b 208 TRP cc_start: 0.8680 (p90) cc_final: 0.8184 (p90) REVERT: f 183 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8149 (mtpp) REVERT: f 194 ASP cc_start: 0.8780 (p0) cc_final: 0.8433 (p0) REVERT: f 208 TRP cc_start: 0.9008 (p90) cc_final: 0.8702 (p90) REVERT: f 237 GLN cc_start: 0.9330 (tp-100) cc_final: 0.9058 (tp-100) REVERT: A 16 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8066 (m-80) REVERT: A 248 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8221 (p0) REVERT: C 164 GLN cc_start: 0.9177 (mm110) cc_final: 0.8635 (mm-40) REVERT: C 199 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9177 (tt) REVERT: C 242 MET cc_start: 0.8391 (mtp) cc_final: 0.7936 (mtm) REVERT: E 158 MET cc_start: 0.5899 (mmp) cc_final: 0.5315 (mmt) REVERT: G 38 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8223 (mm110) REVERT: G 56 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9012 (tp) REVERT: I 158 MET cc_start: 0.8216 (pmm) cc_final: 0.7483 (pmm) REVERT: M 158 MET cc_start: 0.8135 (tpp) cc_final: 0.7596 (tpp) REVERT: K 59 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8499 (mm-30) REVERT: K 166 LEU cc_start: 0.8577 (mm) cc_final: 0.8372 (mt) REVERT: K 207 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9163 (mm) REVERT: K 242 MET cc_start: 0.8763 (mmm) cc_final: 0.8417 (tmm) REVERT: O 158 ASP cc_start: 0.7127 (p0) cc_final: 0.6902 (p0) REVERT: O 211 GLN cc_start: 0.8848 (tp-100) cc_final: 0.8413 (tp-100) REVERT: B 78 MET cc_start: 0.8967 (mmm) cc_final: 0.8676 (mmt) REVERT: B 164 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8513 (mm-40) REVERT: B 179 ASP cc_start: 0.8770 (m-30) cc_final: 0.8504 (m-30) REVERT: B 211 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8764 (mp10) REVERT: D 41 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8966 (mm) REVERT: D 75 MET cc_start: 0.9299 (mmm) cc_final: 0.8901 (mmm) REVERT: D 164 GLN cc_start: 0.9265 (mm-40) cc_final: 0.9025 (mm-40) REVERT: F 167 MET cc_start: 0.8042 (pmm) cc_final: 0.7609 (pmm) REVERT: H 2 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.8443 (m110) REVERT: H 117 MET cc_start: 0.8151 (mpp) cc_final: 0.7772 (mpp) REVERT: H 158 MET cc_start: 0.8453 (mmt) cc_final: 0.8089 (mmm) REVERT: J 41 ASN cc_start: 0.8852 (t0) cc_final: 0.8649 (t0) REVERT: N 117 MET cc_start: 0.8394 (mmm) cc_final: 0.8089 (mmm) REVERT: N 170 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7639 (pptt) REVERT: L 48 TYR cc_start: 0.8300 (OUTLIER) cc_final: 0.8070 (t80) REVERT: L 237 GLN cc_start: 0.8789 (mp10) cc_final: 0.8254 (mp10) REVERT: P 164 GLN cc_start: 0.9243 (tm-30) cc_final: 0.8808 (tm-30) REVERT: P 197 ILE cc_start: 0.9576 (mt) cc_final: 0.9361 (mt) REVERT: P 209 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7898 (ptmt) REVERT: P 239 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7526 (mtp-110) outliers start: 180 outliers final: 74 residues processed: 525 average time/residue: 0.2621 time to fit residues: 230.6413 Evaluate side-chains 420 residues out of total 4812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 329 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 GLU Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 219 LYS Chi-restraints excluded: chain R residue 228 ASN Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 170 THR Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 196 ASN Chi-restraints excluded: chain T residue 211 GLN Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain V residue 91 ASP Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 39 THR Chi-restraints excluded: chain Z residue 158 MET Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 165 ILE Chi-restraints excluded: chain b residue 125 LYS Chi-restraints excluded: chain b residue 131 ASP Chi-restraints excluded: chain b residue 136 ASP Chi-restraints excluded: chain b residue 170 THR Chi-restraints excluded: chain b residue 181 LEU Chi-restraints excluded: chain b residue 195 ILE Chi-restraints excluded: chain f residue 166 LEU Chi-restraints excluded: chain f residue 180 VAL Chi-restraints excluded: chain f residue 183 LYS Chi-restraints excluded: chain f residue 186 LEU Chi-restraints excluded: chain f residue 188 ILE Chi-restraints excluded: chain f residue 195 ILE Chi-restraints excluded: chain f residue 212 LYS Chi-restraints excluded: chain f residue 240 ILE Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 141 GLN Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 137 ASN Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 217 GLN Chi-restraints excluded: chain K residue 222 ILE Chi-restraints excluded: chain O residue 199 LEU Chi-restraints excluded: chain O residue 212 LYS Chi-restraints excluded: chain O residue 220 SER Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 211 GLN Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain F residue 8 ARG Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain H residue 2 ASN Chi-restraints excluded: chain H residue 11 HIS Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 114 CYS Chi-restraints excluded: chain J residue 140 PHE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 133 VAL Chi-restraints excluded: chain N residue 170 LYS Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 155 ILE Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 214 GLU Chi-restraints excluded: chain L residue 215 GLU Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 166 LEU Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 199 LEU Chi-restraints excluded: chain P residue 209 LYS Chi-restraints excluded: chain P residue 212 LYS Chi-restraints excluded: chain P residue 222 ILE Chi-restraints excluded: chain P residue 239 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 258 optimal weight: 1.9990 chunk 445 optimal weight: 10.0000 chunk 298 optimal weight: 9.9990 chunk 524 optimal weight: 5.9990 chunk 240 optimal weight: 9.9990 chunk 268 optimal weight: 9.9990 chunk 480 optimal weight: 0.5980 chunk 291 optimal weight: 20.0000 chunk 373 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 80 HIS T 211 GLN ** T 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 11 HIS ** V 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 74 ASN ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 74 ASN b 3 GLN b 24 ASN b 118 ASN ** b 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 GLN K 3 GLN K 32 GLN ** B 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 HIS F 65 HIS F 82 GLN H 2 ASN ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 127 GLN ** J 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.063205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.042514 restraints weight = 193742.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.044115 restraints weight = 91921.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.045128 restraints weight = 58019.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.045752 restraints weight = 43383.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.046053 restraints weight = 36303.292| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 44652 Z= 0.294 Angle : 0.705 12.215 60228 Z= 0.364 Chirality : 0.048 0.305 6516 Planarity : 0.005 0.086 7668 Dihedral : 6.039 84.977 5864 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.84 % Favored : 94.88 % Rotamer: Outliers : 4.70 % Allowed : 19.99 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.11), residues: 5328 helix: -0.60 (0.10), residues: 2556 sheet: -0.59 (0.16), residues: 1026 loop : -0.81 (0.16), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 8 TYR 0.038 0.002 TYR b 48 PHE 0.041 0.002 PHE Z 76 TRP 0.020 0.002 TRP K 208 HIS 0.007 0.001 HIS J 32 Details of bonding type rmsd covalent geometry : bond 0.00642 (44652) covalent geometry : angle 0.70481 (60228) hydrogen bonds : bond 0.03954 ( 1855) hydrogen bonds : angle 5.11106 ( 5469) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10656 Ramachandran restraints generated. 5328 Oldfield, 0 Emsley, 5328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10656 Ramachandran restraints generated. 5328 Oldfield, 0 Emsley, 5328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 4812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 226 poor density : 327 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 59 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8410 (tp30) REVERT: T 179 ASP cc_start: 0.8478 (m-30) cc_final: 0.8148 (m-30) REVERT: V 69 TYR cc_start: 0.8356 (m-80) cc_final: 0.7975 (m-10) REVERT: V 177 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8510 (tm-30) REVERT: X 10 ARG cc_start: 0.9051 (tpp-160) cc_final: 0.8844 (tpp-160) REVERT: Z 18 LYS cc_start: 0.8762 (tttt) cc_final: 0.8524 (pttm) REVERT: Z 35 ASP cc_start: 0.7979 (t0) cc_final: 0.7668 (t0) REVERT: Z 38 GLN cc_start: 0.8853 (mp10) cc_final: 0.8511 (mp10) REVERT: Z 158 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7252 (ptp) REVERT: Z 167 MET cc_start: 0.7572 (pmm) cc_final: 0.6299 (pmm) REVERT: Z 177 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8769 (pp20) REVERT: d 41 ASN cc_start: 0.9008 (t0) cc_final: 0.8689 (t0) REVERT: d 82 GLN cc_start: 0.8110 (tp40) cc_final: 0.7085 (tp40) REVERT: d 86 ASP cc_start: 0.8514 (p0) cc_final: 0.8197 (p0) REVERT: d 91 ASP cc_start: 0.9275 (m-30) cc_final: 0.8963 (m-30) REVERT: d 117 MET cc_start: 0.8719 (mmm) cc_final: 0.8474 (mmm) REVERT: d 158 MET cc_start: 0.7505 (mpp) cc_final: 0.7229 (mpp) REVERT: b 164 GLN cc_start: 0.9067 (tp40) cc_final: 0.8698 (tp40) REVERT: A 16 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.7879 (m-80) REVERT: A 224 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9221 (mm) REVERT: C 164 GLN cc_start: 0.9284 (mm110) cc_final: 0.8792 (mm-40) REVERT: C 199 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9200 (tt) REVERT: C 230 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8565 (pt) REVERT: C 242 MET cc_start: 0.8562 (mtp) cc_final: 0.8112 (mtm) REVERT: G 38 GLN cc_start: 0.8625 (mm-40) cc_final: 0.8293 (mm-40) REVERT: G 56 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9014 (tp) REVERT: I 158 MET cc_start: 0.8151 (pmm) cc_final: 0.7351 (pmm) REVERT: M 158 MET cc_start: 0.8296 (tpp) cc_final: 0.7657 (tpp) REVERT: K 78 MET cc_start: 0.9380 (mmp) cc_final: 0.9174 (mmp) REVERT: K 108 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.8038 (m-80) REVERT: K 166 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8214 (mt) REVERT: K 207 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9114 (mm) REVERT: K 242 MET cc_start: 0.8519 (mmm) cc_final: 0.8253 (tpt) REVERT: O 158 ASP cc_start: 0.7570 (p0) cc_final: 0.7225 (p0) REVERT: O 194 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8316 (p0) REVERT: O 211 GLN cc_start: 0.8607 (tp-100) cc_final: 0.8304 (tp-100) REVERT: B 78 MET cc_start: 0.9115 (mmm) cc_final: 0.8788 (mmt) REVERT: B 179 ASP cc_start: 0.8738 (m-30) cc_final: 0.8433 (m-30) REVERT: B 211 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8930 (mp10) REVERT: D 16 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.7820 (m-80) REVERT: D 75 MET cc_start: 0.9296 (mmm) cc_final: 0.8858 (mmm) REVERT: F 82 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8544 (tm-30) REVERT: F 167 MET cc_start: 0.8081 (pmm) cc_final: 0.7082 (pmm) REVERT: H 2 ASN cc_start: 0.8904 (m-40) cc_final: 0.8607 (m-40) REVERT: H 117 MET cc_start: 0.8325 (mpp) cc_final: 0.8048 (mpp) REVERT: H 158 MET cc_start: 0.8611 (mmt) cc_final: 0.8163 (mmm) REVERT: J 41 ASN cc_start: 0.8801 (t0) cc_final: 0.8503 (t0) REVERT: N 82 GLN cc_start: 0.8392 (mm110) cc_final: 0.8148 (mm-40) REVERT: N 117 MET cc_start: 0.8649 (mmm) cc_final: 0.8274 (mmm) REVERT: N 170 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7763 (pptt) REVERT: L 237 GLN cc_start: 0.9022 (mp10) cc_final: 0.8392 (mp10) REVERT: P 48 TYR cc_start: 0.8049 (OUTLIER) cc_final: 0.7517 (m-80) REVERT: P 164 GLN cc_start: 0.9279 (tm-30) cc_final: 0.8634 (tm-30) REVERT: P 181 LEU cc_start: 0.9253 (tt) cc_final: 0.8981 (pp) REVERT: P 204 LEU cc_start: 0.9338 (mt) cc_final: 0.9052 (mt) REVERT: P 242 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7654 (ptt) outliers start: 226 outliers final: 122 residues processed: 521 average time/residue: 0.2253 time to fit residues: 200.8720 Evaluate side-chains 446 residues out of total 4812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 305 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 GLU Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 219 LYS Chi-restraints excluded: chain T residue 16 PHE Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 51 PHE Chi-restraints excluded: chain T residue 170 THR Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 195 ILE Chi-restraints excluded: chain T residue 196 ASN Chi-restraints excluded: chain T residue 207 LEU Chi-restraints excluded: chain T residue 211 GLN Chi-restraints excluded: chain V residue 11 HIS Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain V residue 91 ASP Chi-restraints excluded: chain V residue 130 ILE Chi-restraints excluded: chain V residue 177 GLU Chi-restraints excluded: chain X residue 33 SER Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 39 THR Chi-restraints excluded: chain Z residue 130 ILE Chi-restraints excluded: chain Z residue 158 MET Chi-restraints excluded: chain Z residue 177 GLU Chi-restraints excluded: chain d residue 6 ILE Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 165 ILE Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 37 ILE Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 125 LYS Chi-restraints excluded: chain b residue 155 ILE Chi-restraints excluded: chain b residue 170 THR Chi-restraints excluded: chain b residue 181 LEU Chi-restraints excluded: chain b residue 195 ILE Chi-restraints excluded: chain b residue 215 GLU Chi-restraints excluded: chain f residue 166 LEU Chi-restraints excluded: chain f residue 180 VAL Chi-restraints excluded: chain f residue 186 LEU Chi-restraints excluded: chain f residue 188 ILE Chi-restraints excluded: chain f residue 195 ILE Chi-restraints excluded: chain f residue 212 LYS Chi-restraints excluded: chain f residue 222 ILE Chi-restraints excluded: chain f residue 240 ILE Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain M residue 11 HIS Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 166 SER Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain K residue 137 ASN Chi-restraints excluded: chain K residue 166 LEU Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 217 GLN Chi-restraints excluded: chain O residue 180 VAL Chi-restraints excluded: chain O residue 194 ASP Chi-restraints excluded: chain O residue 199 LEU Chi-restraints excluded: chain O residue 212 LYS Chi-restraints excluded: chain O residue 222 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 211 GLN Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 114 CYS Chi-restraints excluded: chain J residue 140 PHE Chi-restraints excluded: chain J residue 177 GLU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 133 VAL Chi-restraints excluded: chain N residue 170 LYS Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 155 ILE Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 214 GLU Chi-restraints excluded: chain L residue 215 GLU Chi-restraints excluded: chain P residue 48 TYR Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 166 LEU Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 199 LEU Chi-restraints excluded: chain P residue 212 LYS Chi-restraints excluded: chain P residue 222 ILE Chi-restraints excluded: chain P residue 242 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 110 optimal weight: 1.9990 chunk 415 optimal weight: 7.9990 chunk 374 optimal weight: 0.8980 chunk 214 optimal weight: 6.9990 chunk 452 optimal weight: 9.9990 chunk 455 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 82 optimal weight: 20.0000 chunk 423 optimal weight: 10.0000 chunk 189 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 80 HIS T 211 GLN ** T 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 141 GLN ** E 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 HIS ** M 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 GLN K 32 GLN ** D 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 GLN ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN L 164 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.064450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.043868 restraints weight = 191480.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.045531 restraints weight = 89225.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.046562 restraints weight = 55590.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.047206 restraints weight = 41443.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.047564 restraints weight = 34667.834| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 44652 Z= 0.154 Angle : 0.596 10.890 60228 Z= 0.306 Chirality : 0.046 0.301 6516 Planarity : 0.004 0.085 7668 Dihedral : 5.613 81.415 5847 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.30 % Favored : 95.46 % Rotamer: Outliers : 3.64 % Allowed : 21.05 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.12), residues: 5328 helix: -0.24 (0.10), residues: 2550 sheet: -0.53 (0.16), residues: 1038 loop : -0.68 (0.16), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 8 TYR 0.049 0.001 TYR K 48 PHE 0.027 0.001 PHE Z 76 TRP 0.050 0.001 TRP f 208 HIS 0.007 0.001 HIS J 32 Details of bonding type rmsd covalent geometry : bond 0.00348 (44652) covalent geometry : angle 0.59568 (60228) hydrogen bonds : bond 0.03399 ( 1855) hydrogen bonds : angle 4.84756 ( 5469) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10656 Ramachandran restraints generated. 5328 Oldfield, 0 Emsley, 5328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10656 Ramachandran restraints generated. 5328 Oldfield, 0 Emsley, 5328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 4812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 349 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 179 ASP cc_start: 0.8447 (m-30) cc_final: 0.8082 (m-30) REVERT: T 211 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8013 (pm20) REVERT: V 69 TYR cc_start: 0.8369 (m-80) cc_final: 0.7942 (m-80) REVERT: V 177 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8508 (tm-30) REVERT: Z 18 LYS cc_start: 0.8779 (tttt) cc_final: 0.8543 (pttm) REVERT: Z 35 ASP cc_start: 0.7967 (t0) cc_final: 0.7653 (t0) REVERT: Z 38 GLN cc_start: 0.8800 (mp10) cc_final: 0.8438 (mp10) REVERT: Z 158 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7557 (ptp) REVERT: Z 167 MET cc_start: 0.7743 (pmm) cc_final: 0.6343 (pmm) REVERT: d 41 ASN cc_start: 0.8960 (t0) cc_final: 0.8590 (t0) REVERT: d 82 GLN cc_start: 0.7976 (tp40) cc_final: 0.7538 (tp40) REVERT: d 87 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8584 (tppt) REVERT: d 91 ASP cc_start: 0.9239 (m-30) cc_final: 0.8919 (p0) REVERT: d 117 MET cc_start: 0.8602 (mmm) cc_final: 0.8344 (mmm) REVERT: b 164 GLN cc_start: 0.9010 (tp40) cc_final: 0.8585 (tp40) REVERT: f 201 PHE cc_start: 0.9443 (m-80) cc_final: 0.9182 (m-80) REVERT: f 237 GLN cc_start: 0.9457 (tp-100) cc_final: 0.9221 (tp-100) REVERT: A 16 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.7946 (m-80) REVERT: A 224 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9223 (mm) REVERT: A 248 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8360 (p0) REVERT: C 164 GLN cc_start: 0.9286 (mm110) cc_final: 0.8659 (mm-40) REVERT: C 242 MET cc_start: 0.8483 (mtp) cc_final: 0.8001 (mtm) REVERT: G 38 GLN cc_start: 0.8611 (mm-40) cc_final: 0.8202 (mm-40) REVERT: G 43 HIS cc_start: 0.8929 (m-70) cc_final: 0.8607 (m90) REVERT: G 158 MET cc_start: 0.6990 (pmm) cc_final: 0.6147 (pmm) REVERT: M 155 PHE cc_start: 0.7594 (OUTLIER) cc_final: 0.7262 (t80) REVERT: M 158 MET cc_start: 0.8446 (tpp) cc_final: 0.7787 (tpp) REVERT: K 32 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8808 (pm20) REVERT: K 41 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9305 (tt) REVERT: K 78 MET cc_start: 0.9354 (mmp) cc_final: 0.9083 (mmp) REVERT: K 108 TYR cc_start: 0.8798 (OUTLIER) cc_final: 0.7963 (m-80) REVERT: K 166 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8213 (mt) REVERT: K 207 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9138 (mm) REVERT: K 242 MET cc_start: 0.8536 (mmm) cc_final: 0.8258 (tpt) REVERT: O 158 ASP cc_start: 0.7624 (p0) cc_final: 0.7202 (p0) REVERT: O 159 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8071 (tp30) REVERT: O 194 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8097 (p0) REVERT: B 78 MET cc_start: 0.9111 (mmm) cc_final: 0.8806 (mmt) REVERT: B 179 ASP cc_start: 0.8786 (m-30) cc_final: 0.8470 (m-30) REVERT: B 211 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8697 (mp10) REVERT: D 16 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.7782 (m-80) REVERT: D 75 MET cc_start: 0.9222 (mmm) cc_final: 0.8784 (mmm) REVERT: F 167 MET cc_start: 0.8110 (pmm) cc_final: 0.7564 (pmm) REVERT: H 2 ASN cc_start: 0.8920 (m-40) cc_final: 0.8601 (m-40) REVERT: H 158 MET cc_start: 0.8681 (mmt) cc_final: 0.8286 (mmm) REVERT: J 41 ASN cc_start: 0.8839 (t0) cc_final: 0.8499 (t0) REVERT: J 177 GLU cc_start: 0.9509 (OUTLIER) cc_final: 0.9295 (tm-30) REVERT: N 82 GLN cc_start: 0.8417 (mm110) cc_final: 0.8192 (mm-40) REVERT: N 117 MET cc_start: 0.8637 (mmm) cc_final: 0.8307 (mmm) REVERT: N 170 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7783 (pptt) REVERT: L 231 GLN cc_start: 0.9407 (mp10) cc_final: 0.8872 (mp10) REVERT: L 237 GLN cc_start: 0.9005 (mp10) cc_final: 0.8352 (mp10) REVERT: P 48 TYR cc_start: 0.7980 (OUTLIER) cc_final: 0.7627 (m-80) REVERT: P 164 GLN cc_start: 0.9266 (tm-30) cc_final: 0.8736 (tm-30) REVERT: P 181 LEU cc_start: 0.9236 (tt) cc_final: 0.8970 (pp) REVERT: P 242 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7479 (ptt) outliers start: 175 outliers final: 104 residues processed: 501 average time/residue: 0.2379 time to fit residues: 207.2122 Evaluate side-chains 444 residues out of total 4812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 319 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 131 ASP Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain T residue 16 PHE Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 51 PHE Chi-restraints excluded: chain T residue 170 THR Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 195 ILE Chi-restraints excluded: chain T residue 196 ASN Chi-restraints excluded: chain T residue 207 LEU Chi-restraints excluded: chain T residue 211 GLN Chi-restraints excluded: chain V residue 11 HIS Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain V residue 83 ILE Chi-restraints excluded: chain V residue 91 ASP Chi-restraints excluded: chain V residue 133 VAL Chi-restraints excluded: chain V residue 177 GLU Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 80 LEU Chi-restraints excluded: chain Z residue 130 ILE Chi-restraints excluded: chain Z residue 133 VAL Chi-restraints excluded: chain Z residue 141 GLN Chi-restraints excluded: chain Z residue 158 MET Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 87 LYS Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 125 LYS Chi-restraints excluded: chain b residue 155 ILE Chi-restraints excluded: chain b residue 166 LEU Chi-restraints excluded: chain b residue 170 THR Chi-restraints excluded: chain b residue 181 LEU Chi-restraints excluded: chain b residue 195 ILE Chi-restraints excluded: chain b residue 215 GLU Chi-restraints excluded: chain f residue 155 ILE Chi-restraints excluded: chain f residue 180 VAL Chi-restraints excluded: chain f residue 186 LEU Chi-restraints excluded: chain f residue 188 ILE Chi-restraints excluded: chain f residue 195 ILE Chi-restraints excluded: chain f residue 212 LYS Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 177 GLU Chi-restraints excluded: chain M residue 11 HIS Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 155 PHE Chi-restraints excluded: chain M residue 166 SER Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 32 GLN Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain K residue 166 LEU Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 217 GLN Chi-restraints excluded: chain K residue 222 ILE Chi-restraints excluded: chain O residue 155 ILE Chi-restraints excluded: chain O residue 159 GLU Chi-restraints excluded: chain O residue 166 LEU Chi-restraints excluded: chain O residue 194 ASP Chi-restraints excluded: chain O residue 197 ILE Chi-restraints excluded: chain O residue 199 LEU Chi-restraints excluded: chain O residue 212 LYS Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 211 GLN Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 84 PHE Chi-restraints excluded: chain J residue 114 CYS Chi-restraints excluded: chain J residue 140 PHE Chi-restraints excluded: chain J residue 177 GLU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 133 VAL Chi-restraints excluded: chain N residue 170 LYS Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 155 ILE Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 214 GLU Chi-restraints excluded: chain L residue 215 GLU Chi-restraints excluded: chain P residue 48 TYR Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 166 LEU Chi-restraints excluded: chain P residue 199 LEU Chi-restraints excluded: chain P residue 212 LYS Chi-restraints excluded: chain P residue 222 ILE Chi-restraints excluded: chain P residue 242 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 398 optimal weight: 2.9990 chunk 452 optimal weight: 9.9990 chunk 185 optimal weight: 8.9990 chunk 338 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 352 optimal weight: 8.9990 chunk 514 optimal weight: 9.9990 chunk 226 optimal weight: 9.9990 chunk 488 optimal weight: 0.4980 chunk 277 optimal weight: 20.0000 chunk 306 optimal weight: 0.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 32 GLN T 211 GLN V 11 HIS ** V 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 217 GLN ** D 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 GLN ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 249 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.064085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.043567 restraints weight = 192185.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.045212 restraints weight = 89783.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.046243 restraints weight = 56018.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.046881 restraints weight = 41667.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.047254 restraints weight = 34863.165| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 44652 Z= 0.176 Angle : 0.597 11.452 60228 Z= 0.306 Chirality : 0.046 0.230 6516 Planarity : 0.004 0.086 7668 Dihedral : 5.307 73.930 5839 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.60 % Favored : 95.14 % Rotamer: Outliers : 4.14 % Allowed : 20.97 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.12), residues: 5328 helix: -0.09 (0.10), residues: 2550 sheet: -0.50 (0.16), residues: 1038 loop : -0.61 (0.16), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 8 TYR 0.039 0.001 TYR O 48 PHE 0.027 0.001 PHE I 93 TRP 0.028 0.001 TRP f 208 HIS 0.006 0.001 HIS J 32 Details of bonding type rmsd covalent geometry : bond 0.00393 (44652) covalent geometry : angle 0.59682 (60228) hydrogen bonds : bond 0.03282 ( 1855) hydrogen bonds : angle 4.77016 ( 5469) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10656 Ramachandran restraints generated. 5328 Oldfield, 0 Emsley, 5328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10656 Ramachandran restraints generated. 5328 Oldfield, 0 Emsley, 5328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 4812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 335 time to evaluate : 1.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 179 ASP cc_start: 0.8431 (m-30) cc_final: 0.8053 (m-30) REVERT: V 69 TYR cc_start: 0.8312 (m-80) cc_final: 0.7941 (m-80) REVERT: V 117 MET cc_start: 0.8631 (tpp) cc_final: 0.8179 (tpp) REVERT: V 177 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8530 (tm-30) REVERT: Z 18 LYS cc_start: 0.8809 (tttt) cc_final: 0.8550 (pttm) REVERT: Z 35 ASP cc_start: 0.8095 (t0) cc_final: 0.7768 (t0) REVERT: Z 38 GLN cc_start: 0.8791 (mp10) cc_final: 0.8462 (mp10) REVERT: Z 158 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7541 (ptp) REVERT: Z 167 MET cc_start: 0.7782 (pmm) cc_final: 0.6344 (pmm) REVERT: d 41 ASN cc_start: 0.8937 (t0) cc_final: 0.8545 (t0) REVERT: d 82 GLN cc_start: 0.7963 (tp40) cc_final: 0.7507 (tp40) REVERT: d 87 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8564 (tppt) REVERT: d 91 ASP cc_start: 0.9217 (m-30) cc_final: 0.8920 (p0) REVERT: d 117 MET cc_start: 0.8632 (mmm) cc_final: 0.8360 (mmm) REVERT: b 125 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8533 (tptp) REVERT: b 164 GLN cc_start: 0.9044 (tp40) cc_final: 0.8620 (tp40) REVERT: f 201 PHE cc_start: 0.9475 (m-80) cc_final: 0.8929 (m-80) REVERT: f 237 GLN cc_start: 0.9471 (tp-100) cc_final: 0.9233 (tp-100) REVERT: A 16 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.7986 (m-80) REVERT: A 224 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9215 (mm) REVERT: C 164 GLN cc_start: 0.9318 (mm110) cc_final: 0.8681 (mm-40) REVERT: C 242 MET cc_start: 0.8449 (mtp) cc_final: 0.7938 (mtm) REVERT: E 155 PHE cc_start: 0.7143 (OUTLIER) cc_final: 0.6501 (t80) REVERT: G 38 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8254 (mm110) REVERT: G 43 HIS cc_start: 0.8934 (m-70) cc_final: 0.8601 (m90) REVERT: M 155 PHE cc_start: 0.7574 (OUTLIER) cc_final: 0.7255 (t80) REVERT: M 158 MET cc_start: 0.8477 (tpp) cc_final: 0.7763 (tpp) REVERT: K 108 TYR cc_start: 0.8811 (OUTLIER) cc_final: 0.7911 (m-80) REVERT: K 166 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8002 (mt) REVERT: K 207 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9109 (mm) REVERT: K 242 MET cc_start: 0.8475 (mmm) cc_final: 0.8199 (tpt) REVERT: O 158 ASP cc_start: 0.7681 (p0) cc_final: 0.7220 (p0) REVERT: O 159 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8080 (tp30) REVERT: O 194 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8131 (p0) REVERT: O 195 ILE cc_start: 0.9303 (tt) cc_final: 0.9071 (tp) REVERT: O 217 GLN cc_start: 0.8700 (mp10) cc_final: 0.7909 (mp10) REVERT: B 78 MET cc_start: 0.9130 (mmm) cc_final: 0.8803 (mmt) REVERT: B 179 ASP cc_start: 0.8802 (m-30) cc_final: 0.8448 (m-30) REVERT: D 16 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.7897 (m-80) REVERT: D 44 ASP cc_start: 0.9049 (OUTLIER) cc_final: 0.8802 (t70) REVERT: D 75 MET cc_start: 0.9224 (mmm) cc_final: 0.8785 (mmm) REVERT: F 167 MET cc_start: 0.8073 (pmm) cc_final: 0.7487 (pmm) REVERT: H 2 ASN cc_start: 0.8968 (m-40) cc_final: 0.8624 (m-40) REVERT: H 117 MET cc_start: 0.8512 (mpp) cc_final: 0.8022 (mpp) REVERT: H 158 MET cc_start: 0.8685 (mmt) cc_final: 0.8254 (mmm) REVERT: J 41 ASN cc_start: 0.8869 (t0) cc_final: 0.8498 (t0) REVERT: J 125 GLU cc_start: 0.9369 (OUTLIER) cc_final: 0.8670 (tm-30) REVERT: J 177 GLU cc_start: 0.9493 (OUTLIER) cc_final: 0.9285 (tm-30) REVERT: N 117 MET cc_start: 0.8662 (mmm) cc_final: 0.8336 (mmm) REVERT: N 170 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7898 (pttp) REVERT: L 215 GLU cc_start: 0.3140 (OUTLIER) cc_final: 0.2723 (pp20) REVERT: L 231 GLN cc_start: 0.9419 (mp10) cc_final: 0.8882 (mp10) REVERT: L 237 GLN cc_start: 0.9024 (mp10) cc_final: 0.8439 (mp10) REVERT: P 48 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.7588 (m-80) REVERT: P 164 GLN cc_start: 0.9278 (tm-30) cc_final: 0.8676 (tm-30) REVERT: P 181 LEU cc_start: 0.9232 (tt) cc_final: 0.8974 (pp) REVERT: P 231 GLN cc_start: 0.9190 (mp10) cc_final: 0.8809 (mp10) REVERT: P 242 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7514 (ptt) outliers start: 199 outliers final: 122 residues processed: 501 average time/residue: 0.2358 time to fit residues: 205.5959 Evaluate side-chains 469 residues out of total 4812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 326 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 131 ASP Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain T residue 16 PHE Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 41 LEU Chi-restraints excluded: chain T residue 51 PHE Chi-restraints excluded: chain T residue 155 ILE Chi-restraints excluded: chain T residue 170 THR Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 195 ILE Chi-restraints excluded: chain T residue 196 ASN Chi-restraints excluded: chain T residue 207 LEU Chi-restraints excluded: chain T residue 211 GLN Chi-restraints excluded: chain V residue 11 HIS Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain V residue 83 ILE Chi-restraints excluded: chain V residue 91 ASP Chi-restraints excluded: chain V residue 133 VAL Chi-restraints excluded: chain V residue 177 GLU Chi-restraints excluded: chain X residue 33 SER Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 80 LEU Chi-restraints excluded: chain Z residue 130 ILE Chi-restraints excluded: chain Z residue 133 VAL Chi-restraints excluded: chain Z residue 141 GLN Chi-restraints excluded: chain Z residue 158 MET Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 87 LYS Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 125 LYS Chi-restraints excluded: chain b residue 155 ILE Chi-restraints excluded: chain b residue 166 LEU Chi-restraints excluded: chain b residue 170 THR Chi-restraints excluded: chain b residue 181 LEU Chi-restraints excluded: chain b residue 195 ILE Chi-restraints excluded: chain b residue 215 GLU Chi-restraints excluded: chain f residue 155 ILE Chi-restraints excluded: chain f residue 166 LEU Chi-restraints excluded: chain f residue 180 VAL Chi-restraints excluded: chain f residue 186 LEU Chi-restraints excluded: chain f residue 188 ILE Chi-restraints excluded: chain f residue 195 ILE Chi-restraints excluded: chain f residue 212 LYS Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 177 GLU Chi-restraints excluded: chain M residue 11 HIS Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 155 PHE Chi-restraints excluded: chain M residue 166 SER Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain K residue 166 LEU Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 222 ILE Chi-restraints excluded: chain O residue 155 ILE Chi-restraints excluded: chain O residue 159 GLU Chi-restraints excluded: chain O residue 166 LEU Chi-restraints excluded: chain O residue 194 ASP Chi-restraints excluded: chain O residue 197 ILE Chi-restraints excluded: chain O residue 199 LEU Chi-restraints excluded: chain O residue 212 LYS Chi-restraints excluded: chain O residue 220 SER Chi-restraints excluded: chain O residue 222 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 84 PHE Chi-restraints excluded: chain J residue 114 CYS Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 130 ILE Chi-restraints excluded: chain J residue 140 PHE Chi-restraints excluded: chain J residue 177 GLU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 133 VAL Chi-restraints excluded: chain N residue 170 LYS Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 155 ILE Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 214 GLU Chi-restraints excluded: chain L residue 215 GLU Chi-restraints excluded: chain P residue 48 TYR Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 155 ILE Chi-restraints excluded: chain P residue 166 LEU Chi-restraints excluded: chain P residue 199 LEU Chi-restraints excluded: chain P residue 212 LYS Chi-restraints excluded: chain P residue 222 ILE Chi-restraints excluded: chain P residue 242 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 109 optimal weight: 8.9990 chunk 525 optimal weight: 6.9990 chunk 361 optimal weight: 2.9990 chunk 382 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 216 optimal weight: 0.6980 chunk 455 optimal weight: 0.0770 chunk 121 optimal weight: 20.0000 chunk 298 optimal weight: 9.9990 chunk 273 optimal weight: 3.9990 chunk 461 optimal weight: 5.9990 overall best weight: 2.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 211 GLN ** V 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 141 GLN ** E 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 GLN K 32 GLN B 211 GLN ** D 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 GLN H 95 GLN H 141 GLN N 141 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.064685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.044810 restraints weight = 190794.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.046369 restraints weight = 90539.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.047364 restraints weight = 57091.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.047973 restraints weight = 42677.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.048295 restraints weight = 35885.505| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 44652 Z= 0.144 Angle : 0.581 14.258 60228 Z= 0.296 Chirality : 0.045 0.221 6516 Planarity : 0.004 0.087 7668 Dihedral : 5.061 59.797 5834 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.35 % Favored : 95.40 % Rotamer: Outliers : 4.34 % Allowed : 20.99 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.12), residues: 5328 helix: 0.05 (0.10), residues: 2562 sheet: -0.45 (0.16), residues: 1038 loop : -0.60 (0.16), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 8 TYR 0.036 0.001 TYR O 48 PHE 0.021 0.001 PHE Z 76 TRP 0.023 0.001 TRP f 208 HIS 0.005 0.001 HIS J 32 Details of bonding type rmsd covalent geometry : bond 0.00326 (44652) covalent geometry : angle 0.58129 (60228) hydrogen bonds : bond 0.03134 ( 1855) hydrogen bonds : angle 4.67549 ( 5469) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10656 Ramachandran restraints generated. 5328 Oldfield, 0 Emsley, 5328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10656 Ramachandran restraints generated. 5328 Oldfield, 0 Emsley, 5328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 4812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 348 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 252 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8677 (mp0) REVERT: T 179 ASP cc_start: 0.8432 (m-30) cc_final: 0.8056 (m-30) REVERT: V 69 TYR cc_start: 0.8318 (m-80) cc_final: 0.7974 (m-80) REVERT: V 117 MET cc_start: 0.8607 (tpp) cc_final: 0.8128 (mmm) REVERT: V 177 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8518 (tm-30) REVERT: Z 18 LYS cc_start: 0.8797 (tttt) cc_final: 0.8556 (pttm) REVERT: Z 35 ASP cc_start: 0.8077 (t0) cc_final: 0.7756 (t0) REVERT: Z 38 GLN cc_start: 0.8794 (mp10) cc_final: 0.8436 (mp10) REVERT: Z 158 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7516 (ptp) REVERT: Z 167 MET cc_start: 0.7865 (pmm) cc_final: 0.6435 (pmm) REVERT: d 41 ASN cc_start: 0.8953 (t0) cc_final: 0.8553 (t0) REVERT: d 82 GLN cc_start: 0.7995 (tp40) cc_final: 0.7499 (tp40) REVERT: d 87 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8574 (tppt) REVERT: d 91 ASP cc_start: 0.9172 (m-30) cc_final: 0.8884 (p0) REVERT: d 95 GLN cc_start: 0.8813 (pp30) cc_final: 0.8467 (pp30) REVERT: d 117 MET cc_start: 0.8508 (mmm) cc_final: 0.8201 (mmm) REVERT: d 168 ARG cc_start: 0.8838 (mtp180) cc_final: 0.8331 (ttp-170) REVERT: b 63 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9276 (mp) REVERT: b 125 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8549 (tptp) REVERT: b 164 GLN cc_start: 0.9026 (tp40) cc_final: 0.8573 (tp40) REVERT: f 237 GLN cc_start: 0.9434 (tp-100) cc_final: 0.9195 (tp-100) REVERT: A 16 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8091 (m-80) REVERT: A 224 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9206 (mm) REVERT: A 248 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8399 (p0) REVERT: C 16 PHE cc_start: 0.9183 (OUTLIER) cc_final: 0.8100 (m-80) REVERT: C 164 GLN cc_start: 0.9267 (mm110) cc_final: 0.8649 (mm-40) REVERT: C 242 MET cc_start: 0.8425 (mtp) cc_final: 0.7867 (mtm) REVERT: G 38 GLN cc_start: 0.8704 (mm-40) cc_final: 0.8310 (mm110) REVERT: G 43 HIS cc_start: 0.8918 (m-70) cc_final: 0.8586 (m90) REVERT: G 56 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9026 (tp) REVERT: G 158 MET cc_start: 0.6806 (pmm) cc_final: 0.5862 (pmm) REVERT: M 155 PHE cc_start: 0.7547 (OUTLIER) cc_final: 0.7227 (t80) REVERT: M 158 MET cc_start: 0.8451 (tpp) cc_final: 0.7813 (tpp) REVERT: K 32 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8905 (pm20) REVERT: K 78 MET cc_start: 0.9420 (mmp) cc_final: 0.9117 (mmp) REVERT: K 108 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.7910 (m-80) REVERT: K 166 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8098 (mt) REVERT: K 207 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9105 (mm) REVERT: K 242 MET cc_start: 0.8446 (mmm) cc_final: 0.8175 (tpt) REVERT: O 158 ASP cc_start: 0.7620 (p0) cc_final: 0.7146 (p0) REVERT: O 194 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.7996 (p0) REVERT: O 195 ILE cc_start: 0.9151 (tt) cc_final: 0.8923 (tp) REVERT: B 64 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.9030 (mptt) REVERT: B 78 MET cc_start: 0.9126 (mmm) cc_final: 0.8800 (mmt) REVERT: B 179 ASP cc_start: 0.8789 (m-30) cc_final: 0.8428 (m-30) REVERT: D 16 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.7888 (m-80) REVERT: D 75 MET cc_start: 0.9181 (mmm) cc_final: 0.8747 (mmm) REVERT: F 167 MET cc_start: 0.8065 (pmm) cc_final: 0.7469 (pmm) REVERT: H 2 ASN cc_start: 0.8926 (m-40) cc_final: 0.8600 (m-40) REVERT: H 117 MET cc_start: 0.8480 (mpp) cc_final: 0.8030 (mpp) REVERT: H 158 MET cc_start: 0.8699 (mmt) cc_final: 0.8250 (mmm) REVERT: J 41 ASN cc_start: 0.8786 (t0) cc_final: 0.8391 (t0) REVERT: J 125 GLU cc_start: 0.9368 (OUTLIER) cc_final: 0.8657 (tm-30) REVERT: J 177 GLU cc_start: 0.9475 (OUTLIER) cc_final: 0.9193 (tm-30) REVERT: N 117 MET cc_start: 0.8700 (mmm) cc_final: 0.8388 (mmm) REVERT: N 170 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7851 (pttp) REVERT: L 158 ASP cc_start: 0.8540 (m-30) cc_final: 0.8233 (t0) REVERT: L 215 GLU cc_start: 0.3159 (OUTLIER) cc_final: 0.2803 (pp20) REVERT: L 231 GLN cc_start: 0.9409 (mp10) cc_final: 0.8897 (mp10) REVERT: L 237 GLN cc_start: 0.9037 (mp10) cc_final: 0.8408 (mp10) REVERT: P 48 TYR cc_start: 0.7982 (OUTLIER) cc_final: 0.7616 (m-80) REVERT: P 164 GLN cc_start: 0.9354 (tm-30) cc_final: 0.8862 (tm-30) REVERT: P 181 LEU cc_start: 0.9247 (tt) cc_final: 0.8966 (pp) REVERT: P 231 GLN cc_start: 0.9195 (mp10) cc_final: 0.8935 (mp10) REVERT: P 242 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7544 (ptt) outliers start: 209 outliers final: 126 residues processed: 532 average time/residue: 0.2181 time to fit residues: 200.7369 Evaluate side-chains 476 residues out of total 4812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 325 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 131 ASP Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 252 GLU Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain T residue 16 PHE Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 41 LEU Chi-restraints excluded: chain T residue 51 PHE Chi-restraints excluded: chain T residue 170 THR Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 195 ILE Chi-restraints excluded: chain T residue 196 ASN Chi-restraints excluded: chain T residue 211 GLN Chi-restraints excluded: chain V residue 11 HIS Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 91 ASP Chi-restraints excluded: chain V residue 133 VAL Chi-restraints excluded: chain V residue 177 GLU Chi-restraints excluded: chain X residue 33 SER Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 51 LEU Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 80 LEU Chi-restraints excluded: chain Z residue 130 ILE Chi-restraints excluded: chain Z residue 133 VAL Chi-restraints excluded: chain Z residue 158 MET Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 87 LYS Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 125 LYS Chi-restraints excluded: chain b residue 128 SER Chi-restraints excluded: chain b residue 155 ILE Chi-restraints excluded: chain b residue 166 LEU Chi-restraints excluded: chain b residue 170 THR Chi-restraints excluded: chain b residue 181 LEU Chi-restraints excluded: chain b residue 195 ILE Chi-restraints excluded: chain b residue 215 GLU Chi-restraints excluded: chain b residue 222 ILE Chi-restraints excluded: chain f residue 155 ILE Chi-restraints excluded: chain f residue 166 LEU Chi-restraints excluded: chain f residue 180 VAL Chi-restraints excluded: chain f residue 186 LEU Chi-restraints excluded: chain f residue 188 ILE Chi-restraints excluded: chain f residue 195 ILE Chi-restraints excluded: chain f residue 212 LYS Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain C residue 16 PHE Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 177 GLU Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 155 PHE Chi-restraints excluded: chain M residue 166 SER Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 32 GLN Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain K residue 166 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 222 ILE Chi-restraints excluded: chain O residue 155 ILE Chi-restraints excluded: chain O residue 166 LEU Chi-restraints excluded: chain O residue 194 ASP Chi-restraints excluded: chain O residue 197 ILE Chi-restraints excluded: chain O residue 199 LEU Chi-restraints excluded: chain O residue 212 LYS Chi-restraints excluded: chain O residue 220 SER Chi-restraints excluded: chain O residue 222 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 211 GLN Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 84 PHE Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 114 CYS Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 130 ILE Chi-restraints excluded: chain J residue 140 PHE Chi-restraints excluded: chain J residue 177 GLU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 133 VAL Chi-restraints excluded: chain N residue 170 LYS Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 155 ILE Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 214 GLU Chi-restraints excluded: chain L residue 215 GLU Chi-restraints excluded: chain P residue 48 TYR Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 155 ILE Chi-restraints excluded: chain P residue 166 LEU Chi-restraints excluded: chain P residue 199 LEU Chi-restraints excluded: chain P residue 222 ILE Chi-restraints excluded: chain P residue 242 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 484 optimal weight: 3.9990 chunk 373 optimal weight: 7.9990 chunk 63 optimal weight: 0.0070 chunk 144 optimal weight: 1.9990 chunk 119 optimal weight: 0.4980 chunk 314 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 284 optimal weight: 1.9990 chunk 462 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 overall best weight: 1.5004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 211 GLN ** V 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 164 GLN ** E 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 2 ASN K 32 GLN D 217 GLN ** D 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 141 GLN N 163 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.065126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.044789 restraints weight = 189704.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.046413 restraints weight = 90539.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.047430 restraints weight = 57110.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.048084 restraints weight = 42702.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.048400 restraints weight = 35739.021| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 44652 Z= 0.122 Angle : 0.587 13.407 60228 Z= 0.296 Chirality : 0.045 0.299 6516 Planarity : 0.004 0.087 7668 Dihedral : 4.968 58.617 5830 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.24 % Favored : 95.51 % Rotamer: Outliers : 3.91 % Allowed : 21.61 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.12), residues: 5328 helix: 0.15 (0.10), residues: 2562 sheet: -0.38 (0.16), residues: 1038 loop : -0.55 (0.16), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 8 TYR 0.043 0.001 TYR O 48 PHE 0.020 0.001 PHE T 201 TRP 0.023 0.001 TRP H 142 HIS 0.004 0.001 HIS J 32 Details of bonding type rmsd covalent geometry : bond 0.00281 (44652) covalent geometry : angle 0.58701 (60228) hydrogen bonds : bond 0.03029 ( 1855) hydrogen bonds : angle 4.59295 ( 5469) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10656 Ramachandran restraints generated. 5328 Oldfield, 0 Emsley, 5328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10656 Ramachandran restraints generated. 5328 Oldfield, 0 Emsley, 5328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 4812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 357 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 252 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8651 (mp0) REVERT: T 64 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8866 (mmtm) REVERT: T 177 ARG cc_start: 0.8583 (mtm-85) cc_final: 0.8343 (mtm-85) REVERT: T 179 ASP cc_start: 0.8401 (m-30) cc_final: 0.8009 (m-30) REVERT: V 69 TYR cc_start: 0.8297 (m-80) cc_final: 0.7964 (m-80) REVERT: V 117 MET cc_start: 0.8584 (tpp) cc_final: 0.8166 (tpp) REVERT: V 177 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8485 (tm-30) REVERT: Z 18 LYS cc_start: 0.8795 (tttt) cc_final: 0.8548 (pttm) REVERT: Z 35 ASP cc_start: 0.8068 (t0) cc_final: 0.7748 (t0) REVERT: Z 38 GLN cc_start: 0.8751 (mp10) cc_final: 0.8454 (mp10) REVERT: Z 158 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7540 (ptp) REVERT: Z 167 MET cc_start: 0.7963 (pmm) cc_final: 0.6542 (pmm) REVERT: d 41 ASN cc_start: 0.8942 (t0) cc_final: 0.8536 (t0) REVERT: d 82 GLN cc_start: 0.8005 (tp40) cc_final: 0.6829 (tp40) REVERT: d 86 ASP cc_start: 0.8491 (p0) cc_final: 0.8057 (p0) REVERT: d 87 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8645 (tppt) REVERT: d 91 ASP cc_start: 0.9146 (m-30) cc_final: 0.8884 (p0) REVERT: d 95 GLN cc_start: 0.8832 (pp30) cc_final: 0.8488 (pp30) REVERT: d 117 MET cc_start: 0.8458 (mmm) cc_final: 0.8145 (mmm) REVERT: d 168 ARG cc_start: 0.8831 (mtp180) cc_final: 0.8349 (ttp-170) REVERT: b 125 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8606 (tptp) REVERT: b 164 GLN cc_start: 0.8998 (tp40) cc_final: 0.8566 (tp40) REVERT: f 201 PHE cc_start: 0.9404 (m-80) cc_final: 0.9049 (m-80) REVERT: A 16 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.8066 (m-80) REVERT: A 224 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9194 (mm) REVERT: A 248 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8409 (p0) REVERT: C 16 PHE cc_start: 0.9200 (OUTLIER) cc_final: 0.8073 (m-80) REVERT: C 164 GLN cc_start: 0.9222 (mm110) cc_final: 0.8689 (mm-40) REVERT: C 242 MET cc_start: 0.8359 (mtp) cc_final: 0.7769 (mtm) REVERT: E 48 ASP cc_start: 0.9197 (OUTLIER) cc_final: 0.8812 (p0) REVERT: G 38 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8299 (mm110) REVERT: G 43 HIS cc_start: 0.8897 (m-70) cc_final: 0.8550 (m90) REVERT: G 158 MET cc_start: 0.6883 (pmm) cc_final: 0.5886 (pmm) REVERT: M 155 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.7214 (t80) REVERT: M 158 MET cc_start: 0.8486 (tpp) cc_final: 0.7819 (tpp) REVERT: K 78 MET cc_start: 0.9404 (mmp) cc_final: 0.9076 (mmp) REVERT: K 108 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.7852 (m-80) REVERT: K 166 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7910 (mt) REVERT: K 207 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9097 (mm) REVERT: K 242 MET cc_start: 0.8432 (mmm) cc_final: 0.8155 (tpt) REVERT: O 194 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7930 (p0) REVERT: O 195 ILE cc_start: 0.9071 (tt) cc_final: 0.8831 (tp) REVERT: B 64 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.9038 (mptt) REVERT: B 78 MET cc_start: 0.9108 (mmm) cc_final: 0.8773 (mmt) REVERT: B 179 ASP cc_start: 0.8786 (m-30) cc_final: 0.8425 (m-30) REVERT: D 16 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.7832 (m-80) REVERT: D 75 MET cc_start: 0.9144 (mmm) cc_final: 0.8742 (mmm) REVERT: F 8 ARG cc_start: 0.8028 (tpp80) cc_final: 0.7754 (tpp80) REVERT: F 167 MET cc_start: 0.8068 (pmm) cc_final: 0.7064 (pmm) REVERT: H 2 ASN cc_start: 0.8910 (m-40) cc_final: 0.8562 (m-40) REVERT: H 41 ASN cc_start: 0.8463 (t0) cc_final: 0.7978 (t0) REVERT: H 117 MET cc_start: 0.8479 (mpp) cc_final: 0.8055 (mpp) REVERT: H 158 MET cc_start: 0.8674 (mmt) cc_final: 0.8373 (mmm) REVERT: J 41 ASN cc_start: 0.8844 (t0) cc_final: 0.8460 (t0) REVERT: J 125 GLU cc_start: 0.9358 (OUTLIER) cc_final: 0.8623 (tm-30) REVERT: J 177 GLU cc_start: 0.9475 (OUTLIER) cc_final: 0.9219 (tm-30) REVERT: N 117 MET cc_start: 0.8682 (mmm) cc_final: 0.8368 (mmm) REVERT: N 170 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7841 (pttp) REVERT: L 157 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9111 (mt) REVERT: L 158 ASP cc_start: 0.8623 (m-30) cc_final: 0.8355 (t0) REVERT: L 231 GLN cc_start: 0.9419 (mp10) cc_final: 0.8931 (mp10) REVERT: L 237 GLN cc_start: 0.9046 (mp10) cc_final: 0.8433 (mp10) REVERT: P 164 GLN cc_start: 0.9359 (tm-30) cc_final: 0.8864 (tm-30) REVERT: P 181 LEU cc_start: 0.9232 (tt) cc_final: 0.8995 (pp) REVERT: P 231 GLN cc_start: 0.9222 (mp10) cc_final: 0.8921 (mp10) REVERT: P 242 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7574 (ptt) outliers start: 188 outliers final: 115 residues processed: 521 average time/residue: 0.2331 time to fit residues: 208.1740 Evaluate side-chains 466 residues out of total 4812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 328 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 131 ASP Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 252 GLU Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain T residue 16 PHE Chi-restraints excluded: chain T residue 41 LEU Chi-restraints excluded: chain T residue 64 LYS Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 196 ASN Chi-restraints excluded: chain T residue 207 LEU Chi-restraints excluded: chain V residue 11 HIS Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 83 ILE Chi-restraints excluded: chain V residue 91 ASP Chi-restraints excluded: chain V residue 129 THR Chi-restraints excluded: chain V residue 133 VAL Chi-restraints excluded: chain V residue 177 GLU Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 51 LEU Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 80 LEU Chi-restraints excluded: chain Z residue 130 ILE Chi-restraints excluded: chain Z residue 133 VAL Chi-restraints excluded: chain Z residue 158 MET Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 87 LYS Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 125 LYS Chi-restraints excluded: chain b residue 155 ILE Chi-restraints excluded: chain b residue 166 LEU Chi-restraints excluded: chain b residue 170 THR Chi-restraints excluded: chain b residue 181 LEU Chi-restraints excluded: chain b residue 195 ILE Chi-restraints excluded: chain b residue 222 ILE Chi-restraints excluded: chain f residue 155 ILE Chi-restraints excluded: chain f residue 166 LEU Chi-restraints excluded: chain f residue 180 VAL Chi-restraints excluded: chain f residue 186 LEU Chi-restraints excluded: chain f residue 188 ILE Chi-restraints excluded: chain f residue 195 ILE Chi-restraints excluded: chain f residue 212 LYS Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain C residue 16 PHE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain I residue 2 ASN Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 177 GLU Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 155 PHE Chi-restraints excluded: chain M residue 166 SER Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain K residue 166 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 222 ILE Chi-restraints excluded: chain O residue 155 ILE Chi-restraints excluded: chain O residue 166 LEU Chi-restraints excluded: chain O residue 194 ASP Chi-restraints excluded: chain O residue 197 ILE Chi-restraints excluded: chain O residue 212 LYS Chi-restraints excluded: chain O residue 220 SER Chi-restraints excluded: chain O residue 222 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 114 CYS Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 130 ILE Chi-restraints excluded: chain J residue 177 GLU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 133 VAL Chi-restraints excluded: chain N residue 170 LYS Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 155 ILE Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 214 GLU Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 155 ILE Chi-restraints excluded: chain P residue 166 LEU Chi-restraints excluded: chain P residue 199 LEU Chi-restraints excluded: chain P residue 222 ILE Chi-restraints excluded: chain P residue 242 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 515 optimal weight: 8.9990 chunk 434 optimal weight: 6.9990 chunk 73 optimal weight: 20.0000 chunk 386 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 235 optimal weight: 0.9990 chunk 425 optimal weight: 20.0000 chunk 514 optimal weight: 2.9990 chunk 506 optimal weight: 6.9990 chunk 133 optimal weight: 7.9990 chunk 474 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 11 HIS ** V 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN ** G 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 GLN D 217 GLN ** D 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 GLN ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.064659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.044201 restraints weight = 192114.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.045857 restraints weight = 89188.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.046908 restraints weight = 55601.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.047537 restraints weight = 41214.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.047946 restraints weight = 34489.109| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 44652 Z= 0.154 Angle : 0.608 13.371 60228 Z= 0.306 Chirality : 0.046 0.248 6516 Planarity : 0.004 0.088 7668 Dihedral : 4.825 55.719 5825 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.35 % Favored : 95.40 % Rotamer: Outliers : 3.76 % Allowed : 21.65 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.12), residues: 5328 helix: 0.25 (0.10), residues: 2538 sheet: -0.37 (0.16), residues: 1038 loop : -0.55 (0.16), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 8 TYR 0.042 0.001 TYR O 48 PHE 0.019 0.001 PHE R 51 TRP 0.024 0.001 TRP H 142 HIS 0.005 0.001 HIS J 32 Details of bonding type rmsd covalent geometry : bond 0.00351 (44652) covalent geometry : angle 0.60810 (60228) hydrogen bonds : bond 0.03065 ( 1855) hydrogen bonds : angle 4.59199 ( 5469) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10656 Ramachandran restraints generated. 5328 Oldfield, 0 Emsley, 5328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10656 Ramachandran restraints generated. 5328 Oldfield, 0 Emsley, 5328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 4812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 334 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 211 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8781 (mt0) REVERT: R 252 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8702 (mp0) REVERT: T 64 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8854 (mmtm) REVERT: T 177 ARG cc_start: 0.8647 (mtm-85) cc_final: 0.8392 (mtm-85) REVERT: T 179 ASP cc_start: 0.8388 (m-30) cc_final: 0.7959 (m-30) REVERT: V 69 TYR cc_start: 0.8315 (m-80) cc_final: 0.7978 (m-80) REVERT: V 117 MET cc_start: 0.8637 (tpp) cc_final: 0.8274 (tpp) REVERT: V 177 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8535 (tm-30) REVERT: Z 18 LYS cc_start: 0.8832 (tttt) cc_final: 0.8588 (pttm) REVERT: Z 35 ASP cc_start: 0.8112 (t0) cc_final: 0.7801 (t0) REVERT: Z 38 GLN cc_start: 0.8725 (mp10) cc_final: 0.8490 (mp10) REVERT: Z 158 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7556 (ptp) REVERT: Z 167 MET cc_start: 0.7864 (pmm) cc_final: 0.6420 (pmm) REVERT: d 41 ASN cc_start: 0.8907 (t0) cc_final: 0.8491 (t0) REVERT: d 82 GLN cc_start: 0.7957 (tp40) cc_final: 0.6863 (tp40) REVERT: d 86 ASP cc_start: 0.8517 (p0) cc_final: 0.8080 (p0) REVERT: d 87 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8652 (tppt) REVERT: d 91 ASP cc_start: 0.9163 (m-30) cc_final: 0.8910 (p0) REVERT: d 95 GLN cc_start: 0.8883 (pp30) cc_final: 0.8534 (pp30) REVERT: d 117 MET cc_start: 0.8486 (mmm) cc_final: 0.8177 (mmm) REVERT: d 168 ARG cc_start: 0.8859 (mtp180) cc_final: 0.8365 (ttp-170) REVERT: b 63 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9281 (mp) REVERT: b 164 GLN cc_start: 0.9065 (tp40) cc_final: 0.8683 (tp40) REVERT: f 1 MET cc_start: 0.8319 (pmm) cc_final: 0.7933 (pmm) REVERT: f 23 MET cc_start: 0.9110 (tmm) cc_final: 0.8906 (tmm) REVERT: A 16 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8093 (m-80) REVERT: A 224 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9167 (mm) REVERT: A 248 ASP cc_start: 0.8650 (OUTLIER) cc_final: 0.8418 (p0) REVERT: C 16 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8132 (m-80) REVERT: C 206 LYS cc_start: 0.9247 (ttmt) cc_final: 0.8948 (ttpt) REVERT: C 242 MET cc_start: 0.8434 (mtp) cc_final: 0.7817 (mtm) REVERT: E 48 ASP cc_start: 0.9216 (OUTLIER) cc_final: 0.8875 (p0) REVERT: E 163 ASN cc_start: 0.7705 (OUTLIER) cc_final: 0.7065 (p0) REVERT: G 38 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8271 (mm-40) REVERT: G 43 HIS cc_start: 0.8915 (m-70) cc_final: 0.8581 (m90) REVERT: G 56 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9068 (tp) REVERT: G 158 MET cc_start: 0.6963 (pmm) cc_final: 0.5967 (pmm) REVERT: M 155 PHE cc_start: 0.7532 (OUTLIER) cc_final: 0.7225 (t80) REVERT: M 158 MET cc_start: 0.8519 (tpp) cc_final: 0.7835 (tpp) REVERT: K 78 MET cc_start: 0.9393 (mmp) cc_final: 0.9060 (mmp) REVERT: K 108 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.7873 (m-80) REVERT: K 166 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8108 (mt) REVERT: K 207 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9086 (mm) REVERT: K 242 MET cc_start: 0.8370 (mmm) cc_final: 0.8109 (tpt) REVERT: O 159 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.7929 (tp30) REVERT: O 194 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7983 (p0) REVERT: O 195 ILE cc_start: 0.9092 (tt) cc_final: 0.8852 (tp) REVERT: B 64 LYS cc_start: 0.9349 (OUTLIER) cc_final: 0.9019 (mptt) REVERT: B 75 MET cc_start: 0.9163 (tpp) cc_final: 0.8764 (tpp) REVERT: B 78 MET cc_start: 0.9176 (mmm) cc_final: 0.8835 (mmt) REVERT: B 179 ASP cc_start: 0.8824 (m-30) cc_final: 0.8443 (m-30) REVERT: D 16 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.7868 (m-80) REVERT: D 64 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.9022 (mmtm) REVERT: D 75 MET cc_start: 0.9183 (mmm) cc_final: 0.8771 (mmm) REVERT: F 8 ARG cc_start: 0.8050 (tpp80) cc_final: 0.7776 (tpp80) REVERT: F 167 MET cc_start: 0.8076 (pmm) cc_final: 0.7462 (pmm) REVERT: H 2 ASN cc_start: 0.8947 (m-40) cc_final: 0.8505 (m-40) REVERT: H 41 ASN cc_start: 0.8455 (t0) cc_final: 0.7974 (t0) REVERT: H 117 MET cc_start: 0.8525 (mpp) cc_final: 0.8021 (mpp) REVERT: H 158 MET cc_start: 0.8716 (mmt) cc_final: 0.8408 (mmm) REVERT: J 41 ASN cc_start: 0.8844 (t0) cc_final: 0.8456 (t0) REVERT: J 125 GLU cc_start: 0.9367 (OUTLIER) cc_final: 0.8627 (tm-30) REVERT: J 177 GLU cc_start: 0.9469 (OUTLIER) cc_final: 0.9216 (tm-30) REVERT: N 117 MET cc_start: 0.8682 (mmm) cc_final: 0.8361 (mmm) REVERT: N 170 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7881 (pttp) REVERT: L 158 ASP cc_start: 0.8596 (m-30) cc_final: 0.8293 (t0) REVERT: L 231 GLN cc_start: 0.9438 (mp10) cc_final: 0.8898 (mp10) REVERT: L 237 GLN cc_start: 0.9085 (mp10) cc_final: 0.8433 (mp10) REVERT: P 164 GLN cc_start: 0.9378 (tm-30) cc_final: 0.8881 (tm-30) REVERT: P 181 LEU cc_start: 0.9276 (tt) cc_final: 0.9025 (pp) outliers start: 181 outliers final: 127 residues processed: 492 average time/residue: 0.2182 time to fit residues: 186.0082 Evaluate side-chains 480 residues out of total 4812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 327 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 131 ASP Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 211 GLN Chi-restraints excluded: chain R residue 252 GLU Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 16 PHE Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 41 LEU Chi-restraints excluded: chain T residue 64 LYS Chi-restraints excluded: chain T residue 170 THR Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain V residue 11 HIS Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 83 ILE Chi-restraints excluded: chain V residue 91 ASP Chi-restraints excluded: chain V residue 129 THR Chi-restraints excluded: chain V residue 133 VAL Chi-restraints excluded: chain V residue 177 GLU Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 51 LEU Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 80 LEU Chi-restraints excluded: chain Z residue 130 ILE Chi-restraints excluded: chain Z residue 133 VAL Chi-restraints excluded: chain Z residue 158 MET Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 87 LYS Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 125 LYS Chi-restraints excluded: chain b residue 128 SER Chi-restraints excluded: chain b residue 155 ILE Chi-restraints excluded: chain b residue 166 LEU Chi-restraints excluded: chain b residue 170 THR Chi-restraints excluded: chain b residue 181 LEU Chi-restraints excluded: chain b residue 195 ILE Chi-restraints excluded: chain b residue 222 ILE Chi-restraints excluded: chain f residue 155 ILE Chi-restraints excluded: chain f residue 166 LEU Chi-restraints excluded: chain f residue 180 VAL Chi-restraints excluded: chain f residue 186 LEU Chi-restraints excluded: chain f residue 188 ILE Chi-restraints excluded: chain f residue 195 ILE Chi-restraints excluded: chain f residue 212 LYS Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain C residue 16 PHE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 177 GLU Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 155 PHE Chi-restraints excluded: chain M residue 166 SER Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain K residue 166 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 222 ILE Chi-restraints excluded: chain O residue 155 ILE Chi-restraints excluded: chain O residue 159 GLU Chi-restraints excluded: chain O residue 166 LEU Chi-restraints excluded: chain O residue 191 SER Chi-restraints excluded: chain O residue 194 ASP Chi-restraints excluded: chain O residue 197 ILE Chi-restraints excluded: chain O residue 212 LYS Chi-restraints excluded: chain O residue 220 SER Chi-restraints excluded: chain O residue 222 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 84 PHE Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 114 CYS Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 130 ILE Chi-restraints excluded: chain J residue 140 PHE Chi-restraints excluded: chain J residue 177 GLU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 133 VAL Chi-restraints excluded: chain N residue 170 LYS Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 155 ILE Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain L residue 173 ASP Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 214 GLU Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 155 ILE Chi-restraints excluded: chain P residue 166 LEU Chi-restraints excluded: chain P residue 199 LEU Chi-restraints excluded: chain P residue 222 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 251 optimal weight: 6.9990 chunk 186 optimal weight: 4.9990 chunk 498 optimal weight: 1.9990 chunk 408 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 517 optimal weight: 9.9990 chunk 449 optimal weight: 0.0470 chunk 290 optimal weight: 7.9990 chunk 288 optimal weight: 10.0000 chunk 158 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 overall best weight: 4.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 11 HIS ** V 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 164 GLN ** E 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN ** G 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 2 ASN ** M 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN ** D 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.063616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.043238 restraints weight = 192269.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.044796 restraints weight = 93000.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.045768 restraints weight = 59226.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.046390 restraints weight = 44682.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.046672 restraints weight = 37597.847| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 44652 Z= 0.225 Angle : 0.650 12.623 60228 Z= 0.329 Chirality : 0.047 0.260 6516 Planarity : 0.004 0.090 7668 Dihedral : 4.894 53.641 5825 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.67 % Favored : 95.06 % Rotamer: Outliers : 3.91 % Allowed : 21.57 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.12), residues: 5328 helix: 0.23 (0.10), residues: 2550 sheet: -0.51 (0.16), residues: 1014 loop : -0.45 (0.16), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 8 TYR 0.063 0.002 TYR O 48 PHE 0.024 0.001 PHE R 51 TRP 0.026 0.001 TRP H 142 HIS 0.009 0.001 HIS V 11 Details of bonding type rmsd covalent geometry : bond 0.00502 (44652) covalent geometry : angle 0.65010 (60228) hydrogen bonds : bond 0.03246 ( 1855) hydrogen bonds : angle 4.68752 ( 5469) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10656 Ramachandran restraints generated. 5328 Oldfield, 0 Emsley, 5328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10656 Ramachandran restraints generated. 5328 Oldfield, 0 Emsley, 5328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 4812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 319 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 252 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8667 (mp0) REVERT: T 64 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.9056 (mmtm) REVERT: T 179 ASP cc_start: 0.8349 (m-30) cc_final: 0.7958 (m-30) REVERT: V 69 TYR cc_start: 0.8305 (m-80) cc_final: 0.7985 (m-80) REVERT: V 117 MET cc_start: 0.8678 (tpp) cc_final: 0.8333 (tpp) REVERT: V 155 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7565 (m-80) REVERT: V 177 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8458 (tm-30) REVERT: Z 18 LYS cc_start: 0.8856 (tttt) cc_final: 0.8620 (pttm) REVERT: Z 35 ASP cc_start: 0.8051 (t0) cc_final: 0.7740 (t0) REVERT: Z 38 GLN cc_start: 0.8708 (mp10) cc_final: 0.8507 (mp10) REVERT: Z 158 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7359 (ptp) REVERT: d 41 ASN cc_start: 0.8963 (t0) cc_final: 0.8547 (t0) REVERT: d 82 GLN cc_start: 0.8063 (tp40) cc_final: 0.7026 (tp40) REVERT: d 86 ASP cc_start: 0.8553 (p0) cc_final: 0.8192 (p0) REVERT: d 87 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8779 (tppt) REVERT: d 91 ASP cc_start: 0.9156 (m-30) cc_final: 0.8904 (p0) REVERT: d 95 GLN cc_start: 0.8881 (pp30) cc_final: 0.8532 (pp30) REVERT: d 117 MET cc_start: 0.8536 (mmm) cc_final: 0.8266 (mmm) REVERT: d 168 ARG cc_start: 0.8866 (mtp180) cc_final: 0.8286 (ttp-170) REVERT: b 63 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9293 (mp) REVERT: b 164 GLN cc_start: 0.9064 (tp40) cc_final: 0.8632 (tp-100) REVERT: f 1 MET cc_start: 0.8393 (pmm) cc_final: 0.8049 (pmm) REVERT: f 201 PHE cc_start: 0.9428 (m-80) cc_final: 0.9119 (m-80) REVERT: A 16 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8197 (m-80) REVERT: A 224 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9206 (mm) REVERT: C 16 PHE cc_start: 0.9230 (OUTLIER) cc_final: 0.8195 (m-80) REVERT: C 164 GLN cc_start: 0.9100 (mm110) cc_final: 0.8637 (mm-40) REVERT: C 242 MET cc_start: 0.8563 (mtp) cc_final: 0.8025 (mtm) REVERT: E 48 ASP cc_start: 0.9167 (OUTLIER) cc_final: 0.8883 (p0) REVERT: E 155 PHE cc_start: 0.6930 (OUTLIER) cc_final: 0.6197 (t80) REVERT: E 163 ASN cc_start: 0.7759 (OUTLIER) cc_final: 0.7224 (p0) REVERT: G 38 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8283 (mm-40) REVERT: G 43 HIS cc_start: 0.8918 (m-70) cc_final: 0.8562 (m90) REVERT: G 56 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9033 (tp) REVERT: G 158 MET cc_start: 0.7059 (pmm) cc_final: 0.5963 (pmm) REVERT: M 155 PHE cc_start: 0.7544 (OUTLIER) cc_final: 0.7298 (t80) REVERT: M 158 MET cc_start: 0.8537 (tpp) cc_final: 0.7842 (tpp) REVERT: K 78 MET cc_start: 0.9414 (mmp) cc_final: 0.9143 (mmp) REVERT: K 108 TYR cc_start: 0.8845 (OUTLIER) cc_final: 0.7915 (m-80) REVERT: K 207 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9216 (mm) REVERT: K 242 MET cc_start: 0.8375 (mmm) cc_final: 0.8098 (tpt) REVERT: O 158 ASP cc_start: 0.7967 (p0) cc_final: 0.7534 (p0) REVERT: O 159 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8126 (tp30) REVERT: O 194 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.8016 (p0) REVERT: O 195 ILE cc_start: 0.9175 (tt) cc_final: 0.8935 (tp) REVERT: O 211 GLN cc_start: 0.8346 (tp-100) cc_final: 0.8144 (tp40) REVERT: B 64 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.9003 (mptt) REVERT: B 75 MET cc_start: 0.9192 (tpp) cc_final: 0.8713 (tpp) REVERT: B 78 MET cc_start: 0.9151 (mmm) cc_final: 0.8829 (mmt) REVERT: B 179 ASP cc_start: 0.8793 (m-30) cc_final: 0.8440 (m-30) REVERT: D 16 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.8297 (m-80) REVERT: D 64 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.9051 (mmtm) REVERT: D 75 MET cc_start: 0.9195 (mmm) cc_final: 0.8784 (mmm) REVERT: F 167 MET cc_start: 0.8086 (pmm) cc_final: 0.7381 (pmm) REVERT: H 2 ASN cc_start: 0.8877 (m-40) cc_final: 0.8542 (m110) REVERT: H 117 MET cc_start: 0.8562 (mpp) cc_final: 0.8043 (mpp) REVERT: H 158 MET cc_start: 0.8697 (mmt) cc_final: 0.8401 (mmm) REVERT: J 41 ASN cc_start: 0.8819 (t0) cc_final: 0.8408 (t0) REVERT: J 125 GLU cc_start: 0.9381 (OUTLIER) cc_final: 0.8650 (tm-30) REVERT: J 177 GLU cc_start: 0.9476 (OUTLIER) cc_final: 0.9203 (tm-30) REVERT: N 117 MET cc_start: 0.8697 (mmm) cc_final: 0.8374 (mmm) REVERT: N 170 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7886 (pttp) REVERT: L 158 ASP cc_start: 0.8483 (m-30) cc_final: 0.8227 (t0) REVERT: L 231 GLN cc_start: 0.9381 (mp10) cc_final: 0.8828 (mp10) REVERT: L 237 GLN cc_start: 0.9141 (mp10) cc_final: 0.8491 (mp10) REVERT: P 164 GLN cc_start: 0.9369 (tm-30) cc_final: 0.8859 (tm-30) REVERT: P 231 GLN cc_start: 0.9233 (mp10) cc_final: 0.8950 (mp10) outliers start: 188 outliers final: 143 residues processed: 486 average time/residue: 0.2246 time to fit residues: 190.1027 Evaluate side-chains 485 residues out of total 4812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 317 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 131 ASP Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 252 GLU Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 16 PHE Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 41 LEU Chi-restraints excluded: chain T residue 64 LYS Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain T residue 170 THR Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain T residue 195 ILE Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 83 ILE Chi-restraints excluded: chain V residue 91 ASP Chi-restraints excluded: chain V residue 129 THR Chi-restraints excluded: chain V residue 130 ILE Chi-restraints excluded: chain V residue 133 VAL Chi-restraints excluded: chain V residue 155 PHE Chi-restraints excluded: chain V residue 177 GLU Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 51 LEU Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 80 LEU Chi-restraints excluded: chain Z residue 130 ILE Chi-restraints excluded: chain Z residue 133 VAL Chi-restraints excluded: chain Z residue 143 ASP Chi-restraints excluded: chain Z residue 158 MET Chi-restraints excluded: chain d residue 6 ILE Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 87 LYS Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 125 LYS Chi-restraints excluded: chain b residue 128 SER Chi-restraints excluded: chain b residue 155 ILE Chi-restraints excluded: chain b residue 166 LEU Chi-restraints excluded: chain b residue 170 THR Chi-restraints excluded: chain b residue 181 LEU Chi-restraints excluded: chain b residue 195 ILE Chi-restraints excluded: chain b residue 222 ILE Chi-restraints excluded: chain f residue 155 ILE Chi-restraints excluded: chain f residue 166 LEU Chi-restraints excluded: chain f residue 180 VAL Chi-restraints excluded: chain f residue 186 LEU Chi-restraints excluded: chain f residue 188 ILE Chi-restraints excluded: chain f residue 195 ILE Chi-restraints excluded: chain f residue 212 LYS Chi-restraints excluded: chain f residue 254 LEU Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain C residue 16 PHE Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 162 LYS Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain I residue 2 ASN Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 177 GLU Chi-restraints excluded: chain M residue 11 HIS Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 155 PHE Chi-restraints excluded: chain M residue 166 SER Chi-restraints excluded: chain M residue 167 MET Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 222 ILE Chi-restraints excluded: chain O residue 155 ILE Chi-restraints excluded: chain O residue 159 GLU Chi-restraints excluded: chain O residue 166 LEU Chi-restraints excluded: chain O residue 191 SER Chi-restraints excluded: chain O residue 194 ASP Chi-restraints excluded: chain O residue 197 ILE Chi-restraints excluded: chain O residue 212 LYS Chi-restraints excluded: chain O residue 220 SER Chi-restraints excluded: chain O residue 222 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 84 PHE Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 114 CYS Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 130 ILE Chi-restraints excluded: chain J residue 140 PHE Chi-restraints excluded: chain J residue 177 GLU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 133 VAL Chi-restraints excluded: chain N residue 170 LYS Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 155 ILE Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 173 ASP Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 214 GLU Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 155 ILE Chi-restraints excluded: chain P residue 166 LEU Chi-restraints excluded: chain P residue 199 LEU Chi-restraints excluded: chain P residue 222 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 155 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 290 optimal weight: 6.9990 chunk 449 optimal weight: 8.9990 chunk 470 optimal weight: 5.9990 chunk 437 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 305 optimal weight: 6.9990 chunk 319 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 440 optimal weight: 20.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 2 ASN ** M 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 GLN ** B 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 17 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.063515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.043332 restraints weight = 192822.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.044860 restraints weight = 93248.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.045847 restraints weight = 59533.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.046434 restraints weight = 44783.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.046820 restraints weight = 37794.101| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.182 44652 Z= 0.228 Angle : 0.751 59.193 60228 Z= 0.413 Chirality : 0.047 0.483 6516 Planarity : 0.004 0.145 7668 Dihedral : 4.896 53.618 5825 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.54 % Favored : 95.18 % Rotamer: Outliers : 3.62 % Allowed : 21.99 % Favored : 74.40 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.12), residues: 5328 helix: 0.24 (0.10), residues: 2550 sheet: -0.52 (0.16), residues: 1014 loop : -0.46 (0.16), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 177 TYR 0.054 0.002 TYR O 48 PHE 0.027 0.001 PHE R 51 TRP 0.023 0.001 TRP H 142 HIS 0.008 0.001 HIS V 11 Details of bonding type rmsd covalent geometry : bond 0.00509 (44652) covalent geometry : angle 0.75140 (60228) hydrogen bonds : bond 0.03243 ( 1855) hydrogen bonds : angle 4.68828 ( 5469) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10656 Ramachandran restraints generated. 5328 Oldfield, 0 Emsley, 5328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10656 Ramachandran restraints generated. 5328 Oldfield, 0 Emsley, 5328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 4812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 317 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 252 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8667 (mp0) REVERT: T 64 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.8775 (mppt) REVERT: T 179 ASP cc_start: 0.8351 (m-30) cc_final: 0.7941 (m-30) REVERT: V 69 TYR cc_start: 0.8292 (m-80) cc_final: 0.7977 (m-80) REVERT: V 117 MET cc_start: 0.8685 (tpp) cc_final: 0.8350 (tpp) REVERT: V 155 PHE cc_start: 0.7833 (OUTLIER) cc_final: 0.7544 (m-80) REVERT: V 177 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8436 (tm-30) REVERT: Z 18 LYS cc_start: 0.8851 (tttt) cc_final: 0.8622 (pttm) REVERT: Z 35 ASP cc_start: 0.8043 (t0) cc_final: 0.7735 (t0) REVERT: Z 158 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7332 (ptp) REVERT: d 41 ASN cc_start: 0.8963 (t0) cc_final: 0.8547 (t0) REVERT: d 82 GLN cc_start: 0.8116 (tp40) cc_final: 0.7022 (tp40) REVERT: d 86 ASP cc_start: 0.8549 (p0) cc_final: 0.8188 (p0) REVERT: d 87 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8782 (tppt) REVERT: d 91 ASP cc_start: 0.9135 (m-30) cc_final: 0.8887 (p0) REVERT: d 95 GLN cc_start: 0.8870 (pp30) cc_final: 0.8524 (pp30) REVERT: d 117 MET cc_start: 0.8535 (mmm) cc_final: 0.8263 (mmm) REVERT: d 168 ARG cc_start: 0.8855 (mtp180) cc_final: 0.8279 (ttp-170) REVERT: b 63 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9292 (mp) REVERT: b 164 GLN cc_start: 0.9061 (tp40) cc_final: 0.8627 (tp-100) REVERT: f 1 MET cc_start: 0.8376 (pmm) cc_final: 0.8036 (pmm) REVERT: A 16 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.8190 (m-80) REVERT: A 224 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9205 (mm) REVERT: C 16 PHE cc_start: 0.9230 (OUTLIER) cc_final: 0.8190 (m-80) REVERT: C 164 GLN cc_start: 0.9096 (mm110) cc_final: 0.8630 (mm-40) REVERT: C 242 MET cc_start: 0.8576 (mtp) cc_final: 0.8028 (mtm) REVERT: E 48 ASP cc_start: 0.9162 (OUTLIER) cc_final: 0.8876 (p0) REVERT: E 155 PHE cc_start: 0.6935 (OUTLIER) cc_final: 0.6189 (t80) REVERT: E 163 ASN cc_start: 0.7721 (OUTLIER) cc_final: 0.6419 (p0) REVERT: G 38 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8280 (mm-40) REVERT: G 43 HIS cc_start: 0.8914 (m-70) cc_final: 0.8556 (m90) REVERT: G 56 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9033 (tp) REVERT: G 158 MET cc_start: 0.6978 (pmm) cc_final: 0.5867 (pmm) REVERT: M 155 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.7273 (t80) REVERT: M 158 MET cc_start: 0.8532 (tpp) cc_final: 0.7847 (tpp) REVERT: K 78 MET cc_start: 0.9417 (mmp) cc_final: 0.9146 (mmp) REVERT: K 108 TYR cc_start: 0.8833 (OUTLIER) cc_final: 0.7915 (m-80) REVERT: K 207 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9216 (mm) REVERT: K 242 MET cc_start: 0.8381 (mmm) cc_final: 0.8104 (tpt) REVERT: O 158 ASP cc_start: 0.7970 (p0) cc_final: 0.7532 (p0) REVERT: O 159 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8125 (tp30) REVERT: O 194 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8019 (p0) REVERT: O 195 ILE cc_start: 0.9176 (tt) cc_final: 0.8936 (tp) REVERT: O 211 GLN cc_start: 0.8342 (tp-100) cc_final: 0.8141 (tp40) REVERT: B 64 LYS cc_start: 0.9349 (OUTLIER) cc_final: 0.9005 (mptt) REVERT: B 78 MET cc_start: 0.9146 (mmm) cc_final: 0.8823 (mmt) REVERT: B 179 ASP cc_start: 0.8793 (m-30) cc_final: 0.8437 (m-30) REVERT: D 16 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8293 (m-80) REVERT: D 64 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.9053 (mmtm) REVERT: D 75 MET cc_start: 0.9195 (mmm) cc_final: 0.8783 (mmm) REVERT: F 167 MET cc_start: 0.8091 (pmm) cc_final: 0.7377 (pmm) REVERT: H 2 ASN cc_start: 0.8873 (m-40) cc_final: 0.8541 (m110) REVERT: H 117 MET cc_start: 0.8566 (mpp) cc_final: 0.8042 (mpp) REVERT: H 158 MET cc_start: 0.8680 (mmt) cc_final: 0.8386 (mmm) REVERT: J 41 ASN cc_start: 0.8819 (t0) cc_final: 0.8405 (t0) REVERT: J 125 GLU cc_start: 0.9365 (OUTLIER) cc_final: 0.8640 (tm-30) REVERT: J 177 GLU cc_start: 0.9474 (OUTLIER) cc_final: 0.9201 (tm-30) REVERT: N 117 MET cc_start: 0.8694 (mmm) cc_final: 0.8374 (mmm) REVERT: N 170 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7873 (pttp) REVERT: L 158 ASP cc_start: 0.8483 (m-30) cc_final: 0.8236 (t0) REVERT: L 231 GLN cc_start: 0.9376 (mp10) cc_final: 0.8825 (mp10) REVERT: L 237 GLN cc_start: 0.9138 (mp10) cc_final: 0.8489 (mp10) REVERT: P 164 GLN cc_start: 0.9366 (tm-30) cc_final: 0.8857 (tm-30) REVERT: P 231 GLN cc_start: 0.9227 (mp10) cc_final: 0.8945 (mp10) outliers start: 174 outliers final: 146 residues processed: 472 average time/residue: 0.2137 time to fit residues: 176.4035 Evaluate side-chains 485 residues out of total 4812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 314 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 131 ASP Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 252 GLU Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 16 PHE Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 41 LEU Chi-restraints excluded: chain T residue 51 PHE Chi-restraints excluded: chain T residue 64 LYS Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain T residue 170 THR Chi-restraints excluded: chain T residue 185 VAL Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 83 ILE Chi-restraints excluded: chain V residue 91 ASP Chi-restraints excluded: chain V residue 129 THR Chi-restraints excluded: chain V residue 130 ILE Chi-restraints excluded: chain V residue 133 VAL Chi-restraints excluded: chain V residue 155 PHE Chi-restraints excluded: chain V residue 177 GLU Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 51 LEU Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 80 LEU Chi-restraints excluded: chain Z residue 130 ILE Chi-restraints excluded: chain Z residue 133 VAL Chi-restraints excluded: chain Z residue 143 ASP Chi-restraints excluded: chain Z residue 158 MET Chi-restraints excluded: chain d residue 6 ILE Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 87 LYS Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 125 LYS Chi-restraints excluded: chain b residue 128 SER Chi-restraints excluded: chain b residue 155 ILE Chi-restraints excluded: chain b residue 166 LEU Chi-restraints excluded: chain b residue 170 THR Chi-restraints excluded: chain b residue 181 LEU Chi-restraints excluded: chain b residue 195 ILE Chi-restraints excluded: chain b residue 222 ILE Chi-restraints excluded: chain f residue 155 ILE Chi-restraints excluded: chain f residue 166 LEU Chi-restraints excluded: chain f residue 180 VAL Chi-restraints excluded: chain f residue 186 LEU Chi-restraints excluded: chain f residue 188 ILE Chi-restraints excluded: chain f residue 195 ILE Chi-restraints excluded: chain f residue 212 LYS Chi-restraints excluded: chain f residue 254 LEU Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain C residue 16 PHE Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 144 CYS Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 177 GLU Chi-restraints excluded: chain M residue 11 HIS Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 155 PHE Chi-restraints excluded: chain M residue 166 SER Chi-restraints excluded: chain M residue 167 MET Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain K residue 137 ASN Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 222 ILE Chi-restraints excluded: chain O residue 155 ILE Chi-restraints excluded: chain O residue 159 GLU Chi-restraints excluded: chain O residue 166 LEU Chi-restraints excluded: chain O residue 191 SER Chi-restraints excluded: chain O residue 194 ASP Chi-restraints excluded: chain O residue 197 ILE Chi-restraints excluded: chain O residue 212 LYS Chi-restraints excluded: chain O residue 220 SER Chi-restraints excluded: chain O residue 222 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 84 PHE Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 114 CYS Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 130 ILE Chi-restraints excluded: chain J residue 140 PHE Chi-restraints excluded: chain J residue 177 GLU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 133 VAL Chi-restraints excluded: chain N residue 170 LYS Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 155 ILE Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 173 ASP Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 214 GLU Chi-restraints excluded: chain P residue 48 TYR Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 155 ILE Chi-restraints excluded: chain P residue 166 LEU Chi-restraints excluded: chain P residue 199 LEU Chi-restraints excluded: chain P residue 222 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 265 optimal weight: 6.9990 chunk 518 optimal weight: 0.9980 chunk 431 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 525 optimal weight: 3.9990 chunk 182 optimal weight: 9.9990 chunk 234 optimal weight: 8.9990 chunk 289 optimal weight: 20.0000 chunk 398 optimal weight: 1.9990 chunk 309 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 2 ASN ** M 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 17 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.063652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.043248 restraints weight = 193742.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.044820 restraints weight = 93442.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.045795 restraints weight = 59370.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.046403 restraints weight = 44748.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.046769 restraints weight = 37863.197| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.182 44652 Z= 0.228 Angle : 0.751 59.193 60228 Z= 0.413 Chirality : 0.047 0.483 6516 Planarity : 0.004 0.145 7668 Dihedral : 4.896 53.618 5825 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.54 % Favored : 95.18 % Rotamer: Outliers : 3.55 % Allowed : 22.03 % Favored : 74.42 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.12), residues: 5328 helix: 0.24 (0.10), residues: 2550 sheet: -0.52 (0.16), residues: 1014 loop : -0.46 (0.16), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 177 TYR 0.054 0.002 TYR O 48 PHE 0.027 0.001 PHE R 51 TRP 0.023 0.001 TRP H 142 HIS 0.008 0.001 HIS V 11 Details of bonding type rmsd covalent geometry : bond 0.00509 (44652) covalent geometry : angle 0.75140 (60228) hydrogen bonds : bond 0.03243 ( 1855) hydrogen bonds : angle 4.68828 ( 5469) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8116.06 seconds wall clock time: 141 minutes 37.78 seconds (8497.78 seconds total)