Starting phenix.real_space_refine on Thu Nov 20 23:03:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5mpe_3535/11_2025/5mpe_3535.cif Found real_map, /net/cci-nas-00/data/ceres_data/5mpe_3535/11_2025/5mpe_3535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5mpe_3535/11_2025/5mpe_3535.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5mpe_3535/11_2025/5mpe_3535.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5mpe_3535/11_2025/5mpe_3535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5mpe_3535/11_2025/5mpe_3535.map" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 151 5.16 5 C 26021 2.51 5 N 6810 2.21 5 O 7992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 217 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40974 Number of models: 1 Model: "" Number of chains: 13 Chain: "W" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1534 Classifications: {'peptide': 197} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 187} Chain: "V" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2274 Classifications: {'peptide': 289} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 282} Chain: "T" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2192 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 7, 'TRANS': 258} Chain: "X" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1032 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 9, 'TRANS': 117} Chain: "Y" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 435 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain breaks: 1 Chain: "Z" Number of atoms: 7005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 7005 Classifications: {'peptide': 906} Link IDs: {'PTRANS': 30, 'TRANS': 875} Chain breaks: 1 Chain: "N" Number of atoms: 6882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 6882 Classifications: {'peptide': 890} Link IDs: {'PTRANS': 23, 'TRANS': 866} Chain breaks: 1 Chain: "S" Number of atoms: 3894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3894 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 11, 'TRANS': 463} Chain: "P" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3608 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 9, 'TRANS': 430} Chain: "Q" Number of atoms: 3499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3499 Classifications: {'peptide': 434} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 425} Chain: "R" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3060 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 7, 'TRANS': 373} Chain breaks: 1 Chain: "U" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2373 Classifications: {'peptide': 298} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 288} Chain: "O" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3186 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 378} Time building chain proxies: 9.37, per 1000 atoms: 0.23 Number of scatterers: 40974 At special positions: 0 Unit cell: (231.84, 200.1, 218.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 151 16.00 O 7992 8.00 N 6810 7.00 C 26021 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: 3.43 Conformation dependent library (CDL) restraints added in 1.6 seconds 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9824 Finding SS restraints... Secondary structure from input PDB file: 260 helices and 16 sheets defined 71.5% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'W' and resid 24 through 44 removed outlier: 4.138A pdb=" N ILE W 30 " --> pdb=" O PHE W 26 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP W 31 " --> pdb=" O GLU W 27 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER W 43 " --> pdb=" O ALA W 39 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN W 44 " --> pdb=" O LYS W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 68 through 78 removed outlier: 3.881A pdb=" N ILE W 72 " --> pdb=" O GLU W 68 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP W 78 " --> pdb=" O ALA W 74 " (cutoff:3.500A) Processing helix chain 'W' and resid 86 through 99 removed outlier: 3.554A pdb=" N ALA W 90 " --> pdb=" O HIS W 86 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN W 92 " --> pdb=" O ALA W 88 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU W 96 " --> pdb=" O GLN W 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 135 removed outlier: 3.645A pdb=" N LEU W 125 " --> pdb=" O SER W 121 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS W 133 " --> pdb=" O ALA W 129 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS W 134 " --> pdb=" O LYS W 130 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN W 135 " --> pdb=" O THR W 131 " (cutoff:3.500A) Processing helix chain 'W' and resid 145 through 149 removed outlier: 3.540A pdb=" N GLU W 148 " --> pdb=" O GLY W 145 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN W 149 " --> pdb=" O GLU W 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 145 through 149' Processing helix chain 'W' and resid 153 through 162 removed outlier: 3.873A pdb=" N PHE W 157 " --> pdb=" O LEU W 153 " (cutoff:3.500A) Processing helix chain 'W' and resid 180 through 188 Processing helix chain 'V' and resid 30 through 45 removed outlier: 3.502A pdb=" N GLY V 44 " --> pdb=" O HIS V 40 " (cutoff:3.500A) Processing helix chain 'V' and resid 84 through 98 removed outlier: 3.696A pdb=" N GLN V 97 " --> pdb=" O ASP V 93 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR V 98 " --> pdb=" O MET V 94 " (cutoff:3.500A) Processing helix chain 'V' and resid 119 through 133 removed outlier: 3.562A pdb=" N ASN V 124 " --> pdb=" O SER V 120 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE V 129 " --> pdb=" O THR V 125 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN V 131 " --> pdb=" O LYS V 127 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU V 132 " --> pdb=" O SER V 128 " (cutoff:3.500A) Processing helix chain 'V' and resid 143 through 148 removed outlier: 3.789A pdb=" N VAL V 147 " --> pdb=" O ILE V 144 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS V 148 " --> pdb=" O GLN V 145 " (cutoff:3.500A) Processing helix chain 'V' and resid 160 through 166 removed outlier: 3.825A pdb=" N LEU V 164 " --> pdb=" O ASP V 160 " (cutoff:3.500A) Processing helix chain 'V' and resid 168 through 174 removed outlier: 3.718A pdb=" N THR V 174 " --> pdb=" O ARG V 171 " (cutoff:3.500A) Processing helix chain 'V' and resid 185 through 194 Processing helix chain 'V' and resid 206 through 215 Processing helix chain 'V' and resid 229 through 255 removed outlier: 3.635A pdb=" N LYS V 233 " --> pdb=" O ASP V 229 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL V 245 " --> pdb=" O THR V 241 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS V 246 " --> pdb=" O LYS V 242 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLN V 250 " --> pdb=" O LYS V 246 " (cutoff:3.500A) Processing helix chain 'V' and resid 262 through 270 Processing helix chain 'V' and resid 275 through 306 removed outlier: 3.545A pdb=" N ILE V 292 " --> pdb=" O LEU V 288 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 18 removed outlier: 4.074A pdb=" N SER T 12 " --> pdb=" O THR T 8 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU T 16 " --> pdb=" O SER T 12 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY T 18 " --> pdb=" O ALA T 14 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 41 removed outlier: 3.909A pdb=" N CYS T 23 " --> pdb=" O ASP T 19 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU T 24 " --> pdb=" O TYR T 20 " (cutoff:3.500A) Proline residue: T 28 - end of helix removed outlier: 3.767A pdb=" N ILE T 32 " --> pdb=" O PRO T 28 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU T 33 " --> pdb=" O PRO T 29 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE T 35 " --> pdb=" O LYS T 31 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS T 36 " --> pdb=" O ILE T 32 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN T 37 " --> pdb=" O GLU T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 72 removed outlier: 4.261A pdb=" N ASN T 53 " --> pdb=" O ASP T 49 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP T 54 " --> pdb=" O ILE T 50 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR T 58 " --> pdb=" O ASP T 54 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE T 61 " --> pdb=" O ILE T 57 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 91 removed outlier: 3.615A pdb=" N PHE T 78 " --> pdb=" O ASN T 74 " (cutoff:3.500A) Proline residue: T 87 - end of helix Processing helix chain 'T' and resid 99 through 116 Processing helix chain 'T' and resid 118 through 130 removed outlier: 3.803A pdb=" N SER T 124 " --> pdb=" O THR T 120 " (cutoff:3.500A) Processing helix chain 'T' and resid 131 through 133 No H-bonds generated for 'chain 'T' and resid 131 through 133' Processing helix chain 'T' and resid 142 through 155 removed outlier: 3.747A pdb=" N ILE T 146 " --> pdb=" O LEU T 142 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU T 152 " --> pdb=" O LEU T 148 " (cutoff:3.500A) Processing helix chain 'T' and resid 156 through 167 removed outlier: 3.510A pdb=" N LEU T 164 " --> pdb=" O ALA T 160 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN T 165 " --> pdb=" O TRP T 161 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 170 No H-bonds generated for 'chain 'T' and resid 168 through 170' Processing helix chain 'T' and resid 174 through 197 removed outlier: 5.065A pdb=" N ILE T 180 " --> pdb=" O SER T 176 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS T 182 " --> pdb=" O THR T 178 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER T 183 " --> pdb=" O ASP T 179 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN T 192 " --> pdb=" O GLU T 188 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU T 194 " --> pdb=" O ALA T 190 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU T 195 " --> pdb=" O LYS T 191 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER T 196 " --> pdb=" O ASN T 192 " (cutoff:3.500A) Processing helix chain 'T' and resid 201 through 210 Processing helix chain 'T' and resid 213 through 224 removed outlier: 3.552A pdb=" N GLU T 218 " --> pdb=" O GLU T 214 " (cutoff:3.500A) Processing helix chain 'T' and resid 235 through 248 removed outlier: 4.077A pdb=" N SER T 239 " --> pdb=" O PHE T 235 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS T 240 " --> pdb=" O ASN T 236 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU T 248 " --> pdb=" O ASP T 244 " (cutoff:3.500A) Processing helix chain 'T' and resid 252 through 257 Processing helix chain 'T' and resid 258 through 271 removed outlier: 3.689A pdb=" N ALA T 263 " --> pdb=" O ILE T 259 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET T 264 " --> pdb=" O ILE T 260 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE T 268 " --> pdb=" O MET T 264 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER T 269 " --> pdb=" O ASP T 265 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE T 270 " --> pdb=" O TYR T 266 " (cutoff:3.500A) Processing helix chain 'X' and resid 118 through 131 removed outlier: 3.503A pdb=" N TYR X 122 " --> pdb=" O ASP X 118 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS X 124 " --> pdb=" O GLU X 120 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN X 131 " --> pdb=" O GLY X 127 " (cutoff:3.500A) Processing helix chain 'Y' and resid 18 through 31 removed outlier: 4.406A pdb=" N GLU Y 22 " --> pdb=" O LYS Y 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 42 removed outlier: 3.630A pdb=" N ILE Y 40 " --> pdb=" O GLU Y 36 " (cutoff:3.500A) Processing helix chain 'Y' and resid 71 through 88 removed outlier: 3.909A pdb=" N LEU Y 77 " --> pdb=" O PHE Y 73 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS Y 85 " --> pdb=" O LEU Y 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 19 removed outlier: 3.605A pdb=" N GLU Z 14 " --> pdb=" O GLN Z 10 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE Z 18 " --> pdb=" O GLU Z 14 " (cutoff:3.500A) Processing helix chain 'Z' and resid 24 through 34 Processing helix chain 'Z' and resid 35 through 42 removed outlier: 3.857A pdb=" N SER Z 39 " --> pdb=" O GLU Z 35 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU Z 40 " --> pdb=" O GLU Z 36 " (cutoff:3.500A) Processing helix chain 'Z' and resid 44 through 58 removed outlier: 3.579A pdb=" N GLU Z 50 " --> pdb=" O LYS Z 46 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU Z 51 " --> pdb=" O THR Z 47 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU Z 52 " --> pdb=" O ASP Z 48 " (cutoff:3.500A) Processing helix chain 'Z' and resid 61 through 66 Processing helix chain 'Z' and resid 70 through 75 removed outlier: 4.481A pdb=" N SER Z 74 " --> pdb=" O ALA Z 70 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE Z 75 " --> pdb=" O LEU Z 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 70 through 75' Processing helix chain 'Z' and resid 85 through 90 removed outlier: 3.599A pdb=" N LEU Z 89 " --> pdb=" O VAL Z 85 " (cutoff:3.500A) Processing helix chain 'Z' and resid 95 through 104 removed outlier: 4.097A pdb=" N ILE Z 102 " --> pdb=" O ASP Z 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 108 through 127 removed outlier: 3.537A pdb=" N SER Z 114 " --> pdb=" O ASN Z 110 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP Z 117 " --> pdb=" O SER Z 113 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL Z 118 " --> pdb=" O SER Z 114 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE Z 121 " --> pdb=" O ASP Z 117 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 141 removed outlier: 3.601A pdb=" N LEU Z 135 " --> pdb=" O LYS Z 131 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG Z 138 " --> pdb=" O SER Z 134 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU Z 139 " --> pdb=" O LEU Z 135 " (cutoff:3.500A) Processing helix chain 'Z' and resid 148 through 164 removed outlier: 5.014A pdb=" N ILE Z 154 " --> pdb=" O GLY Z 150 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU Z 157 " --> pdb=" O TYR Z 153 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU Z 160 " --> pdb=" O HIS Z 156 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE Z 161 " --> pdb=" O LEU Z 157 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL Z 164 " --> pdb=" O GLU Z 160 " (cutoff:3.500A) Processing helix chain 'Z' and resid 164 through 170 removed outlier: 3.980A pdb=" N GLN Z 168 " --> pdb=" O VAL Z 164 " (cutoff:3.500A) Processing helix chain 'Z' and resid 185 through 188 removed outlier: 4.438A pdb=" N ALA Z 188 " --> pdb=" O ASP Z 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 185 through 188' Processing helix chain 'Z' and resid 189 through 203 removed outlier: 3.743A pdb=" N PHE Z 195 " --> pdb=" O SER Z 191 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU Z 198 " --> pdb=" O GLU Z 194 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU Z 201 " --> pdb=" O LYS Z 197 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG Z 202 " --> pdb=" O GLU Z 198 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU Z 203 " --> pdb=" O ASP Z 199 " (cutoff:3.500A) Processing helix chain 'Z' and resid 207 through 216 removed outlier: 3.607A pdb=" N ASN Z 215 " --> pdb=" O PHE Z 211 " (cutoff:3.500A) Processing helix chain 'Z' and resid 217 through 232 removed outlier: 3.970A pdb=" N VAL Z 221 " --> pdb=" O GLU Z 217 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU Z 226 " --> pdb=" O ASP Z 222 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE Z 227 " --> pdb=" O LEU Z 223 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP Z 231 " --> pdb=" O ILE Z 227 " (cutoff:3.500A) Processing helix chain 'Z' and resid 237 through 252 removed outlier: 3.614A pdb=" N GLN Z 243 " --> pdb=" O GLU Z 239 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG Z 244 " --> pdb=" O ASN Z 240 " (cutoff:3.500A) Processing helix chain 'Z' and resid 257 through 275 removed outlier: 3.767A pdb=" N VAL Z 262 " --> pdb=" O PRO Z 258 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA Z 263 " --> pdb=" O PRO Z 259 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU Z 265 " --> pdb=" O ASP Z 261 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR Z 267 " --> pdb=" O ALA Z 263 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER Z 270 " --> pdb=" O LYS Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 277 through 289 removed outlier: 4.370A pdb=" N ALA Z 281 " --> pdb=" O GLU Z 277 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE Z 282 " --> pdb=" O LEU Z 278 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA Z 283 " --> pdb=" O THR Z 279 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU Z 284 " --> pdb=" O ASP Z 280 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL Z 286 " --> pdb=" O ILE Z 282 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG Z 287 " --> pdb=" O ALA Z 283 " (cutoff:3.500A) Processing helix chain 'Z' and resid 290 through 303 removed outlier: 3.682A pdb=" N ILE Z 294 " --> pdb=" O GLU Z 290 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL Z 297 " --> pdb=" O MET Z 293 " (cutoff:3.500A) Processing helix chain 'Z' and resid 308 through 321 removed outlier: 3.699A pdb=" N TYR Z 312 " --> pdb=" O LYS Z 308 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE Z 313 " --> pdb=" O GLN Z 309 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE Z 321 " --> pdb=" O GLN Z 317 " (cutoff:3.500A) Processing helix chain 'Z' and resid 325 through 332 removed outlier: 3.625A pdb=" N ILE Z 330 " --> pdb=" O VAL Z 326 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASN Z 332 " --> pdb=" O ASP Z 328 " (cutoff:3.500A) Processing helix chain 'Z' and resid 333 through 339 removed outlier: 3.566A pdb=" N PHE Z 339 " --> pdb=" O LEU Z 335 " (cutoff:3.500A) Processing helix chain 'Z' and resid 342 through 350 removed outlier: 3.816A pdb=" N ASN Z 347 " --> pdb=" O ALA Z 343 " (cutoff:3.500A) Processing helix chain 'Z' and resid 351 through 366 removed outlier: 3.659A pdb=" N GLU Z 355 " --> pdb=" O PRO Z 351 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP Z 356 " --> pdb=" O LYS Z 352 " (cutoff:3.500A) Processing helix chain 'Z' and resid 378 through 391 removed outlier: 3.596A pdb=" N SER Z 384 " --> pdb=" O ASN Z 380 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN Z 387 " --> pdb=" O SER Z 383 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY Z 388 " --> pdb=" O SER Z 384 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN Z 391 " --> pdb=" O ASN Z 387 " (cutoff:3.500A) Processing helix chain 'Z' and resid 397 through 402 removed outlier: 3.781A pdb=" N VAL Z 401 " --> pdb=" O ASP Z 397 " (cutoff:3.500A) Processing helix chain 'Z' and resid 404 through 409 Processing helix chain 'Z' and resid 413 through 424 removed outlier: 3.597A pdb=" N SER Z 417 " --> pdb=" O ASP Z 413 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE Z 422 " --> pdb=" O ALA Z 418 " (cutoff:3.500A) Processing helix chain 'Z' and resid 425 through 427 No H-bonds generated for 'chain 'Z' and resid 425 through 427' Processing helix chain 'Z' and resid 432 through 441 removed outlier: 3.758A pdb=" N LEU Z 436 " --> pdb=" O GLY Z 432 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS Z 438 " --> pdb=" O GLN Z 434 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR Z 439 " --> pdb=" O GLN Z 435 " (cutoff:3.500A) Processing helix chain 'Z' and resid 444 through 459 removed outlier: 3.786A pdb=" N LYS Z 448 " --> pdb=" O GLU Z 444 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY Z 450 " --> pdb=" O GLU Z 446 " (cutoff:3.500A) Processing helix chain 'Z' and resid 469 through 480 removed outlier: 4.284A pdb=" N LEU Z 473 " --> pdb=" O PRO Z 469 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP Z 476 " --> pdb=" O LEU Z 472 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR Z 477 " --> pdb=" O LEU Z 473 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR Z 479 " --> pdb=" O GLN Z 475 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN Z 480 " --> pdb=" O ASP Z 476 " (cutoff:3.500A) Processing helix chain 'Z' and resid 482 through 498 removed outlier: 3.904A pdb=" N LEU Z 493 " --> pdb=" O ALA Z 489 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE Z 497 " --> pdb=" O LEU Z 493 " (cutoff:3.500A) Processing helix chain 'Z' and resid 502 through 510 removed outlier: 3.648A pdb=" N LEU Z 508 " --> pdb=" O GLU Z 504 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU Z 509 " --> pdb=" O VAL Z 505 " (cutoff:3.500A) Processing helix chain 'Z' and resid 520 through 523 Processing helix chain 'Z' and resid 524 through 535 removed outlier: 3.705A pdb=" N LEU Z 528 " --> pdb=" O ALA Z 524 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU Z 530 " --> pdb=" O ALA Z 526 " (cutoff:3.500A) Processing helix chain 'Z' and resid 543 through 556 removed outlier: 3.649A pdb=" N ASP Z 548 " --> pdb=" O THR Z 544 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA Z 555 " --> pdb=" O LEU Z 551 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE Z 556 " --> pdb=" O GLU Z 552 " (cutoff:3.500A) Processing helix chain 'Z' and resid 559 through 575 removed outlier: 3.796A pdb=" N VAL Z 563 " --> pdb=" O LYS Z 559 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE Z 565 " --> pdb=" O ASP Z 561 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR Z 574 " --> pdb=" O LEU Z 570 " (cutoff:3.500A) Processing helix chain 'Z' and resid 582 through 589 removed outlier: 3.991A pdb=" N GLU Z 586 " --> pdb=" O ASP Z 582 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR Z 587 " --> pdb=" O ASP Z 583 " (cutoff:3.500A) Processing helix chain 'Z' and resid 593 through 608 removed outlier: 3.542A pdb=" N SER Z 597 " --> pdb=" O HIS Z 593 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE Z 599 " --> pdb=" O MET Z 595 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL Z 601 " --> pdb=" O SER Z 597 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU Z 602 " --> pdb=" O ALA Z 598 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS Z 606 " --> pdb=" O LEU Z 602 " (cutoff:3.500A) Processing helix chain 'Z' and resid 614 through 635 removed outlier: 3.546A pdb=" N LEU Z 620 " --> pdb=" O LEU Z 616 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG Z 623 " --> pdb=" O ASP Z 619 " (cutoff:3.500A) Proline residue: Z 626 - end of helix Processing helix chain 'Z' and resid 701 through 727 removed outlier: 3.527A pdb=" N ASP Z 712 " --> pdb=" O GLY Z 708 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS Z 713 " --> pdb=" O LYS Z 709 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU Z 725 " --> pdb=" O ASN Z 721 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU Z 726 " --> pdb=" O ASP Z 722 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU Z 727 " --> pdb=" O ASP Z 723 " (cutoff:3.500A) Processing helix chain 'Z' and resid 728 through 750 removed outlier: 4.012A pdb=" N VAL Z 733 " --> pdb=" O GLU Z 729 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP Z 734 " --> pdb=" O ALA Z 730 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL Z 740 " --> pdb=" O LEU Z 736 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU Z 741 " --> pdb=" O ALA Z 737 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA Z 744 " --> pdb=" O VAL Z 740 " (cutoff:3.500A) Processing helix chain 'Z' and resid 750 through 769 removed outlier: 3.917A pdb=" N LYS Z 754 " --> pdb=" O GLU Z 750 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU Z 755 " --> pdb=" O ASP Z 751 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET Z 756 " --> pdb=" O ILE Z 752 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG Z 759 " --> pdb=" O GLU Z 755 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY Z 762 " --> pdb=" O LEU Z 758 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N HIS Z 763 " --> pdb=" O ARG Z 759 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET Z 765 " --> pdb=" O PHE Z 761 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS Z 766 " --> pdb=" O GLY Z 762 " (cutoff:3.500A) Processing helix chain 'Z' and resid 775 through 787 removed outlier: 3.736A pdb=" N VAL Z 783 " --> pdb=" O ALA Z 779 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER Z 786 " --> pdb=" O ILE Z 782 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP Z 787 " --> pdb=" O VAL Z 783 " (cutoff:3.500A) Processing helix chain 'Z' and resid 790 through 800 removed outlier: 4.168A pdb=" N ASP Z 794 " --> pdb=" O MET Z 790 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG Z 798 " --> pdb=" O ASP Z 794 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE Z 799 " --> pdb=" O THR Z 795 " (cutoff:3.500A) Processing helix chain 'Z' and resid 806 through 822 removed outlier: 3.900A pdb=" N ASN Z 810 " --> pdb=" O GLU Z 806 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY Z 816 " --> pdb=" O ILE Z 812 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU Z 817 " --> pdb=" O PHE Z 813 " (cutoff:3.500A) Processing helix chain 'Z' and resid 825 through 840 removed outlier: 3.741A pdb=" N SER Z 836 " --> pdb=" O ARG Z 832 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG Z 840 " --> pdb=" O SER Z 836 " (cutoff:3.500A) Processing helix chain 'Z' and resid 864 through 869 removed outlier: 4.229A pdb=" N ASN Z 868 " --> pdb=" O MET Z 864 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP Z 869 " --> pdb=" O ASP Z 865 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 864 through 869' Processing helix chain 'Z' and resid 877 through 884 Processing helix chain 'N' and resid 6 through 15 Processing helix chain 'N' and resid 17 through 30 removed outlier: 3.748A pdb=" N LYS N 21 " --> pdb=" O GLN N 17 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR N 23 " --> pdb=" O SER N 19 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU N 25 " --> pdb=" O LYS N 21 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU N 26 " --> pdb=" O THR N 22 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER N 27 " --> pdb=" O TYR N 23 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN N 30 " --> pdb=" O GLU N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 41 removed outlier: 3.501A pdb=" N ASN N 41 " --> pdb=" O GLU N 38 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 52 removed outlier: 3.620A pdb=" N TYR N 50 " --> pdb=" O ILE N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 73 Processing helix chain 'N' and resid 74 through 86 removed outlier: 3.556A pdb=" N ALA N 78 " --> pdb=" O GLU N 74 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU N 83 " --> pdb=" O VAL N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 94 Processing helix chain 'N' and resid 99 through 118 removed outlier: 3.554A pdb=" N GLN N 111 " --> pdb=" O GLU N 107 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS N 115 " --> pdb=" O GLN N 111 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR N 118 " --> pdb=" O SER N 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 148 removed outlier: 3.505A pdb=" N SER N 135 " --> pdb=" O PRO N 131 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA N 147 " --> pdb=" O LYS N 143 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 161 removed outlier: 3.637A pdb=" N ALA N 157 " --> pdb=" O ALA N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 163 through 173 removed outlier: 3.512A pdb=" N LEU N 170 " --> pdb=" O ILE N 166 " (cutoff:3.500A) Processing helix chain 'N' and resid 178 through 197 removed outlier: 3.578A pdb=" N ASN N 182 " --> pdb=" O SER N 178 " (cutoff:3.500A) Processing helix chain 'N' and resid 199 through 217 removed outlier: 3.552A pdb=" N ARG N 203 " --> pdb=" O ASN N 199 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP N 212 " --> pdb=" O ARG N 208 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET N 217 " --> pdb=" O PHE N 213 " (cutoff:3.500A) Processing helix chain 'N' and resid 222 through 233 removed outlier: 3.589A pdb=" N LYS N 227 " --> pdb=" O LEU N 223 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL N 228 " --> pdb=" O THR N 224 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL N 229 " --> pdb=" O LEU N 225 " (cutoff:3.500A) Processing helix chain 'N' and resid 234 through 246 removed outlier: 3.571A pdb=" N ALA N 238 " --> pdb=" O ASP N 234 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN N 240 " --> pdb=" O GLY N 236 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU N 241 " --> pdb=" O LEU N 237 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE N 242 " --> pdb=" O ALA N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 265 removed outlier: 3.805A pdb=" N SER N 263 " --> pdb=" O PHE N 259 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER N 264 " --> pdb=" O ASP N 260 " (cutoff:3.500A) Processing helix chain 'N' and resid 266 through 281 removed outlier: 3.544A pdb=" N LEU N 270 " --> pdb=" O SER N 266 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR N 275 " --> pdb=" O GLU N 271 " (cutoff:3.500A) Processing helix chain 'N' and resid 283 through 292 removed outlier: 4.019A pdb=" N LEU N 287 " --> pdb=" O ASP N 283 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE N 289 " --> pdb=" O ALA N 285 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY N 292 " --> pdb=" O ASN N 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 292 through 307 Processing helix chain 'N' and resid 311 through 321 removed outlier: 3.570A pdb=" N ASN N 315 " --> pdb=" O ILE N 311 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS N 318 " --> pdb=" O LEU N 314 " (cutoff:3.500A) Processing helix chain 'N' and resid 325 through 340 Processing helix chain 'N' and resid 346 through 352 removed outlier: 3.531A pdb=" N ALA N 351 " --> pdb=" O SER N 347 " (cutoff:3.500A) Processing helix chain 'N' and resid 352 through 358 removed outlier: 3.520A pdb=" N LYS N 358 " --> pdb=" O PRO N 354 " (cutoff:3.500A) Processing helix chain 'N' and resid 361 through 375 removed outlier: 3.700A pdb=" N PHE N 365 " --> pdb=" O ASN N 361 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU N 371 " --> pdb=" O ALA N 367 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY N 372 " --> pdb=" O THR N 368 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL N 373 " --> pdb=" O ALA N 369 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE N 374 " --> pdb=" O SER N 370 " (cutoff:3.500A) Processing helix chain 'N' and resid 378 through 387 removed outlier: 4.366A pdb=" N LYS N 383 " --> pdb=" O LEU N 379 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYS N 384 " --> pdb=" O LEU N 380 " (cutoff:3.500A) Processing helix chain 'N' and resid 397 through 413 removed outlier: 3.716A pdb=" N LYS N 401 " --> pdb=" O SER N 397 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU N 405 " --> pdb=" O LYS N 401 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU N 408 " --> pdb=" O SER N 404 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY N 409 " --> pdb=" O LEU N 405 " (cutoff:3.500A) Processing helix chain 'N' and resid 418 through 430 removed outlier: 4.147A pdb=" N TYR N 422 " --> pdb=" O ASP N 418 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU N 423 " --> pdb=" O THR N 419 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE N 426 " --> pdb=" O TYR N 422 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN N 430 " --> pdb=" O ILE N 426 " (cutoff:3.500A) Processing helix chain 'N' and resid 436 through 454 removed outlier: 3.992A pdb=" N VAL N 441 " --> pdb=" O GLU N 437 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU N 442 " --> pdb=" O ASP N 438 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY N 445 " --> pdb=" O VAL N 441 " (cutoff:3.500A) Processing helix chain 'N' and resid 459 through 473 removed outlier: 3.803A pdb=" N VAL N 469 " --> pdb=" O ALA N 465 " (cutoff:3.500A) Processing helix chain 'N' and resid 476 through 489 removed outlier: 3.762A pdb=" N ALA N 480 " --> pdb=" O THR N 476 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY N 486 " --> pdb=" O ALA N 482 " (cutoff:3.500A) Processing helix chain 'N' and resid 494 through 508 removed outlier: 4.204A pdb=" N GLN N 506 " --> pdb=" O PHE N 502 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU N 507 " --> pdb=" O THR N 503 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR N 508 " --> pdb=" O TYR N 504 " (cutoff:3.500A) Processing helix chain 'N' and resid 510 through 525 removed outlier: 3.614A pdb=" N THR N 514 " --> pdb=" O HIS N 510 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA N 522 " --> pdb=" O ALA N 518 " (cutoff:3.500A) Processing helix chain 'N' and resid 528 through 531 Processing helix chain 'N' and resid 532 through 542 Processing helix chain 'N' and resid 544 through 559 removed outlier: 3.555A pdb=" N GLY N 550 " --> pdb=" O LEU N 546 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE N 553 " --> pdb=" O TYR N 549 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE N 555 " --> pdb=" O GLY N 551 " (cutoff:3.500A) Processing helix chain 'N' and resid 564 through 578 Processing helix chain 'N' and resid 580 through 595 removed outlier: 3.745A pdb=" N VAL N 588 " --> pdb=" O ARG N 584 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU N 591 " --> pdb=" O ALA N 587 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY N 592 " --> pdb=" O VAL N 588 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE N 593 " --> pdb=" O ILE N 589 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL N 594 " --> pdb=" O ALA N 590 " (cutoff:3.500A) Processing helix chain 'N' and resid 601 through 606 Processing helix chain 'N' and resid 606 through 612 Processing helix chain 'N' and resid 614 through 629 removed outlier: 3.527A pdb=" N PHE N 623 " --> pdb=" O CYS N 619 " (cutoff:3.500A) Processing helix chain 'N' and resid 634 through 646 removed outlier: 3.704A pdb=" N ILE N 638 " --> pdb=" O LEU N 634 " (cutoff:3.500A) Proline residue: N 643 - end of helix removed outlier: 4.017A pdb=" N LYS N 646 " --> pdb=" O ASP N 642 " (cutoff:3.500A) Processing helix chain 'N' and resid 649 through 664 removed outlier: 3.546A pdb=" N ARG N 653 " --> pdb=" O VAL N 649 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER N 661 " --> pdb=" O MET N 657 " (cutoff:3.500A) Processing helix chain 'N' and resid 673 through 688 removed outlier: 3.901A pdb=" N ASP N 677 " --> pdb=" O PRO N 673 " (cutoff:3.500A) Processing helix chain 'N' and resid 692 through 707 removed outlier: 3.504A pdb=" N LYS N 696 " --> pdb=" O GLU N 692 " (cutoff:3.500A) Processing helix chain 'N' and resid 708 through 711 Processing helix chain 'N' and resid 726 through 738 removed outlier: 3.649A pdb=" N VAL N 730 " --> pdb=" O ASP N 726 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL N 731 " --> pdb=" O THR N 727 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN N 738 " --> pdb=" O VAL N 734 " (cutoff:3.500A) Processing helix chain 'N' and resid 742 through 751 removed outlier: 3.731A pdb=" N LEU N 745 " --> pdb=" O TRP N 742 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N HIS N 747 " --> pdb=" O PRO N 744 " (cutoff:3.500A) Processing helix chain 'N' and resid 779 through 783 removed outlier: 3.794A pdb=" N PHE N 782 " --> pdb=" O GLU N 779 " (cutoff:3.500A) Processing helix chain 'N' and resid 789 through 821 removed outlier: 3.605A pdb=" N VAL N 796 " --> pdb=" O SER N 792 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU N 797 " --> pdb=" O GLY N 793 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER N 805 " --> pdb=" O THR N 801 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA N 810 " --> pdb=" O THR N 806 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS N 811 " --> pdb=" O THR N 807 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG N 813 " --> pdb=" O ARG N 809 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA N 814 " --> pdb=" O ALA N 810 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR N 817 " --> pdb=" O ARG N 813 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU N 820 " --> pdb=" O LYS N 816 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS N 821 " --> pdb=" O THR N 817 " (cutoff:3.500A) Processing helix chain 'N' and resid 875 through 880 removed outlier: 3.952A pdb=" N ARG N 880 " --> pdb=" O PRO N 876 " (cutoff:3.500A) Processing helix chain 'N' and resid 919 through 925 removed outlier: 4.220A pdb=" N MET N 923 " --> pdb=" O THR N 919 " (cutoff:3.500A) Processing helix chain 'S' and resid 19 through 42 Processing helix chain 'S' and resid 47 through 65 removed outlier: 3.609A pdb=" N ASP S 59 " --> pdb=" O ARG S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 79 Processing helix chain 'S' and resid 84 through 96 removed outlier: 3.606A pdb=" N ILE S 96 " --> pdb=" O LEU S 92 " (cutoff:3.500A) Processing helix chain 'S' and resid 119 through 126 removed outlier: 3.641A pdb=" N GLU S 124 " --> pdb=" O SER S 120 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS S 125 " --> pdb=" O VAL S 121 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS S 126 " --> pdb=" O ASN S 122 " (cutoff:3.500A) Processing helix chain 'S' and resid 131 through 150 Processing helix chain 'S' and resid 152 through 168 removed outlier: 3.618A pdb=" N VAL S 156 " --> pdb=" O LEU S 152 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU S 157 " --> pdb=" O GLU S 153 " (cutoff:3.500A) Proline residue: S 165 - end of helix Processing helix chain 'S' and resid 173 through 198 removed outlier: 3.791A pdb=" N ILE S 179 " --> pdb=" O SER S 175 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYS S 182 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU S 183 " --> pdb=" O ILE S 179 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N PHE S 185 " --> pdb=" O ALA S 181 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR S 186 " --> pdb=" O LYS S 182 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU S 194 " --> pdb=" O SER S 190 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER S 198 " --> pdb=" O LEU S 194 " (cutoff:3.500A) Processing helix chain 'S' and resid 200 through 224 removed outlier: 3.862A pdb=" N ASP S 204 " --> pdb=" O GLU S 200 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE S 208 " --> pdb=" O ASP S 204 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE S 209 " --> pdb=" O ASN S 205 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE S 220 " --> pdb=" O LYS S 216 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER S 222 " --> pdb=" O LEU S 218 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU S 223 " --> pdb=" O LYS S 219 " (cutoff:3.500A) Processing helix chain 'S' and resid 226 through 245 removed outlier: 3.515A pdb=" N LYS S 230 " --> pdb=" O ASP S 226 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN S 244 " --> pdb=" O ASP S 240 " (cutoff:3.500A) Processing helix chain 'S' and resid 246 through 255 removed outlier: 3.687A pdb=" N SER S 255 " --> pdb=" O SER S 251 " (cutoff:3.500A) Processing helix chain 'S' and resid 265 through 283 removed outlier: 3.566A pdb=" N ARG S 271 " --> pdb=" O SER S 267 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE S 282 " --> pdb=" O LYS S 278 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLN S 283 " --> pdb=" O ILE S 279 " (cutoff:3.500A) Processing helix chain 'S' and resid 286 through 300 removed outlier: 3.889A pdb=" N GLU S 291 " --> pdb=" O SER S 287 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE S 297 " --> pdb=" O ILE S 293 " (cutoff:3.500A) Processing helix chain 'S' and resid 306 through 325 Processing helix chain 'S' and resid 330 through 336 removed outlier: 3.655A pdb=" N HIS S 334 " --> pdb=" O LEU S 330 " (cutoff:3.500A) Processing helix chain 'S' and resid 342 through 355 removed outlier: 3.739A pdb=" N HIS S 347 " --> pdb=" O LEU S 343 " (cutoff:3.500A) Processing helix chain 'S' and resid 356 through 367 removed outlier: 3.592A pdb=" N PHE S 360 " --> pdb=" O ASP S 356 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR S 365 " --> pdb=" O THR S 361 " (cutoff:3.500A) Processing helix chain 'S' and resid 367 through 374 removed outlier: 3.665A pdb=" N LYS S 373 " --> pdb=" O GLN S 369 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASP S 374 " --> pdb=" O LEU S 370 " (cutoff:3.500A) Processing helix chain 'S' and resid 376 through 399 removed outlier: 3.748A pdb=" N ARG S 382 " --> pdb=" O GLN S 378 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG S 384 " --> pdb=" O CYS S 380 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N SER S 385 " --> pdb=" O VAL S 381 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN S 386 " --> pdb=" O ARG S 382 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL S 387 " --> pdb=" O LEU S 383 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE S 388 " --> pdb=" O ARG S 384 " (cutoff:3.500A) Processing helix chain 'S' and resid 404 through 411 removed outlier: 3.582A pdb=" N CYS S 408 " --> pdb=" O LEU S 404 " (cutoff:3.500A) Processing helix chain 'S' and resid 415 through 430 removed outlier: 3.553A pdb=" N VAL S 419 " --> pdb=" O SER S 415 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG S 428 " --> pdb=" O SER S 424 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP S 429 " --> pdb=" O ARG S 425 " (cutoff:3.500A) Processing helix chain 'S' and resid 455 through 489 removed outlier: 3.773A pdb=" N GLN S 459 " --> pdb=" O GLU S 455 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU S 463 " --> pdb=" O GLN S 459 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG S 464 " --> pdb=" O VAL S 460 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN S 469 " --> pdb=" O ILE S 465 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET S 479 " --> pdb=" O TYR S 475 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG S 480 " --> pdb=" O LEU S 476 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR S 481 " --> pdb=" O VAL S 477 " (cutoff:3.500A) Proline residue: S 482 - end of helix removed outlier: 3.773A pdb=" N LYS S 485 " --> pdb=" O TYR S 481 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 20 removed outlier: 4.287A pdb=" N LYS P 8 " --> pdb=" O ASP P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 29 removed outlier: 3.663A pdb=" N GLN P 29 " --> pdb=" O ASP P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 31 through 43 removed outlier: 4.017A pdb=" N ALA P 35 " --> pdb=" O ASP P 31 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU P 39 " --> pdb=" O ALA P 35 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 68 removed outlier: 3.519A pdb=" N ALA P 53 " --> pdb=" O ALA P 49 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS P 56 " --> pdb=" O LEU P 52 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLU P 57 " --> pdb=" O ALA P 53 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL P 58 " --> pdb=" O SER P 54 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP P 64 " --> pdb=" O ALA P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 71 through 79 removed outlier: 3.990A pdb=" N LEU P 75 " --> pdb=" O LYS P 71 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN P 76 " --> pdb=" O TRP P 72 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU P 77 " --> pdb=" O ASP P 73 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU P 79 " --> pdb=" O LEU P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 86 removed outlier: 3.780A pdb=" N HIS P 86 " --> pdb=" O LEU P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 108 removed outlier: 3.982A pdb=" N TYR P 95 " --> pdb=" O LEU P 91 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N MET P 96 " --> pdb=" O SER P 92 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN P 98 " --> pdb=" O GLN P 94 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LYS P 108 " --> pdb=" O LEU P 104 " (cutoff:3.500A) Processing helix chain 'P' and resid 110 through 126 Processing helix chain 'P' and resid 131 through 150 removed outlier: 4.322A pdb=" N GLU P 135 " --> pdb=" O PHE P 131 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG P 138 " --> pdb=" O VAL P 134 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS P 141 " --> pdb=" O ALA P 137 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP P 142 " --> pdb=" O ARG P 138 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU P 143 " --> pdb=" O VAL P 139 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU P 150 " --> pdb=" O ILE P 146 " (cutoff:3.500A) Processing helix chain 'P' and resid 152 through 164 removed outlier: 3.648A pdb=" N ALA P 157 " --> pdb=" O ILE P 153 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP P 158 " --> pdb=" O ASP P 154 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE P 159 " --> pdb=" O GLU P 155 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU P 162 " --> pdb=" O ASP P 158 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN P 164 " --> pdb=" O LEU P 160 " (cutoff:3.500A) Processing helix chain 'P' and resid 172 through 191 removed outlier: 3.659A pdb=" N LEU P 189 " --> pdb=" O GLU P 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 192 through 201 removed outlier: 3.600A pdb=" N ALA P 196 " --> pdb=" O ASP P 192 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL P 198 " --> pdb=" O SER P 194 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG P 201 " --> pdb=" O THR P 197 " (cutoff:3.500A) Processing helix chain 'P' and resid 206 through 210 removed outlier: 3.662A pdb=" N LYS P 209 " --> pdb=" O LYS P 206 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN P 210 " --> pdb=" O THR P 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 206 through 210' Processing helix chain 'P' and resid 213 through 231 Processing helix chain 'P' and resid 233 through 247 removed outlier: 3.777A pdb=" N VAL P 237 " --> pdb=" O GLU P 233 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE P 244 " --> pdb=" O TYR P 240 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR P 247 " --> pdb=" O GLU P 243 " (cutoff:3.500A) Processing helix chain 'P' and resid 247 through 253 Processing helix chain 'P' and resid 253 through 271 Proline residue: P 259 - end of helix Processing helix chain 'P' and resid 274 through 287 removed outlier: 3.816A pdb=" N ASN P 278 " --> pdb=" O GLY P 274 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP P 279 " --> pdb=" O ASN P 275 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS P 283 " --> pdb=" O ASP P 279 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP P 287 " --> pdb=" O LYS P 283 " (cutoff:3.500A) Processing helix chain 'P' and resid 288 through 293 removed outlier: 3.548A pdb=" N LYS P 292 " --> pdb=" O ASN P 289 " (cutoff:3.500A) Processing helix chain 'P' and resid 294 through 304 removed outlier: 3.808A pdb=" N LEU P 299 " --> pdb=" O SER P 295 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL P 300 " --> pdb=" O GLN P 296 " (cutoff:3.500A) Processing helix chain 'P' and resid 310 through 319 removed outlier: 4.113A pdb=" N LYS P 316 " --> pdb=" O PRO P 312 " (cutoff:3.500A) Processing helix chain 'P' and resid 331 through 339 removed outlier: 3.812A pdb=" N HIS P 336 " --> pdb=" O GLU P 332 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N HIS P 337 " --> pdb=" O ALA P 333 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU P 339 " --> pdb=" O LYS P 335 " (cutoff:3.500A) Processing helix chain 'P' and resid 340 through 356 removed outlier: 3.694A pdb=" N GLU P 355 " --> pdb=" O ARG P 351 " (cutoff:3.500A) Processing helix chain 'P' and resid 362 through 370 Processing helix chain 'P' and resid 372 through 387 Processing helix chain 'P' and resid 407 through 440 removed outlier: 3.652A pdb=" N LEU P 411 " --> pdb=" O ASN P 407 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU P 427 " --> pdb=" O LEU P 423 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS P 435 " --> pdb=" O HIS P 431 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU P 437 " --> pdb=" O ILE P 433 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE P 438 " --> pdb=" O THR P 434 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 16 Processing helix chain 'Q' and resid 19 through 39 removed outlier: 3.705A pdb=" N ALA Q 23 " --> pdb=" O GLN Q 19 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN Q 25 " --> pdb=" O ASN Q 21 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL Q 26 " --> pdb=" O GLU Q 22 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 66 removed outlier: 3.653A pdb=" N GLU Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN Q 63 " --> pdb=" O LEU Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 78 removed outlier: 3.594A pdb=" N GLU Q 76 " --> pdb=" O ASP Q 72 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE Q 77 " --> pdb=" O LYS Q 73 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE Q 78 " --> pdb=" O LEU Q 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 89 removed outlier: 3.698A pdb=" N MET Q 86 " --> pdb=" O THR Q 82 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA Q 89 " --> pdb=" O MET Q 85 " (cutoff:3.500A) Processing helix chain 'Q' and resid 92 through 107 Processing helix chain 'Q' and resid 109 through 124 removed outlier: 4.610A pdb=" N ASP Q 113 " --> pdb=" O ASP Q 109 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN Q 114 " --> pdb=" O SER Q 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 130 through 148 removed outlier: 4.051A pdb=" N SER Q 136 " --> pdb=" O PHE Q 132 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS Q 140 " --> pdb=" O SER Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 150 through 162 removed outlier: 3.808A pdb=" N SER Q 154 " --> pdb=" O GLN Q 150 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU Q 157 " --> pdb=" O ASP Q 153 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE Q 158 " --> pdb=" O SER Q 154 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU Q 161 " --> pdb=" O LEU Q 157 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU Q 162 " --> pdb=" O ILE Q 158 " (cutoff:3.500A) Processing helix chain 'Q' and resid 171 through 188 removed outlier: 4.020A pdb=" N VAL Q 175 " --> pdb=" O LYS Q 171 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL Q 177 " --> pdb=" O SER Q 173 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS Q 178 " --> pdb=" O LEU Q 174 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS Q 183 " --> pdb=" O LEU Q 179 " (cutoff:3.500A) Processing helix chain 'Q' and resid 191 through 205 Processing helix chain 'Q' and resid 211 through 229 removed outlier: 3.604A pdb=" N VAL Q 215 " --> pdb=" O PRO Q 211 " (cutoff:3.500A) Processing helix chain 'Q' and resid 233 through 249 Processing helix chain 'Q' and resid 254 through 273 removed outlier: 3.970A pdb=" N LYS Q 269 " --> pdb=" O MET Q 265 " (cutoff:3.500A) Processing helix chain 'Q' and resid 275 through 282 removed outlier: 4.007A pdb=" N LYS Q 279 " --> pdb=" O ILE Q 275 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU Q 282 " --> pdb=" O VAL Q 278 " (cutoff:3.500A) Processing helix chain 'Q' and resid 286 through 291 removed outlier: 3.863A pdb=" N TYR Q 291 " --> pdb=" O THR Q 287 " (cutoff:3.500A) Processing helix chain 'Q' and resid 293 through 309 removed outlier: 3.850A pdb=" N ASP Q 297 " --> pdb=" O SER Q 293 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS Q 300 " --> pdb=" O ILE Q 296 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU Q 304 " --> pdb=" O LYS Q 300 " (cutoff:3.500A) Processing helix chain 'Q' and resid 310 through 320 removed outlier: 3.545A pdb=" N PHE Q 314 " --> pdb=" O SER Q 310 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN Q 320 " --> pdb=" O THR Q 316 " (cutoff:3.500A) Processing helix chain 'Q' and resid 321 through 328 Processing helix chain 'Q' and resid 328 through 352 removed outlier: 3.530A pdb=" N ARG Q 332 " --> pdb=" O ASP Q 328 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA Q 337 " --> pdb=" O SER Q 333 " (cutoff:3.500A) Processing helix chain 'Q' and resid 359 through 367 removed outlier: 3.822A pdb=" N ILE Q 365 " --> pdb=" O HIS Q 361 " (cutoff:3.500A) Processing helix chain 'Q' and resid 369 through 384 removed outlier: 3.758A pdb=" N GLN Q 379 " --> pdb=" O GLY Q 375 " (cutoff:3.500A) Processing helix chain 'Q' and resid 406 through 432 removed outlier: 3.841A pdb=" N ASP Q 410 " --> pdb=" O ASP Q 406 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS Q 421 " --> pdb=" O GLY Q 417 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU Q 428 " --> pdb=" O ASP Q 424 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL Q 432 " --> pdb=" O GLU Q 428 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 434 No H-bonds generated for 'chain 'Q' and resid 433 through 434' Processing helix chain 'R' and resid 20 through 20 No H-bonds generated for 'chain 'R' and resid 20 through 20' Processing helix chain 'R' and resid 21 through 35 removed outlier: 4.980A pdb=" N SER R 27 " --> pdb=" O ASN R 23 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU R 32 " --> pdb=" O GLU R 28 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU R 33 " --> pdb=" O LYS R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 58 removed outlier: 3.569A pdb=" N ALA R 47 " --> pdb=" O ARG R 43 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU R 48 " --> pdb=" O LYS R 44 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE R 49 " --> pdb=" O GLU R 45 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS R 53 " --> pdb=" O PHE R 49 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS R 55 " --> pdb=" O LEU R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 69 removed outlier: 3.570A pdb=" N LYS R 64 " --> pdb=" O ALA R 60 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYR R 65 " --> pdb=" O PRO R 61 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU R 68 " --> pdb=" O LYS R 64 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU R 69 " --> pdb=" O TYR R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 123 removed outlier: 3.598A pdb=" N GLU R 115 " --> pdb=" O LYS R 111 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU R 122 " --> pdb=" O GLN R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 145 Processing helix chain 'R' and resid 146 through 160 removed outlier: 3.867A pdb=" N ALA R 150 " --> pdb=" O ASP R 146 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS R 152 " --> pdb=" O ASP R 148 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR R 153 " --> pdb=" O ASN R 149 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS R 156 " --> pdb=" O LYS R 152 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER R 157 " --> pdb=" O THR R 153 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU R 158 " --> pdb=" O LEU R 154 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS R 160 " --> pdb=" O LYS R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 182 removed outlier: 3.531A pdb=" N ASP R 169 " --> pdb=" O GLY R 165 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY R 178 " --> pdb=" O ILE R 174 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE R 179 " --> pdb=" O ALA R 175 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE R 180 " --> pdb=" O ARG R 176 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR R 181 " --> pdb=" O LEU R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 202 removed outlier: 3.785A pdb=" N VAL R 187 " --> pdb=" O ASP R 183 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU R 189 " --> pdb=" O LEU R 185 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS R 190 " --> pdb=" O TYR R 186 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU R 192 " --> pdb=" O LYS R 188 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA R 193 " --> pdb=" O GLU R 189 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL R 194 " --> pdb=" O LYS R 190 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN R 195 " --> pdb=" O LEU R 191 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER R 196 " --> pdb=" O GLU R 192 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET R 197 " --> pdb=" O ALA R 193 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLU R 199 " --> pdb=" O ASN R 195 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LYS R 200 " --> pdb=" O SER R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 204 through 221 removed outlier: 3.842A pdb=" N ARG R 209 " --> pdb=" O GLU R 205 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL R 221 " --> pdb=" O HIS R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 234 removed outlier: 3.952A pdb=" N LYS R 229 " --> pdb=" O LYS R 225 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP R 233 " --> pdb=" O LYS R 229 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 261 removed outlier: 3.510A pdb=" N PHE R 259 " --> pdb=" O VAL R 255 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 270 Processing helix chain 'R' and resid 273 through 279 removed outlier: 3.895A pdb=" N LEU R 277 " --> pdb=" O SER R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 298 Processing helix chain 'R' and resid 303 through 315 Processing helix chain 'R' and resid 325 through 344 removed outlier: 3.814A pdb=" N ARG R 331 " --> pdb=" O ASP R 327 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER R 344 " --> pdb=" O GLN R 340 " (cutoff:3.500A) Processing helix chain 'R' and resid 350 through 358 Processing helix chain 'R' and resid 360 through 375 removed outlier: 3.798A pdb=" N LYS R 370 " --> pdb=" O ASN R 366 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE R 371 " --> pdb=" O ASP R 367 " (cutoff:3.500A) Proline residue: R 373 - end of helix Processing helix chain 'R' and resid 395 through 424 removed outlier: 3.501A pdb=" N LYS R 405 " --> pdb=" O HIS R 401 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS R 413 " --> pdb=" O GLY R 409 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU R 423 " --> pdb=" O ALA R 419 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR R 424 " --> pdb=" O ALA R 420 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 25 removed outlier: 3.719A pdb=" N LEU U 15 " --> pdb=" O ALA U 11 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR U 22 " --> pdb=" O ALA U 18 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU U 23 " --> pdb=" O LEU U 19 " (cutoff:3.500A) Processing helix chain 'U' and resid 70 through 84 removed outlier: 4.086A pdb=" N GLU U 74 " --> pdb=" O HIS U 70 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN U 75 " --> pdb=" O ASN U 71 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET U 79 " --> pdb=" O ASN U 75 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS U 82 " --> pdb=" O GLU U 78 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE U 83 " --> pdb=" O MET U 79 " (cutoff:3.500A) Processing helix chain 'U' and resid 102 through 114 removed outlier: 3.758A pdb=" N ILE U 106 " --> pdb=" O SER U 102 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU U 108 " --> pdb=" O LEU U 104 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU U 109 " --> pdb=" O LYS U 105 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE U 110 " --> pdb=" O ILE U 106 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS U 112 " --> pdb=" O GLU U 108 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR U 113 " --> pdb=" O LEU U 109 " (cutoff:3.500A) Processing helix chain 'U' and resid 164 through 175 Processing helix chain 'U' and resid 185 through 215 removed outlier: 3.729A pdb=" N LEU U 194 " --> pdb=" O LEU U 190 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS U 203 " --> pdb=" O GLY U 199 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP U 212 " --> pdb=" O VAL U 208 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS U 213 " --> pdb=" O GLU U 209 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE U 215 " --> pdb=" O LEU U 211 " (cutoff:3.500A) Processing helix chain 'U' and resid 222 through 235 removed outlier: 3.947A pdb=" N LEU U 226 " --> pdb=" O ASN U 222 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP U 231 " --> pdb=" O GLY U 227 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL U 232 " --> pdb=" O LYS U 228 " (cutoff:3.500A) Processing helix chain 'U' and resid 241 through 298 removed outlier: 3.714A pdb=" N ASP U 245 " --> pdb=" O THR U 241 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR U 266 " --> pdb=" O GLN U 262 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL U 267 " --> pdb=" O LYS U 263 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS U 268 " --> pdb=" O ALA U 264 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE U 285 " --> pdb=" O LEU U 281 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU U 291 " --> pdb=" O ALA U 287 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE U 292 " --> pdb=" O PHE U 288 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 18 Processing helix chain 'O' and resid 22 through 36 removed outlier: 3.660A pdb=" N PHE O 26 " --> pdb=" O LEU O 22 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU O 27 " --> pdb=" O HIS O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 49 removed outlier: 3.557A pdb=" N GLU O 43 " --> pdb=" O PHE O 39 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU O 45 " --> pdb=" O LEU O 41 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS O 47 " --> pdb=" O GLU O 43 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE O 48 " --> pdb=" O SER O 44 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 68 removed outlier: 3.830A pdb=" N ARG O 60 " --> pdb=" O PRO O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 88 removed outlier: 3.771A pdb=" N VAL O 78 " --> pdb=" O ASN O 74 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP O 88 " --> pdb=" O ALA O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 118 removed outlier: 3.535A pdb=" N LYS O 97 " --> pdb=" O ASP O 93 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN O 107 " --> pdb=" O LYS O 103 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU O 108 " --> pdb=" O ALA O 104 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER O 111 " --> pdb=" O GLN O 107 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS O 112 " --> pdb=" O GLU O 108 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG O 115 " --> pdb=" O SER O 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 122 through 139 removed outlier: 4.298A pdb=" N ILE O 126 " --> pdb=" O HIS O 122 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU O 127 " --> pdb=" O GLY O 123 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU O 139 " --> pdb=" O ARG O 135 " (cutoff:3.500A) Processing helix chain 'O' and resid 142 through 160 removed outlier: 3.590A pdb=" N LYS O 159 " --> pdb=" O LYS O 155 " (cutoff:3.500A) Processing helix chain 'O' and resid 164 through 183 removed outlier: 4.137A pdb=" N THR O 168 " --> pdb=" O PRO O 164 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS O 182 " --> pdb=" O TYR O 178 " (cutoff:3.500A) Processing helix chain 'O' and resid 184 through 198 removed outlier: 4.139A pdb=" N TYR O 190 " --> pdb=" O ASN O 186 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR O 191 " --> pdb=" O SER O 187 " (cutoff:3.500A) Processing helix chain 'O' and resid 206 through 223 removed outlier: 3.503A pdb=" N LEU O 223 " --> pdb=" O ILE O 219 " (cutoff:3.500A) Processing helix chain 'O' and resid 229 through 235 removed outlier: 3.967A pdb=" N LEU O 234 " --> pdb=" O PHE O 230 " (cutoff:3.500A) Processing helix chain 'O' and resid 236 through 241 Processing helix chain 'O' and resid 245 through 248 Processing helix chain 'O' and resid 249 through 261 removed outlier: 3.589A pdb=" N VAL O 260 " --> pdb=" O ASN O 256 " (cutoff:3.500A) Processing helix chain 'O' and resid 262 through 277 removed outlier: 3.543A pdb=" N PHE O 266 " --> pdb=" O ASP O 262 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL O 272 " --> pdb=" O SER O 268 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER O 275 " --> pdb=" O LYS O 271 " (cutoff:3.500A) Processing helix chain 'O' and resid 278 through 283 Processing helix chain 'O' and resid 283 through 303 removed outlier: 4.229A pdb=" N ILE O 291 " --> pdb=" O LEU O 287 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N CYS O 292 " --> pdb=" O ARG O 288 " (cutoff:3.500A) Processing helix chain 'O' and resid 310 through 318 Processing helix chain 'O' and resid 321 through 335 removed outlier: 3.893A pdb=" N GLU O 325 " --> pdb=" O LYS O 321 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS O 326 " --> pdb=" O ASP O 322 " (cutoff:3.500A) Processing helix chain 'O' and resid 359 through 387 removed outlier: 3.630A pdb=" N THR O 364 " --> pdb=" O GLY O 360 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS O 367 " --> pdb=" O ILE O 363 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS O 383 " --> pdb=" O LYS O 379 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET O 384 " --> pdb=" O LEU O 380 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'W' and resid 61 through 66 removed outlier: 7.298A pdb=" N LEU W 62 " --> pdb=" O SER W 53 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N SER W 53 " --> pdb=" O LEU W 62 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N THR W 64 " --> pdb=" O LEU W 51 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU W 51 " --> pdb=" O THR W 64 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLU W 4 " --> pdb=" O THR W 48 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLY W 50 " --> pdb=" O GLU W 4 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N THR W 6 " --> pdb=" O GLY W 50 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE W 52 " --> pdb=" O THR W 6 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LEU W 8 " --> pdb=" O ILE W 52 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG W 109 " --> pdb=" O ALA W 5 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL W 9 " --> pdb=" O VAL W 111 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLN W 108 " --> pdb=" O ALA W 138 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ASP W 140 " --> pdb=" O GLN W 108 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE W 110 " --> pdb=" O ASP W 140 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ILE W 142 " --> pdb=" O ILE W 110 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA W 112 " --> pdb=" O ILE W 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'V' and resid 196 through 198 removed outlier: 3.700A pdb=" N VAL V 137 " --> pdb=" O VAL V 105 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL V 104 " --> pdb=" O GLY V 55 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N GLY V 55 " --> pdb=" O VAL V 104 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL V 49 " --> pdb=" O SER V 110 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE V 69 " --> pdb=" O LEU V 52 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N GLU V 56 " --> pdb=" O VAL V 65 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL V 65 " --> pdb=" O GLU V 56 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL V 58 " --> pdb=" O VAL V 63 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N VAL V 63 " --> pdb=" O VAL V 58 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL V 63 " --> pdb=" O THR V 26 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'X' and resid 8 through 10 removed outlier: 3.918A pdb=" N ILE X 8 " --> pdb=" O ILE X 35 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE X 35 " --> pdb=" O ILE X 8 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU X 49 " --> pdb=" O GLU X 34 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS X 36 " --> pdb=" O ASP X 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'X' and resid 13 through 15 removed outlier: 4.264A pdb=" N PHE X 98 " --> pdb=" O CYS X 15 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR X 97 " --> pdb=" O LEU X 89 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU X 89 " --> pdb=" O TYR X 97 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA X 88 " --> pdb=" O VAL X 76 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Z' and resid 894 through 895 removed outlier: 3.754A pdb=" N THR Z 967 " --> pdb=" O LEU Z 895 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLU Z 966 " --> pdb=" O VAL Z 955 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Z' and resid 927 through 929 Processing sheet with id=AA7, first strand: chain 'N' and resid 713 through 715 Processing sheet with id=AA8, first strand: chain 'N' and resid 872 through 873 removed outlier: 4.481A pdb=" N THR N 872 " --> pdb=" O VAL N 758 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL N 758 " --> pdb=" O THR N 872 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N VAL N 903 " --> pdb=" O THR N 757 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE N 759 " --> pdb=" O VAL N 903 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU N 905 " --> pdb=" O ILE N 759 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE N 761 " --> pdb=" O LEU N 905 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 768 through 769 removed outlier: 3.740A pdb=" N ILE N 768 " --> pdb=" O ILE N 917 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 865 through 869 Processing sheet with id=AB2, first strand: chain 'S' and resid 401 through 403 Processing sheet with id=AB3, first strand: chain 'P' and resid 391 through 392 removed outlier: 4.810A pdb=" N SER P 358 " --> pdb=" O PHE P 402 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TYR P 357 " --> pdb=" O GLY O 339 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE O 341 " --> pdb=" O TYR P 357 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS O 338 " --> pdb=" O SER O 351 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU O 308 " --> pdb=" O VAL O 348 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 357 through 358 removed outlier: 3.535A pdb=" N VAL Q 357 " --> pdb=" O LEU Q 397 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 347 through 349 removed outlier: 3.502A pdb=" N ILE R 387 " --> pdb=" O ASP R 382 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'U' and resid 7 through 10 removed outlier: 5.394A pdb=" N VAL U 48 " --> pdb=" O ASP U 40 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ASP U 40 " --> pdb=" O VAL U 48 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY U 91 " --> pdb=" O ILE U 37 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY U 39 " --> pdb=" O LEU U 89 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU U 89 " --> pdb=" O GLY U 39 " (cutoff:3.500A) removed outlier: 9.558A pdb=" N LEU U 119 " --> pdb=" O LYS U 88 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE U 90 " --> pdb=" O LEU U 119 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU U 121 " --> pdb=" O ILE U 90 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TRP U 92 " --> pdb=" O LEU U 121 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL U 123 " --> pdb=" O TRP U 92 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N HIS U 94 " --> pdb=" O VAL U 123 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA U 136 " --> pdb=" O LEU U 157 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL U 138 " --> pdb=" O LEU U 155 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'U' and resid 57 through 58 removed outlier: 3.687A pdb=" N GLU U 57 " --> pdb=" O PHE U 67 " (cutoff:3.500A) 2182 hydrogen bonds defined for protein. 6453 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: 8.11 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.22: 1719 1.22 - 1.44: 17195 1.44 - 1.65: 22480 1.65 - 1.87: 249 1.87 - 2.09: 19 Bond restraints: 41662 Sorted by residual: bond pdb=" CZ TYR R 99 " pdb=" OH TYR R 99 " ideal model delta sigma weight residual 1.376 2.041 -0.665 2.10e-02 2.27e+03 1.00e+03 bond pdb=" C GLN P 78 " pdb=" N LEU P 79 " ideal model delta sigma weight residual 1.332 1.754 -0.421 1.40e-02 5.10e+03 9.05e+02 bond pdb=" CE1 TYR R 99 " pdb=" CZ TYR R 99 " ideal model delta sigma weight residual 1.378 2.089 -0.711 2.40e-02 1.74e+03 8.77e+02 bond pdb=" CA ASP S 59 " pdb=" CB ASP S 59 " ideal model delta sigma weight residual 1.529 1.098 0.431 1.55e-02 4.16e+03 7.72e+02 bond pdb=" CA THR S 127 " pdb=" CB THR S 127 " ideal model delta sigma weight residual 1.532 1.984 -0.452 1.65e-02 3.67e+03 7.51e+02 ... (remaining 41657 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.72: 56240 13.72 - 27.44: 35 27.44 - 41.16: 3 41.16 - 54.88: 0 54.88 - 68.60: 1 Bond angle restraints: 56279 Sorted by residual: angle pdb=" CE1 TYR R 99 " pdb=" CZ TYR R 99 " pdb=" OH TYR R 99 " ideal model delta sigma weight residual 119.90 51.30 68.60 3.00e+00 1.11e-01 5.23e+02 angle pdb=" C TYR O 62 " pdb=" CA TYR O 62 " pdb=" CB TYR O 62 " ideal model delta sigma weight residual 110.81 78.61 32.20 1.60e+00 3.91e-01 4.05e+02 angle pdb=" C PHE Q 77 " pdb=" N ILE Q 78 " pdb=" CA ILE Q 78 " ideal model delta sigma weight residual 120.24 131.35 -11.11 6.30e-01 2.52e+00 3.11e+02 angle pdb=" O GLN P 78 " pdb=" C GLN P 78 " pdb=" N LEU P 79 " ideal model delta sigma weight residual 122.59 99.48 23.11 1.33e+00 5.65e-01 3.02e+02 angle pdb=" C ALA Z 188 " pdb=" CA ALA Z 188 " pdb=" CB ALA Z 188 " ideal model delta sigma weight residual 110.56 82.62 27.94 1.69e+00 3.50e-01 2.73e+02 ... (remaining 56274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.88: 23238 18.88 - 37.75: 1542 37.75 - 56.63: 344 56.63 - 75.51: 250 75.51 - 94.38: 127 Dihedral angle restraints: 25501 sinusoidal: 10350 harmonic: 15151 Sorted by residual: dihedral pdb=" CA HIS T 251 " pdb=" C HIS T 251 " pdb=" N GLU T 252 " pdb=" CA GLU T 252 " ideal model delta harmonic sigma weight residual -180.00 -85.62 -94.38 0 5.00e+00 4.00e-02 3.56e+02 dihedral pdb=" C ALA Z 188 " pdb=" N ALA Z 188 " pdb=" CA ALA Z 188 " pdb=" CB ALA Z 188 " ideal model delta harmonic sigma weight residual -122.60 -82.24 -40.36 0 2.50e+00 1.60e-01 2.61e+02 dihedral pdb=" CA SER T 91 " pdb=" C SER T 91 " pdb=" N ASN T 92 " pdb=" CA ASN T 92 " ideal model delta harmonic sigma weight residual 180.00 103.20 76.80 0 5.00e+00 4.00e-02 2.36e+02 ... (remaining 25498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.196: 4644 0.196 - 0.393: 1522 0.393 - 0.589: 235 0.589 - 0.785: 37 0.785 - 0.981: 9 Chirality restraints: 6447 Sorted by residual: chirality pdb=" CA ASP S 375 " pdb=" N ASP S 375 " pdb=" C ASP S 375 " pdb=" CB ASP S 375 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.41e+01 chirality pdb=" CA ASN R 182 " pdb=" N ASN R 182 " pdb=" C ASN R 182 " pdb=" CB ASN R 182 " both_signs ideal model delta sigma weight residual False 2.51 1.62 0.90 2.00e-01 2.50e+01 2.00e+01 chirality pdb=" CA ASP S 59 " pdb=" N ASP S 59 " pdb=" C ASP S 59 " pdb=" CB ASP S 59 " both_signs ideal model delta sigma weight residual False 2.51 1.62 0.89 2.00e-01 2.50e+01 1.96e+01 ... (remaining 6444 not shown) Planarity restraints: 7202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 99 " 0.366 2.00e-02 2.50e+03 2.97e-01 1.77e+03 pdb=" CG TYR R 99 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR R 99 " -0.307 2.00e-02 2.50e+03 pdb=" CD2 TYR R 99 " -0.079 2.00e-02 2.50e+03 pdb=" CE1 TYR R 99 " -0.392 2.00e-02 2.50e+03 pdb=" CE2 TYR R 99 " -0.070 2.00e-02 2.50e+03 pdb=" CZ TYR R 99 " -0.079 2.00e-02 2.50e+03 pdb=" OH TYR R 99 " 0.555 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 65 " 0.249 2.00e-02 2.50e+03 1.40e-01 3.90e+02 pdb=" CG TYR R 65 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR R 65 " -0.131 2.00e-02 2.50e+03 pdb=" CD2 TYR R 65 " -0.095 2.00e-02 2.50e+03 pdb=" CE1 TYR R 65 " -0.063 2.00e-02 2.50e+03 pdb=" CE2 TYR R 65 " -0.112 2.00e-02 2.50e+03 pdb=" CZ TYR R 65 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR R 65 " 0.220 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Z 64 " -0.240 2.00e-02 2.50e+03 1.39e-01 3.86e+02 pdb=" CG TYR Z 64 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR Z 64 " 0.124 2.00e-02 2.50e+03 pdb=" CD2 TYR Z 64 " 0.115 2.00e-02 2.50e+03 pdb=" CE1 TYR Z 64 " 0.080 2.00e-02 2.50e+03 pdb=" CE2 TYR Z 64 " 0.115 2.00e-02 2.50e+03 pdb=" CZ TYR Z 64 " -0.016 2.00e-02 2.50e+03 pdb=" OH TYR Z 64 " -0.216 2.00e-02 2.50e+03 ... (remaining 7199 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.91: 7 1.91 - 2.65: 1033 2.65 - 3.40: 55880 3.40 - 4.15: 95668 4.15 - 4.90: 170141 Nonbonded interactions: 322729 Sorted by model distance: nonbonded pdb=" CE1 TYR O 33 " pdb=" CE2 PHE O 69 " model vdw 1.158 3.640 nonbonded pdb=" CE1 PHE O 69 " pdb=" CD LYS O 72 " model vdw 1.316 3.740 nonbonded pdb=" CD1 LEU O 14 " pdb=" CD1 LEU O 61 " model vdw 1.341 3.880 nonbonded pdb=" O ASP Y 33 " pdb=" N PHE Y 35 " model vdw 1.428 3.120 nonbonded pdb=" CE1 TYR O 33 " pdb=" CZ PHE O 69 " model vdw 1.507 3.640 ... (remaining 322724 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 36.020 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4150 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 : 0.034 0.711 41662 Z= 2.214 Angle : 3.323 68.596 56279 Z= 2.303 Chirality : 0.190 0.981 6447 Planarity : 0.027 0.326 7202 Dihedral : 17.162 94.381 15677 Min Nonbonded Distance : 1.158 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 2.19 % Allowed : 5.23 % Favored : 92.58 % Rotamer: Outliers : 2.25 % Allowed : 5.79 % Favored : 91.95 % Cbeta Deviations : 6.05 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.86 (0.10), residues: 5108 helix: -0.51 (0.08), residues: 3156 sheet: -1.01 (0.35), residues: 171 loop : -2.49 (0.12), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.109 0.010 ARG Z 832 TYR 0.555 0.044 TYR R 99 PHE 0.166 0.037 PHE O 106 TRP 0.190 0.041 TRP P 72 HIS 0.060 0.014 HIS U 252 Details of bonding type rmsd covalent geometry : bond 0.03394 (41662) covalent geometry : angle 3.32283 (56279) hydrogen bonds : bond 0.32752 ( 2182) hydrogen bonds : angle 8.15159 ( 6453) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1728 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 1625 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 72 ILE cc_start: 0.6797 (mm) cc_final: 0.6596 (mm) REVERT: W 105 VAL cc_start: 0.5855 (OUTLIER) cc_final: 0.5512 (t) REVERT: W 133 LYS cc_start: 0.5783 (pttm) cc_final: 0.5494 (pttm) REVERT: W 137 VAL cc_start: 0.7457 (t) cc_final: 0.7099 (t) REVERT: W 149 GLN cc_start: 0.3882 (OUTLIER) cc_final: 0.1995 (pp30) REVERT: V 34 LEU cc_start: 0.7533 (tp) cc_final: 0.7003 (tp) REVERT: V 173 THR cc_start: 0.6453 (p) cc_final: 0.5959 (p) REVERT: V 198 SER cc_start: 0.6879 (m) cc_final: 0.6639 (t) REVERT: V 215 ASN cc_start: 0.4967 (m-40) cc_final: 0.4646 (m-40) REVERT: V 235 GLU cc_start: 0.7335 (tm-30) cc_final: 0.7078 (tm-30) REVERT: T 249 MET cc_start: 0.4303 (ptt) cc_final: 0.3861 (ptp) REVERT: T 265 ASP cc_start: 0.7101 (m-30) cc_final: 0.6531 (m-30) REVERT: X 14 VAL cc_start: 0.6507 (OUTLIER) cc_final: 0.6078 (m) REVERT: Z 138 ARG cc_start: 0.3611 (ptt180) cc_final: 0.1192 (tmt170) REVERT: Z 249 MET cc_start: 0.3745 (mmt) cc_final: 0.3174 (mmm) REVERT: Z 425 ILE cc_start: 0.4064 (mm) cc_final: 0.3399 (mm) REVERT: Z 595 MET cc_start: 0.4837 (mtm) cc_final: 0.4300 (mtm) REVERT: Z 793 PHE cc_start: 0.1024 (m-80) cc_final: 0.0808 (m-10) REVERT: N 294 PRO cc_start: 0.6033 (OUTLIER) cc_final: 0.3708 (Cg_endo) REVERT: N 428 VAL cc_start: 0.8132 (m) cc_final: 0.7764 (p) REVERT: N 485 MET cc_start: 0.6871 (mtm) cc_final: 0.6558 (mtm) REVERT: N 521 LEU cc_start: 0.6322 (mt) cc_final: 0.6010 (mt) REVERT: N 543 ASP cc_start: 0.7016 (t70) cc_final: 0.6803 (t70) REVERT: N 546 LEU cc_start: 0.7626 (mm) cc_final: 0.7293 (mm) REVERT: N 616 HIS cc_start: 0.6397 (m90) cc_final: 0.5965 (m90) REVERT: N 650 ASP cc_start: 0.5333 (m-30) cc_final: 0.4935 (t0) REVERT: N 683 LEU cc_start: 0.8293 (mt) cc_final: 0.8024 (mt) REVERT: N 742 TRP cc_start: 0.5359 (t-100) cc_final: 0.4651 (t-100) REVERT: S 456 ASP cc_start: 0.6631 (m-30) cc_final: 0.6281 (m-30) REVERT: S 465 ILE cc_start: 0.7560 (mt) cc_final: 0.6713 (mt) REVERT: P 16 ILE cc_start: 0.7230 (mt) cc_final: 0.6778 (mt) REVERT: P 224 LEU cc_start: 0.8334 (mt) cc_final: 0.7862 (mm) REVERT: P 308 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6437 (tp) REVERT: P 346 ILE cc_start: 0.6463 (mt) cc_final: 0.6022 (mt) REVERT: Q 52 ASN cc_start: 0.4291 (p0) cc_final: 0.3298 (t0) REVERT: Q 229 ASP cc_start: 0.6132 (m-30) cc_final: 0.5707 (t0) REVERT: Q 230 LYS cc_start: 0.6588 (mmtt) cc_final: 0.5759 (mmtm) REVERT: Q 234 THR cc_start: 0.6674 (p) cc_final: 0.5089 (p) REVERT: Q 381 ILE cc_start: 0.6467 (mt) cc_final: 0.6127 (mt) REVERT: Q 389 VAL cc_start: 0.6111 (m) cc_final: 0.5373 (m) REVERT: Q 434 TYR cc_start: 0.4966 (m-10) cc_final: 0.4187 (m-80) REVERT: R 333 MET cc_start: 0.7166 (mmm) cc_final: 0.6894 (mmm) REVERT: R 364 LEU cc_start: 0.6654 (tp) cc_final: 0.6266 (tp) REVERT: R 404 VAL cc_start: 0.7990 (m) cc_final: 0.7561 (p) REVERT: U 1 MET cc_start: 0.5211 (mtt) cc_final: 0.4964 (mtt) REVERT: U 15 LEU cc_start: 0.7838 (mt) cc_final: 0.7304 (mt) REVERT: U 17 SER cc_start: 0.7507 (m) cc_final: 0.6574 (t) REVERT: U 45 THR cc_start: 0.7439 (t) cc_final: 0.6929 (p) REVERT: U 65 VAL cc_start: 0.7731 (t) cc_final: 0.6341 (t) REVERT: U 73 ILE cc_start: 0.5669 (mt) cc_final: 0.5347 (mt) REVERT: U 116 ASN cc_start: 0.5949 (p0) cc_final: 0.5429 (p0) REVERT: U 171 VAL cc_start: 0.8436 (t) cc_final: 0.7478 (t) REVERT: U 229 LEU cc_start: 0.8005 (mt) cc_final: 0.7786 (mm) REVERT: U 247 ILE cc_start: 0.8559 (mt) cc_final: 0.8176 (mt) REVERT: O 112 LYS cc_start: 0.5789 (mttt) cc_final: 0.5564 (mttt) REVERT: O 173 SER cc_start: 0.5850 (t) cc_final: 0.4905 (p) REVERT: O 284 GLU cc_start: 0.4423 (tt0) cc_final: 0.3733 (tt0) outliers start: 103 outliers final: 18 residues processed: 1698 average time/residue: 0.2679 time to fit residues: 730.2487 Evaluate side-chains 879 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 856 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 494 optimal weight: 8.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 207 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: W 95 GLN V 40 HIS V 73 GLN V 102 GLN V 131 GLN V 193 ASN V 195 HIS V 200 ASN V 274 GLN V 301 ASN ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 112 ASN T 123 HIS T 132 HIS ** T 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 230 ASN ** T 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 38 ASN Z 17 GLN ** Z 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 235 GLN Z 247 GLN Z 332 ASN Z 347 ASN Z 361 HIS Z 387 ASN ** Z 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 769 ASN ** Z 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 823 ASN Z 917 ASN Z 926 ASN Z 931 GLN N 111 GLN ** N 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 256 GLN N 268 GLN N 306 ASN N 340 HIS N 375 HIS N 378 ASN N 425 ASN N 444 HIS N 525 ASN ** N 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 772 GLN N 878 GLN N 900 ASN S 20 HIS S 112 ASN S 159 ASN ** S 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 191 HIS S 243 ASN S 334 HIS ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 450 ASN ** S 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 296 GLN P 306 ASN P 323 ASN ** P 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 336 HIS ** P 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 349 ASN P 417 HIS Q 87 GLN Q 186 HIS Q 280 ASN ** Q 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 361 HIS R 35 GLN R 217 HIS ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 397 ASN R 401 HIS R 415 GLN U 21 HIS U 94 HIS ** U 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 260 ASN U 294 ASN ** O 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 ASN ** O 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 273 GLN ** O 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.171900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.143881 restraints weight = 160515.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.146968 restraints weight = 118668.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.148629 restraints weight = 86105.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.150198 restraints weight = 64845.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.150560 restraints weight = 51774.878| |-----------------------------------------------------------------------------| r_work (final): 0.4382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 41662 Z= 0.215 Angle : 0.805 17.765 56279 Z= 0.431 Chirality : 0.045 0.440 6447 Planarity : 0.006 0.078 7202 Dihedral : 5.858 55.089 5504 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.11 % Favored : 95.44 % Rotamer: Outliers : 0.33 % Allowed : 4.04 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.11), residues: 5108 helix: 0.67 (0.09), residues: 3264 sheet: -0.83 (0.34), residues: 187 loop : -1.88 (0.14), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 387 TYR 0.038 0.003 TYR V 197 PHE 0.037 0.003 PHE S 241 TRP 0.023 0.002 TRP S 184 HIS 0.016 0.002 HIS V 40 Details of bonding type rmsd covalent geometry : bond 0.00379 (41662) covalent geometry : angle 0.80487 (56279) hydrogen bonds : bond 0.06787 ( 2182) hydrogen bonds : angle 5.05351 ( 6453) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1156 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 1141 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 1 MET cc_start: 0.0702 (ttt) cc_final: -0.0238 (ttm) REVERT: V 28 TYR cc_start: 0.8705 (m-80) cc_final: 0.8141 (m-80) REVERT: V 53 MET cc_start: 0.7652 (mtp) cc_final: 0.7387 (mtp) REVERT: V 64 ASN cc_start: 0.8483 (m-40) cc_final: 0.8092 (t0) REVERT: V 95 LEU cc_start: 0.9043 (mt) cc_final: 0.8787 (mt) REVERT: V 116 CYS cc_start: 0.8787 (m) cc_final: 0.8192 (p) REVERT: V 126 GLN cc_start: 0.8001 (tp40) cc_final: 0.7720 (tp40) REVERT: V 134 SER cc_start: 0.8759 (p) cc_final: 0.8391 (t) REVERT: V 159 ILE cc_start: 0.7489 (pt) cc_final: 0.7087 (pt) REVERT: V 197 TYR cc_start: 0.6455 (t80) cc_final: 0.5921 (t80) REVERT: V 227 MET cc_start: 0.8569 (pmm) cc_final: 0.8341 (pmm) REVERT: V 275 ASP cc_start: 0.7775 (p0) cc_final: 0.7348 (p0) REVERT: V 277 LYS cc_start: 0.8834 (ttpt) cc_final: 0.8563 (ttpt) REVERT: V 291 ASN cc_start: 0.9240 (m110) cc_final: 0.8997 (m-40) REVERT: T 40 LEU cc_start: 0.7041 (mt) cc_final: 0.6802 (mm) REVERT: T 122 PHE cc_start: 0.6361 (t80) cc_final: 0.5998 (t80) REVERT: T 196 SER cc_start: 0.5986 (m) cc_final: 0.5777 (p) REVERT: T 226 TRP cc_start: 0.8094 (m-10) cc_final: 0.7238 (m-10) REVERT: Z 392 LEU cc_start: 0.6439 (mt) cc_final: 0.6233 (mt) REVERT: Z 724 GLU cc_start: 0.5836 (OUTLIER) cc_final: 0.5604 (mm-30) REVERT: Z 815 MET cc_start: 0.5798 (ppp) cc_final: 0.5566 (ppp) REVERT: Z 841 GLU cc_start: 0.6200 (mt-10) cc_final: 0.5971 (mt-10) REVERT: Z 864 MET cc_start: 0.1321 (mmp) cc_final: 0.0915 (mpp) REVERT: Z 945 ILE cc_start: 0.6739 (tp) cc_final: 0.6078 (tp) REVERT: N 60 MET cc_start: 0.6620 (tpt) cc_final: 0.6082 (tpp) REVERT: N 89 PHE cc_start: 0.8091 (t80) cc_final: 0.7840 (t80) REVERT: N 222 TYR cc_start: 0.7249 (m-80) cc_final: 0.6979 (m-80) REVERT: N 270 LEU cc_start: 0.8908 (tp) cc_final: 0.8658 (tp) REVERT: N 271 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8626 (mm-30) REVERT: N 408 LEU cc_start: 0.8574 (tp) cc_final: 0.7270 (tp) REVERT: N 412 TYR cc_start: 0.7585 (m-80) cc_final: 0.6744 (m-80) REVERT: N 436 ASP cc_start: 0.7190 (m-30) cc_final: 0.6898 (t70) REVERT: N 581 ASP cc_start: 0.8128 (m-30) cc_final: 0.7421 (m-30) REVERT: N 616 HIS cc_start: 0.7928 (m90) cc_final: 0.7302 (m90) REVERT: N 677 ASP cc_start: 0.8613 (t0) cc_final: 0.8281 (t0) REVERT: N 678 ILE cc_start: 0.9172 (mt) cc_final: 0.8858 (mt) REVERT: N 706 MET cc_start: 0.7991 (tpt) cc_final: 0.7608 (tpt) REVERT: N 735 MET cc_start: 0.7994 (mmp) cc_final: 0.7786 (mmp) REVERT: N 787 MET cc_start: 0.7561 (ppp) cc_final: 0.6841 (tmm) REVERT: S 32 GLN cc_start: 0.7856 (tt0) cc_final: 0.7620 (tm-30) REVERT: S 178 LEU cc_start: 0.6643 (mt) cc_final: 0.6223 (mt) REVERT: S 228 GLU cc_start: 0.8581 (tt0) cc_final: 0.8216 (pm20) REVERT: S 232 MET cc_start: 0.7985 (mmp) cc_final: 0.7356 (mmp) REVERT: S 269 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8327 (mt-10) REVERT: S 276 LEU cc_start: 0.9394 (mt) cc_final: 0.9178 (mt) REVERT: S 297 ILE cc_start: 0.8150 (mt) cc_final: 0.7856 (mt) REVERT: P 120 GLU cc_start: 0.8397 (tp30) cc_final: 0.7852 (tp30) REVERT: P 131 PHE cc_start: 0.7549 (t80) cc_final: 0.7043 (t80) REVERT: P 264 ILE cc_start: 0.8974 (mt) cc_final: 0.8381 (tp) REVERT: P 281 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.7982 (mp) REVERT: P 285 GLN cc_start: 0.8257 (tp40) cc_final: 0.7492 (mm-40) REVERT: P 412 LEU cc_start: 0.9375 (mt) cc_final: 0.9090 (mt) REVERT: P 414 GLU cc_start: 0.8541 (mp0) cc_final: 0.8330 (mp0) REVERT: Q 52 ASN cc_start: 0.4753 (p0) cc_final: 0.4158 (t0) REVERT: Q 96 VAL cc_start: 0.8506 (t) cc_final: 0.8275 (p) REVERT: Q 110 SER cc_start: 0.4598 (m) cc_final: 0.4211 (t) REVERT: Q 210 CYS cc_start: 0.6577 (m) cc_final: 0.6242 (m) REVERT: Q 234 THR cc_start: 0.6695 (p) cc_final: 0.5644 (p) REVERT: Q 267 LEU cc_start: 0.8161 (mt) cc_final: 0.7676 (mt) REVERT: Q 335 PHE cc_start: 0.6664 (m-80) cc_final: 0.6353 (m-80) REVERT: Q 354 PHE cc_start: 0.7787 (m-10) cc_final: 0.7252 (m-80) REVERT: Q 426 LEU cc_start: 0.9042 (mm) cc_final: 0.8799 (tp) REVERT: R 213 TYR cc_start: 0.9173 (m-10) cc_final: 0.8971 (m-80) REVERT: R 300 ASP cc_start: 0.7546 (p0) cc_final: 0.7263 (p0) REVERT: R 304 TYR cc_start: 0.7247 (t80) cc_final: 0.7029 (t80) REVERT: R 405 LYS cc_start: 0.8806 (mmmt) cc_final: 0.8199 (mmtt) REVERT: U 17 SER cc_start: 0.8850 (m) cc_final: 0.8027 (t) REVERT: U 209 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8085 (pm20) REVERT: U 251 ASN cc_start: 0.8756 (m-40) cc_final: 0.8476 (m-40) REVERT: O 64 ASN cc_start: 0.8278 (m-40) cc_final: 0.8018 (m-40) REVERT: O 76 LEU cc_start: 0.9033 (tp) cc_final: 0.8775 (tp) REVERT: O 94 GLU cc_start: 0.7883 (tt0) cc_final: 0.7626 (pt0) REVERT: O 138 LEU cc_start: 0.8448 (mm) cc_final: 0.8064 (mm) REVERT: O 173 SER cc_start: 0.8359 (t) cc_final: 0.7848 (p) REVERT: O 223 LEU cc_start: 0.8006 (mt) cc_final: 0.7548 (mt) REVERT: O 244 ASN cc_start: 0.8299 (m-40) cc_final: 0.8064 (m-40) outliers start: 15 outliers final: 3 residues processed: 1154 average time/residue: 0.2470 time to fit residues: 469.9712 Evaluate side-chains 756 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 750 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 418 optimal weight: 7.9990 chunk 233 optimal weight: 9.9990 chunk 467 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 310 optimal weight: 0.7980 chunk 444 optimal weight: 20.0000 chunk 337 optimal weight: 8.9990 chunk 407 optimal weight: 3.9990 chunk 165 optimal weight: 9.9990 chunk 158 optimal weight: 0.0060 overall best weight: 4.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 12 ASN W 80 GLN W 106 GLN V 102 GLN V 279 HIS ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 112 ASN T 230 ASN ** T 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 26 ASN Z 549 ASN ** Z 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 231 ASN N 233 ASN N 256 GLN N 336 ASN N 361 ASN N 444 HIS N 529 GLN N 573 HIS ** N 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 667 GLN ** N 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 772 GLN N 900 ASN N 922 GLN ** S 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 312 GLN ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 263 HIS P 289 ASN ** P 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 348 HIS P 413 ASN P 418 ASN P 431 HIS Q 63 GLN ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 145 HIS ** Q 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 405 GLN R 195 ASN R 366 ASN ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 230 GLN ** U 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 238 ASN ** U 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.166148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.138383 restraints weight = 162443.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.141244 restraints weight = 118246.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.142841 restraints weight = 84413.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.144117 restraints weight = 67402.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.144625 restraints weight = 55960.842| |-----------------------------------------------------------------------------| r_work (final): 0.4325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.6251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 41662 Z= 0.183 Angle : 0.727 19.057 56279 Z= 0.387 Chirality : 0.042 0.232 6447 Planarity : 0.005 0.104 7202 Dihedral : 5.433 43.526 5504 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.35 % Favored : 95.30 % Rotamer: Outliers : 0.13 % Allowed : 3.24 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.16 (0.11), residues: 5108 helix: 0.71 (0.09), residues: 3304 sheet: -1.15 (0.32), residues: 206 loop : -1.63 (0.14), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG S 428 TYR 0.045 0.003 TYR T 266 PHE 0.031 0.002 PHE N 697 TRP 0.023 0.002 TRP T 226 HIS 0.015 0.002 HIS Z 361 Details of bonding type rmsd covalent geometry : bond 0.00382 (41662) covalent geometry : angle 0.72658 (56279) hydrogen bonds : bond 0.05539 ( 2182) hydrogen bonds : angle 4.79928 ( 6453) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1013 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1007 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 1 MET cc_start: 0.1441 (ttt) cc_final: 0.1214 (ttt) REVERT: W 25 ARG cc_start: 0.7258 (ttp-170) cc_final: 0.7018 (ttp-170) REVERT: W 26 PHE cc_start: 0.6287 (t80) cc_final: 0.6071 (t80) REVERT: W 29 GLN cc_start: 0.9082 (mt0) cc_final: 0.8632 (mm110) REVERT: V 28 TYR cc_start: 0.8669 (m-80) cc_final: 0.8168 (m-80) REVERT: V 34 LEU cc_start: 0.9407 (tp) cc_final: 0.9170 (tp) REVERT: V 64 ASN cc_start: 0.8381 (m-40) cc_final: 0.8148 (t0) REVERT: V 91 MET cc_start: 0.8443 (mmp) cc_final: 0.8040 (mmm) REVERT: V 116 CYS cc_start: 0.8961 (m) cc_final: 0.8286 (p) REVERT: V 126 GLN cc_start: 0.8187 (tp40) cc_final: 0.7981 (tp40) REVERT: V 157 ARG cc_start: 0.7827 (ppt170) cc_final: 0.7567 (ppt170) REVERT: V 173 THR cc_start: 0.8776 (m) cc_final: 0.8568 (m) REVERT: V 279 HIS cc_start: 0.8652 (m90) cc_final: 0.8380 (m-70) REVERT: T 40 LEU cc_start: 0.6913 (mt) cc_final: 0.6615 (mt) REVERT: T 226 TRP cc_start: 0.7569 (m-10) cc_final: 0.7348 (m-10) REVERT: X 29 VAL cc_start: 0.5906 (t) cc_final: 0.5673 (t) REVERT: Z 48 ASP cc_start: 0.2153 (m-30) cc_final: 0.1069 (t0) REVERT: Z 358 TYR cc_start: 0.3736 (m-10) cc_final: 0.2319 (m-10) REVERT: Z 945 ILE cc_start: 0.6728 (tp) cc_final: 0.6213 (tp) REVERT: N 26 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8833 (mp0) REVERT: N 89 PHE cc_start: 0.8174 (t80) cc_final: 0.7794 (t80) REVERT: N 90 ASP cc_start: 0.8260 (m-30) cc_final: 0.7197 (p0) REVERT: N 270 LEU cc_start: 0.8687 (tp) cc_final: 0.8320 (tp) REVERT: N 271 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8551 (mm-30) REVERT: N 412 TYR cc_start: 0.7697 (m-80) cc_final: 0.6943 (m-80) REVERT: N 436 ASP cc_start: 0.7334 (m-30) cc_final: 0.7019 (t70) REVERT: N 448 LEU cc_start: 0.9072 (mt) cc_final: 0.8306 (mt) REVERT: N 529 GLN cc_start: 0.7891 (tp-100) cc_final: 0.7613 (tp40) REVERT: N 548 ARG cc_start: 0.8883 (mtt180) cc_final: 0.7877 (mmt90) REVERT: N 581 ASP cc_start: 0.8209 (m-30) cc_final: 0.7631 (m-30) REVERT: N 583 VAL cc_start: 0.9409 (t) cc_final: 0.9104 (t) REVERT: N 613 HIS cc_start: 0.6447 (p-80) cc_final: 0.5924 (p-80) REVERT: N 616 HIS cc_start: 0.7766 (m90) cc_final: 0.7449 (m90) REVERT: N 667 GLN cc_start: 0.4127 (OUTLIER) cc_final: 0.3560 (pp30) REVERT: N 787 MET cc_start: 0.7740 (ppp) cc_final: 0.7105 (tmm) REVERT: S 40 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8126 (pt0) REVERT: S 192 GLU cc_start: 0.8466 (pp20) cc_final: 0.8163 (pp20) REVERT: S 232 MET cc_start: 0.7817 (mmp) cc_final: 0.7601 (mmm) REVERT: S 269 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8289 (mt-10) REVERT: S 280 ASN cc_start: 0.8419 (m-40) cc_final: 0.7835 (t0) REVERT: S 297 ILE cc_start: 0.8241 (mt) cc_final: 0.7914 (mt) REVERT: S 338 MET cc_start: 0.7754 (mpp) cc_final: 0.7333 (mpp) REVERT: S 437 ASN cc_start: 0.8996 (t0) cc_final: 0.8678 (t0) REVERT: P 19 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7981 (pp20) REVERT: P 134 VAL cc_start: 0.9101 (m) cc_final: 0.8390 (p) REVERT: P 411 LEU cc_start: 0.8014 (mp) cc_final: 0.7785 (mp) REVERT: P 414 GLU cc_start: 0.8502 (mp0) cc_final: 0.8291 (mp0) REVERT: Q 63 GLN cc_start: 0.8423 (tp-100) cc_final: 0.8001 (tp-100) REVERT: Q 96 VAL cc_start: 0.8616 (t) cc_final: 0.8416 (p) REVERT: Q 210 CYS cc_start: 0.6806 (m) cc_final: 0.6483 (m) REVERT: Q 236 PHE cc_start: 0.7199 (t80) cc_final: 0.6970 (t80) REVERT: Q 281 ILE cc_start: 0.8131 (mm) cc_final: 0.7893 (mm) REVERT: Q 389 VAL cc_start: 0.8134 (m) cc_final: 0.7700 (t) REVERT: Q 426 LEU cc_start: 0.8970 (mm) cc_final: 0.8569 (mm) REVERT: R 172 LEU cc_start: 0.7739 (mt) cc_final: 0.7412 (mt) REVERT: R 197 MET cc_start: 0.2164 (mtm) cc_final: 0.1485 (ptp) REVERT: R 209 ARG cc_start: 0.9000 (mtm180) cc_final: 0.8741 (mtm180) REVERT: R 213 TYR cc_start: 0.9091 (m-10) cc_final: 0.8814 (m-80) REVERT: R 247 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8545 (tm-30) REVERT: R 304 TYR cc_start: 0.7449 (t80) cc_final: 0.7102 (t80) REVERT: R 319 CYS cc_start: 0.7891 (m) cc_final: 0.6593 (t) REVERT: R 405 LYS cc_start: 0.8948 (mmmt) cc_final: 0.8324 (mmtt) REVERT: U 1 MET cc_start: 0.5820 (mtm) cc_final: 0.5496 (mtm) REVERT: U 17 SER cc_start: 0.8814 (m) cc_final: 0.8362 (t) REVERT: U 54 LEU cc_start: 0.8667 (mt) cc_final: 0.8449 (mt) REVERT: U 229 LEU cc_start: 0.9245 (mm) cc_final: 0.8880 (mm) REVERT: U 251 ASN cc_start: 0.8836 (m-40) cc_final: 0.8566 (m-40) REVERT: U 262 GLN cc_start: 0.8673 (pt0) cc_final: 0.7721 (pt0) REVERT: U 263 LYS cc_start: 0.9498 (mtmm) cc_final: 0.9212 (mmtm) REVERT: O 64 ASN cc_start: 0.8732 (m-40) cc_final: 0.8366 (m-40) REVERT: O 76 LEU cc_start: 0.9044 (tp) cc_final: 0.8773 (tp) REVERT: O 129 ILE cc_start: 0.7661 (mt) cc_final: 0.7408 (mt) REVERT: O 244 ASN cc_start: 0.8360 (m-40) cc_final: 0.8027 (m-40) REVERT: O 373 TRP cc_start: 0.8220 (t60) cc_final: 0.7716 (t60) outliers start: 6 outliers final: 0 residues processed: 1012 average time/residue: 0.2533 time to fit residues: 423.1329 Evaluate side-chains 715 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 713 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 80 optimal weight: 30.0000 chunk 105 optimal weight: 4.9990 chunk 200 optimal weight: 30.0000 chunk 423 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 400 optimal weight: 7.9990 chunk 294 optimal weight: 8.9990 chunk 189 optimal weight: 20.0000 chunk 311 optimal weight: 0.4980 chunk 184 optimal weight: 6.9990 chunk 164 optimal weight: 20.0000 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 97 GLN V 222 GLN ** V 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 ASN T 94 HIS T 112 ASN T 116 GLN T 237 ASN ** T 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 240 ASN Z 622 HIS Z 763 HIS Z 771 HIS ** Z 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 842 GLN Z 856 HIS ** Z 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 256 GLN N 305 ASN N 375 HIS ** N 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 772 GLN ** S 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 235 ASN ** S 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 183 GLN ** P 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 337 HIS P 386 GLN ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 150 GLN Q 248 ASN ** Q 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 361 HIS U 230 GLN U 234 ASN U 252 HIS U 256 ASN ** U 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 116 ASN O 117 ASN ** O 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 282 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.160335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.134013 restraints weight = 162190.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.136038 restraints weight = 118675.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.137692 restraints weight = 90765.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.138507 restraints weight = 73156.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.139707 restraints weight = 64774.139| |-----------------------------------------------------------------------------| r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.7314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 41662 Z= 0.203 Angle : 0.753 18.475 56279 Z= 0.397 Chirality : 0.044 0.420 6447 Planarity : 0.005 0.089 7202 Dihedral : 5.517 37.059 5504 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.33 % Favored : 95.34 % Rotamer: Outliers : 0.09 % Allowed : 3.98 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.44 (0.11), residues: 5108 helix: 0.43 (0.09), residues: 3292 sheet: -1.04 (0.32), residues: 225 loop : -1.58 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 58 TYR 0.044 0.003 TYR Z 738 PHE 0.045 0.003 PHE Q 335 TRP 0.027 0.002 TRP Z 149 HIS 0.015 0.002 HIS S 139 Details of bonding type rmsd covalent geometry : bond 0.00429 (41662) covalent geometry : angle 0.75287 (56279) hydrogen bonds : bond 0.04922 ( 2182) hydrogen bonds : angle 4.88059 ( 6453) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 975 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 971 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 25 ARG cc_start: 0.7205 (ttp-170) cc_final: 0.6827 (ttp-170) REVERT: W 35 PHE cc_start: 0.8136 (t80) cc_final: 0.7893 (t80) REVERT: W 182 TYR cc_start: 0.8279 (p90) cc_final: 0.8027 (p90) REVERT: V 34 LEU cc_start: 0.9516 (tp) cc_final: 0.9054 (tp) REVERT: V 58 VAL cc_start: 0.8186 (m) cc_final: 0.7937 (p) REVERT: V 71 MET cc_start: 0.8165 (ttm) cc_final: 0.7909 (ttm) REVERT: V 91 MET cc_start: 0.8365 (mmp) cc_final: 0.8044 (mmp) REVERT: V 126 GLN cc_start: 0.8342 (tp40) cc_final: 0.8125 (tp40) REVERT: V 188 LEU cc_start: 0.7741 (mt) cc_final: 0.7422 (mt) REVERT: V 230 TYR cc_start: 0.7527 (m-80) cc_final: 0.6920 (m-10) REVERT: V 251 TYR cc_start: 0.8682 (t80) cc_final: 0.8408 (t80) REVERT: T 40 LEU cc_start: 0.6972 (mt) cc_final: 0.6664 (mt) REVERT: T 144 TYR cc_start: 0.3069 (t80) cc_final: 0.1782 (m-80) REVERT: T 158 GLN cc_start: 0.8672 (pp30) cc_final: 0.8141 (tp-100) REVERT: T 226 TRP cc_start: 0.7576 (m-10) cc_final: 0.6969 (m-10) REVERT: Y 22 GLU cc_start: 0.7128 (mp0) cc_final: 0.6862 (mp0) REVERT: Y 34 GLU cc_start: 0.3257 (tp30) cc_final: 0.3043 (tp30) REVERT: Z 276 ASN cc_start: 0.6918 (t0) cc_final: 0.6479 (p0) REVERT: Z 736 LEU cc_start: 0.5867 (tt) cc_final: 0.5654 (tt) REVERT: Z 815 MET cc_start: 0.6685 (ppp) cc_final: 0.6042 (ppp) REVERT: Z 832 ARG cc_start: 0.3892 (mtm-85) cc_final: 0.3593 (ttm110) REVERT: Z 945 ILE cc_start: 0.6560 (tp) cc_final: 0.5818 (tp) REVERT: N 26 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8984 (mp0) REVERT: N 89 PHE cc_start: 0.8048 (t80) cc_final: 0.7678 (t80) REVERT: N 90 ASP cc_start: 0.8236 (m-30) cc_final: 0.7173 (p0) REVERT: N 217 MET cc_start: 0.5334 (mmp) cc_final: 0.5045 (mmp) REVERT: N 270 LEU cc_start: 0.8613 (tp) cc_final: 0.8253 (tt) REVERT: N 271 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8503 (mm-30) REVERT: N 339 MET cc_start: 0.6071 (mmm) cc_final: 0.5861 (mmp) REVERT: N 412 TYR cc_start: 0.7550 (m-80) cc_final: 0.6774 (m-80) REVERT: N 436 ASP cc_start: 0.7451 (m-30) cc_final: 0.7068 (t70) REVERT: N 448 LEU cc_start: 0.9170 (mt) cc_final: 0.8475 (mt) REVERT: N 519 VAL cc_start: 0.8836 (t) cc_final: 0.8555 (t) REVERT: N 534 ASP cc_start: 0.8416 (m-30) cc_final: 0.7901 (m-30) REVERT: N 538 LYS cc_start: 0.9354 (mttm) cc_final: 0.9049 (mtmm) REVERT: N 548 ARG cc_start: 0.9014 (mtt180) cc_final: 0.7823 (mmt90) REVERT: N 581 ASP cc_start: 0.8292 (m-30) cc_final: 0.7827 (m-30) REVERT: N 613 HIS cc_start: 0.6643 (p-80) cc_final: 0.6231 (p-80) REVERT: N 616 HIS cc_start: 0.7620 (m90) cc_final: 0.7038 (m90) REVERT: N 634 LEU cc_start: 0.7958 (tp) cc_final: 0.7753 (tp) REVERT: N 658 ILE cc_start: 0.8973 (mt) cc_final: 0.8550 (mt) REVERT: N 678 ILE cc_start: 0.9251 (mm) cc_final: 0.8863 (mm) REVERT: N 679 ASN cc_start: 0.9237 (m110) cc_final: 0.9029 (m-40) REVERT: N 707 ASN cc_start: 0.8361 (m-40) cc_final: 0.7874 (t0) REVERT: N 787 MET cc_start: 0.7843 (ppp) cc_final: 0.7542 (tmm) REVERT: S 138 MET cc_start: 0.8799 (ttt) cc_final: 0.8588 (ttt) REVERT: S 153 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7118 (mp0) REVERT: S 193 THR cc_start: 0.8343 (m) cc_final: 0.7784 (m) REVERT: S 214 MET cc_start: 0.7728 (tmm) cc_final: 0.7511 (tmm) REVERT: S 253 PHE cc_start: 0.8680 (t80) cc_final: 0.8117 (t80) REVERT: S 269 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8377 (mt-10) REVERT: S 273 PHE cc_start: 0.8806 (m-80) cc_final: 0.8483 (m-10) REVERT: S 280 ASN cc_start: 0.8298 (m-40) cc_final: 0.7757 (t0) REVERT: S 297 ILE cc_start: 0.8388 (mt) cc_final: 0.8121 (mt) REVERT: S 316 LEU cc_start: 0.8306 (tp) cc_final: 0.8077 (tp) REVERT: P 98 GLN cc_start: 0.8760 (mt0) cc_final: 0.8317 (mt0) REVERT: P 411 LEU cc_start: 0.8206 (mp) cc_final: 0.7882 (mp) REVERT: Q 110 SER cc_start: 0.4215 (m) cc_final: 0.3855 (t) REVERT: Q 236 PHE cc_start: 0.6900 (t80) cc_final: 0.6375 (t80) REVERT: Q 335 PHE cc_start: 0.7003 (m-80) cc_final: 0.6276 (m-80) REVERT: Q 420 ASN cc_start: 0.8040 (m-40) cc_final: 0.7604 (m110) REVERT: Q 434 TYR cc_start: 0.8448 (m-80) cc_final: 0.7872 (m-80) REVERT: R 192 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8724 (mm-30) REVERT: R 213 TYR cc_start: 0.9111 (m-10) cc_final: 0.8829 (m-80) REVERT: R 297 TYR cc_start: 0.7665 (t80) cc_final: 0.7042 (t80) REVERT: R 300 ASP cc_start: 0.7906 (p0) cc_final: 0.7670 (p0) REVERT: R 405 LYS cc_start: 0.8957 (mmmt) cc_final: 0.8379 (mmtt) REVERT: R 408 ASP cc_start: 0.8407 (t70) cc_final: 0.8124 (t70) REVERT: U 17 SER cc_start: 0.9133 (m) cc_final: 0.8734 (t) REVERT: U 78 GLU cc_start: 0.8493 (pt0) cc_final: 0.8217 (pt0) REVERT: U 251 ASN cc_start: 0.8965 (m-40) cc_final: 0.8751 (m-40) REVERT: U 255 ILE cc_start: 0.8756 (tt) cc_final: 0.8540 (tt) REVERT: U 274 MET cc_start: 0.7510 (ttt) cc_final: 0.7249 (ttt) REVERT: O 64 ASN cc_start: 0.8793 (m-40) cc_final: 0.8451 (m-40) REVERT: O 143 LEU cc_start: 0.8101 (mt) cc_final: 0.7544 (mt) REVERT: O 289 GLN cc_start: 0.8083 (tp-100) cc_final: 0.7579 (tp-100) outliers start: 4 outliers final: 2 residues processed: 974 average time/residue: 0.2497 time to fit residues: 400.2750 Evaluate side-chains 718 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 716 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 262 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 170 optimal weight: 20.0000 chunk 469 optimal weight: 8.9990 chunk 305 optimal weight: 0.0020 chunk 441 optimal weight: 20.0000 chunk 139 optimal weight: 40.0000 chunk 167 optimal weight: 20.0000 chunk 439 optimal weight: 6.9990 chunk 108 optimal weight: 50.0000 chunk 125 optimal weight: 7.9990 overall best weight: 4.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 100 HIS ** T 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 26 ASN Z 766 HIS Z 771 HIS Z 899 GLN ** Z 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 231 ASN N 256 GLN ** N 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 190 ASN ** Q 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 385 ASN U 230 GLN U 234 ASN U 256 ASN ** U 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 ASN ** O 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 282 GLN ** O 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.160364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.134491 restraints weight = 164043.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.136367 restraints weight = 120950.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.137748 restraints weight = 90339.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.139073 restraints weight = 73244.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.139613 restraints weight = 61453.730| |-----------------------------------------------------------------------------| r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.7751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 41662 Z= 0.178 Angle : 0.702 15.712 56279 Z= 0.371 Chirality : 0.042 0.260 6447 Planarity : 0.004 0.069 7202 Dihedral : 5.423 39.207 5504 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.40 % Favored : 95.28 % Rotamer: Outliers : 0.04 % Allowed : 2.40 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.38 (0.11), residues: 5108 helix: 0.48 (0.09), residues: 3330 sheet: -1.07 (0.32), residues: 215 loop : -1.60 (0.15), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 58 TYR 0.032 0.002 TYR Z 738 PHE 0.039 0.002 PHE O 301 TRP 0.023 0.002 TRP S 54 HIS 0.010 0.002 HIS S 139 Details of bonding type rmsd covalent geometry : bond 0.00374 (41662) covalent geometry : angle 0.70234 (56279) hydrogen bonds : bond 0.04623 ( 2182) hydrogen bonds : angle 4.79127 ( 6453) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 947 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 945 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 1 MET cc_start: 0.2322 (ttt) cc_final: 0.1239 (ttm) REVERT: W 25 ARG cc_start: 0.7220 (ttp-170) cc_final: 0.6707 (ttp-170) REVERT: W 35 PHE cc_start: 0.8169 (t80) cc_final: 0.7900 (t80) REVERT: W 68 GLU cc_start: 0.6180 (mm-30) cc_final: 0.5669 (tm-30) REVERT: W 182 TYR cc_start: 0.8328 (p90) cc_final: 0.8108 (p90) REVERT: V 34 LEU cc_start: 0.9650 (tp) cc_final: 0.9206 (tp) REVERT: V 53 MET cc_start: 0.8106 (mtm) cc_final: 0.7364 (mtm) REVERT: V 87 PHE cc_start: 0.8496 (t80) cc_final: 0.8173 (t80) REVERT: V 92 MET cc_start: 0.9000 (mpp) cc_final: 0.8752 (mpp) REVERT: V 96 LYS cc_start: 0.8733 (mttt) cc_final: 0.8454 (mttt) REVERT: V 188 LEU cc_start: 0.7961 (mt) cc_final: 0.7552 (mt) REVERT: V 251 TYR cc_start: 0.9098 (t80) cc_final: 0.8781 (t80) REVERT: V 275 ASP cc_start: 0.7894 (t0) cc_final: 0.7347 (t0) REVERT: V 279 HIS cc_start: 0.8378 (m-70) cc_final: 0.8028 (m-70) REVERT: V 285 ASP cc_start: 0.8553 (t70) cc_final: 0.8285 (t0) REVERT: T 40 LEU cc_start: 0.6841 (mt) cc_final: 0.6566 (mt) REVERT: T 116 GLN cc_start: 0.7736 (pt0) cc_final: 0.7458 (tm-30) REVERT: T 144 TYR cc_start: 0.2864 (t80) cc_final: 0.1783 (m-80) REVERT: Z 736 LEU cc_start: 0.5834 (tt) cc_final: 0.5554 (mt) REVERT: Z 815 MET cc_start: 0.6605 (ppp) cc_final: 0.5995 (ppp) REVERT: Z 832 ARG cc_start: 0.4054 (mtm-85) cc_final: 0.3848 (ttm110) REVERT: Z 945 ILE cc_start: 0.6640 (tp) cc_final: 0.6145 (tp) REVERT: N 26 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8927 (mp0) REVERT: N 89 PHE cc_start: 0.7926 (t80) cc_final: 0.7588 (t80) REVERT: N 90 ASP cc_start: 0.8117 (m-30) cc_final: 0.6970 (p0) REVERT: N 217 MET cc_start: 0.6147 (mmp) cc_final: 0.5845 (mmp) REVERT: N 270 LEU cc_start: 0.8603 (tp) cc_final: 0.8318 (mt) REVERT: N 271 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8701 (mm-30) REVERT: N 339 MET cc_start: 0.6481 (mmm) cc_final: 0.6130 (mmp) REVERT: N 412 TYR cc_start: 0.7326 (m-80) cc_final: 0.6590 (m-80) REVERT: N 436 ASP cc_start: 0.7632 (m-30) cc_final: 0.7292 (t70) REVERT: N 448 LEU cc_start: 0.9104 (mt) cc_final: 0.8399 (mt) REVERT: N 519 VAL cc_start: 0.8831 (t) cc_final: 0.8598 (t) REVERT: N 538 LYS cc_start: 0.9443 (mttm) cc_final: 0.9160 (mtmm) REVERT: N 581 ASP cc_start: 0.8428 (m-30) cc_final: 0.7944 (m-30) REVERT: N 616 HIS cc_start: 0.7524 (m90) cc_final: 0.6947 (m90) REVERT: N 679 ASN cc_start: 0.9247 (m110) cc_final: 0.9029 (m-40) REVERT: N 707 ASN cc_start: 0.8212 (m-40) cc_final: 0.7774 (t0) REVERT: N 782 PHE cc_start: 0.5717 (m-80) cc_final: 0.5462 (m-10) REVERT: N 787 MET cc_start: 0.7821 (ppp) cc_final: 0.7557 (ppp) REVERT: N 896 PHE cc_start: 0.5461 (m-10) cc_final: 0.4966 (t80) REVERT: S 40 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8242 (pt0) REVERT: S 47 THR cc_start: 0.8550 (t) cc_final: 0.8346 (t) REVERT: S 153 GLU cc_start: 0.7291 (mm-30) cc_final: 0.7002 (mp0) REVERT: S 269 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8268 (mt-10) REVERT: S 273 PHE cc_start: 0.8885 (m-80) cc_final: 0.8500 (m-10) REVERT: S 280 ASN cc_start: 0.8284 (m-40) cc_final: 0.7720 (t0) REVERT: S 297 ILE cc_start: 0.8457 (mt) cc_final: 0.8161 (mt) REVERT: S 422 MET cc_start: 0.8474 (mmp) cc_final: 0.8222 (mmm) REVERT: P 98 GLN cc_start: 0.8767 (mt0) cc_final: 0.8356 (mt0) REVERT: P 135 GLU cc_start: 0.8898 (pm20) cc_final: 0.8675 (pm20) REVERT: P 173 MET cc_start: 0.8912 (ptm) cc_final: 0.8629 (ppp) REVERT: P 175 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7907 (tm-30) REVERT: P 316 LYS cc_start: 0.8245 (mmtt) cc_final: 0.7991 (pttm) REVERT: P 356 TYR cc_start: 0.6941 (m-10) cc_final: 0.6638 (m-80) REVERT: P 361 THR cc_start: 0.5533 (m) cc_final: 0.5236 (m) REVERT: P 373 GLU cc_start: 0.8521 (pm20) cc_final: 0.8276 (pm20) REVERT: Q 63 GLN cc_start: 0.8621 (tp-100) cc_final: 0.8204 (tp40) REVERT: Q 110 SER cc_start: 0.4675 (m) cc_final: 0.4398 (t) REVERT: Q 133 LEU cc_start: 0.8537 (tp) cc_final: 0.8272 (tp) REVERT: Q 184 VAL cc_start: 0.7342 (t) cc_final: 0.6883 (t) REVERT: Q 190 ASN cc_start: 0.6608 (OUTLIER) cc_final: 0.6110 (p0) REVERT: Q 210 CYS cc_start: 0.5490 (m) cc_final: 0.5274 (m) REVERT: Q 335 PHE cc_start: 0.6546 (m-80) cc_final: 0.6104 (m-80) REVERT: Q 420 ASN cc_start: 0.7970 (m-40) cc_final: 0.7521 (m110) REVERT: Q 434 TYR cc_start: 0.8392 (m-80) cc_final: 0.8003 (m-80) REVERT: R 40 ILE cc_start: 0.6522 (pt) cc_final: 0.6195 (tp) REVERT: R 333 MET cc_start: 0.8739 (mmm) cc_final: 0.8314 (mmm) REVERT: R 405 LYS cc_start: 0.8868 (mmmt) cc_final: 0.8322 (mmtt) REVERT: U 17 SER cc_start: 0.9181 (m) cc_final: 0.8843 (t) REVERT: U 78 GLU cc_start: 0.8659 (pt0) cc_final: 0.8270 (pt0) REVERT: U 229 LEU cc_start: 0.9342 (mm) cc_final: 0.8986 (mm) REVERT: U 247 ILE cc_start: 0.9061 (tp) cc_final: 0.8736 (tp) REVERT: U 251 ASN cc_start: 0.8971 (m-40) cc_final: 0.8720 (m-40) REVERT: O 64 ASN cc_start: 0.9006 (m-40) cc_final: 0.8493 (m110) REVERT: O 143 LEU cc_start: 0.8197 (mt) cc_final: 0.7870 (mt) REVERT: O 189 TYR cc_start: 0.7958 (t80) cc_final: 0.7756 (t80) REVERT: O 289 GLN cc_start: 0.8287 (tp-100) cc_final: 0.7732 (tp-100) outliers start: 2 outliers final: 0 residues processed: 945 average time/residue: 0.2518 time to fit residues: 391.4398 Evaluate side-chains 729 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 728 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 473 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 487 optimal weight: 2.9990 chunk 401 optimal weight: 5.9990 chunk 138 optimal weight: 20.0000 chunk 75 optimal weight: 7.9990 chunk 340 optimal weight: 9.9990 chunk 304 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 chunk 470 optimal weight: 20.0000 chunk 441 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 58 ASN V 184 ASN ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 26 ASN Z 243 GLN Z 361 HIS ** Z 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 256 GLN N 336 ASN ** N 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 607 GLN N 616 HIS ** N 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 738 GLN ** S 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 235 ASN ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 417 GLN ** S 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 278 ASN ** P 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 178 HIS Q 190 ASN ** Q 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 149 ASN U 230 GLN U 260 ASN ** U 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 282 GLN ** O 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 389 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.156840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.130167 restraints weight = 164546.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.132383 restraints weight = 121267.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.134113 restraints weight = 89115.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.135210 restraints weight = 71775.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.135872 restraints weight = 61137.660| |-----------------------------------------------------------------------------| r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.8396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 41662 Z= 0.205 Angle : 0.750 16.924 56279 Z= 0.394 Chirality : 0.043 0.327 6447 Planarity : 0.005 0.088 7202 Dihedral : 5.553 43.961 5504 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.78 % Favored : 94.87 % Rotamer: Outliers : 0.04 % Allowed : 2.71 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.04 % 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: -0.65 (0.11), residues: 5108 helix: 0.26 (0.09), residues: 3343 sheet: -1.06 (0.31), residues: 226 loop : -1.74 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P 395 TYR 0.032 0.002 TYR T 266 PHE 0.050 0.003 PHE Q 236 TRP 0.027 0.002 TRP S 54 HIS 0.010 0.002 HIS V 40 Details of bonding type rmsd covalent geometry : bond 0.00435 (41662) covalent geometry : angle 0.75008 (56279) hydrogen bonds : bond 0.04667 ( 2182) hydrogen bonds : angle 4.99956 ( 6453) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 930 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 1 MET cc_start: 0.2391 (ttt) cc_final: 0.1953 (ttt) REVERT: V 34 LEU cc_start: 0.9668 (tp) cc_final: 0.9114 (tp) REVERT: V 53 MET cc_start: 0.7696 (mtm) cc_final: 0.7233 (mtm) REVERT: V 96 LYS cc_start: 0.8676 (mttt) cc_final: 0.8473 (mttt) REVERT: V 188 LEU cc_start: 0.7867 (mt) cc_final: 0.7389 (mt) REVERT: V 212 MET cc_start: 0.8566 (ttt) cc_final: 0.8287 (ttm) REVERT: V 251 TYR cc_start: 0.9063 (t80) cc_final: 0.8679 (t80) REVERT: V 278 LYS cc_start: 0.9376 (mttp) cc_final: 0.8733 (mttm) REVERT: V 285 ASP cc_start: 0.8517 (t70) cc_final: 0.8185 (t70) REVERT: T 158 GLN cc_start: 0.8727 (pp30) cc_final: 0.8066 (tp-100) REVERT: Z 358 TYR cc_start: 0.4149 (m-10) cc_final: 0.3085 (m-10) REVERT: Z 406 TRP cc_start: 0.5994 (p-90) cc_final: 0.4693 (t-100) REVERT: Z 455 ILE cc_start: 0.2203 (mm) cc_final: 0.1841 (tp) REVERT: Z 736 LEU cc_start: 0.5440 (tt) cc_final: 0.5210 (mt) REVERT: Z 815 MET cc_start: 0.6518 (ppp) cc_final: 0.5935 (ppp) REVERT: N 26 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8954 (mp0) REVERT: N 89 PHE cc_start: 0.8132 (t80) cc_final: 0.7668 (t80) REVERT: N 90 ASP cc_start: 0.8097 (m-30) cc_final: 0.6680 (p0) REVERT: N 166 ILE cc_start: 0.7308 (mm) cc_final: 0.7083 (mm) REVERT: N 217 MET cc_start: 0.6540 (mmp) cc_final: 0.6247 (mmp) REVERT: N 271 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8634 (mm-30) REVERT: N 289 ILE cc_start: 0.6939 (mm) cc_final: 0.6711 (mm) REVERT: N 309 ILE cc_start: 0.7547 (mp) cc_final: 0.7237 (pt) REVERT: N 339 MET cc_start: 0.6225 (mmm) cc_final: 0.5572 (mmp) REVERT: N 386 MET cc_start: 0.7661 (ppp) cc_final: 0.7367 (ppp) REVERT: N 412 TYR cc_start: 0.7262 (m-80) cc_final: 0.6564 (m-80) REVERT: N 436 ASP cc_start: 0.7536 (m-30) cc_final: 0.7265 (t70) REVERT: N 448 LEU cc_start: 0.9113 (mt) cc_final: 0.8330 (mt) REVERT: N 450 ILE cc_start: 0.8808 (tt) cc_final: 0.8514 (tp) REVERT: N 519 VAL cc_start: 0.8806 (t) cc_final: 0.8594 (t) REVERT: N 570 ARG cc_start: 0.9215 (mmp-170) cc_final: 0.8812 (mmp-170) REVERT: N 580 ASN cc_start: 0.8381 (t0) cc_final: 0.7984 (t0) REVERT: N 582 ASP cc_start: 0.7522 (p0) cc_final: 0.6905 (p0) REVERT: N 707 ASN cc_start: 0.8461 (m-40) cc_final: 0.8009 (t0) REVERT: N 787 MET cc_start: 0.7695 (ppp) cc_final: 0.7400 (ppp) REVERT: N 875 LEU cc_start: 0.8732 (mt) cc_final: 0.8172 (mt) REVERT: N 896 PHE cc_start: 0.5463 (m-10) cc_final: 0.5036 (t80) REVERT: S 40 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8485 (pt0) REVERT: S 47 THR cc_start: 0.8613 (t) cc_final: 0.8406 (t) REVERT: S 58 LYS cc_start: 0.4599 (mtmt) cc_final: 0.4044 (ttmt) REVERT: S 253 PHE cc_start: 0.8666 (t80) cc_final: 0.8151 (t80) REVERT: S 269 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8356 (mt-10) REVERT: S 273 PHE cc_start: 0.8956 (m-80) cc_final: 0.8694 (m-10) REVERT: S 297 ILE cc_start: 0.8773 (mt) cc_final: 0.8548 (mt) REVERT: S 407 ILE cc_start: 0.6323 (mm) cc_final: 0.6041 (mt) REVERT: S 437 ASN cc_start: 0.9217 (t0) cc_final: 0.8739 (t0) REVERT: P 173 MET cc_start: 0.8844 (ppp) cc_final: 0.8595 (ppp) REVERT: P 356 TYR cc_start: 0.6915 (m-10) cc_final: 0.6663 (m-80) REVERT: P 402 PHE cc_start: 0.7555 (m-80) cc_final: 0.6726 (m-10) REVERT: P 414 GLU cc_start: 0.8634 (mp0) cc_final: 0.8375 (mp0) REVERT: Q 63 GLN cc_start: 0.8655 (tp-100) cc_final: 0.8385 (tp40) REVERT: Q 133 LEU cc_start: 0.8510 (tp) cc_final: 0.8256 (tp) REVERT: Q 210 CYS cc_start: 0.5202 (m) cc_final: 0.4861 (m) REVERT: Q 420 ASN cc_start: 0.7875 (m-40) cc_final: 0.7527 (m110) REVERT: Q 434 TYR cc_start: 0.8216 (m-80) cc_final: 0.7645 (m-80) REVERT: R 40 ILE cc_start: 0.6451 (pt) cc_final: 0.6213 (tp) REVERT: R 59 MET cc_start: 0.6094 (mmp) cc_final: 0.5863 (mmp) REVERT: R 226 GLU cc_start: 0.9073 (tp30) cc_final: 0.8442 (tp30) REVERT: R 319 CYS cc_start: 0.7753 (m) cc_final: 0.7397 (t) REVERT: R 405 LYS cc_start: 0.8915 (mmmt) cc_final: 0.8407 (mmtt) REVERT: U 17 SER cc_start: 0.9304 (m) cc_final: 0.8976 (t) REVERT: U 137 TYR cc_start: 0.7615 (m-80) cc_final: 0.7117 (m-80) REVERT: U 229 LEU cc_start: 0.9413 (mm) cc_final: 0.9034 (mm) REVERT: U 233 PHE cc_start: 0.8102 (m-80) cc_final: 0.7662 (m-10) REVERT: U 247 ILE cc_start: 0.9150 (tp) cc_final: 0.8772 (tp) REVERT: U 251 ASN cc_start: 0.9085 (m-40) cc_final: 0.8843 (m-40) REVERT: O 64 ASN cc_start: 0.8965 (m-40) cc_final: 0.8612 (m-40) REVERT: O 77 SER cc_start: 0.8948 (m) cc_final: 0.8607 (p) REVERT: O 143 LEU cc_start: 0.7975 (mt) cc_final: 0.7665 (mt) REVERT: O 289 GLN cc_start: 0.8254 (tp-100) cc_final: 0.7661 (tp-100) outliers start: 2 outliers final: 1 residues processed: 931 average time/residue: 0.2492 time to fit residues: 382.0958 Evaluate side-chains 702 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 701 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 108 optimal weight: 50.0000 chunk 104 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 271 optimal weight: 0.9990 chunk 412 optimal weight: 5.9990 chunk 157 optimal weight: 10.0000 chunk 473 optimal weight: 5.9990 chunk 227 optimal weight: 20.0000 chunk 311 optimal weight: 3.9990 chunk 188 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 86 HIS V 133 ASN V 279 HIS V 290 ASN T 47 GLN ** T 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 116 GLN Z 26 ASN Z 77 ASN Z 243 GLN Z 532 HIS ** Z 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 842 GLN ** Z 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 256 GLN ** N 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 235 ASN ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 469 ASN ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 223 ASN R 287 GLN R 323 ASN U 71 ASN U 230 GLN U 256 ASN U 260 ASN ** U 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 GLN O 211 GLN ** O 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 282 GLN ** O 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.158168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.132301 restraints weight = 166699.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.134389 restraints weight = 120104.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.136052 restraints weight = 92141.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.136836 restraints weight = 74508.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.137896 restraints weight = 62700.436| |-----------------------------------------------------------------------------| r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.8674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 41662 Z= 0.165 Angle : 0.701 14.453 56279 Z= 0.369 Chirality : 0.042 0.235 6447 Planarity : 0.005 0.078 7202 Dihedral : 5.430 41.987 5504 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.66 % Favored : 94.99 % Rotamer: Outliers : 0.04 % Allowed : 1.95 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.04 % 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: -0.57 (0.11), residues: 5108 helix: 0.34 (0.09), residues: 3330 sheet: -1.04 (0.31), residues: 236 loop : -1.73 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG V 254 TYR 0.055 0.002 TYR S 475 PHE 0.044 0.002 PHE O 65 TRP 0.049 0.003 TRP T 151 HIS 0.009 0.001 HIS V 40 Details of bonding type rmsd covalent geometry : bond 0.00352 (41662) covalent geometry : angle 0.70129 (56279) hydrogen bonds : bond 0.04439 ( 2182) hydrogen bonds : angle 4.91714 ( 6453) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 917 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 1 MET cc_start: 0.2392 (ttt) cc_final: 0.1960 (ttt) REVERT: W 79 THR cc_start: 0.7842 (t) cc_final: 0.7555 (t) REVERT: W 92 GLN cc_start: 0.8664 (mp10) cc_final: 0.8399 (mp10) REVERT: V 34 LEU cc_start: 0.9702 (tp) cc_final: 0.9200 (tp) REVERT: V 50 MET cc_start: 0.8546 (mmm) cc_final: 0.8200 (tpp) REVERT: V 53 MET cc_start: 0.7787 (mtm) cc_final: 0.7261 (mtm) REVERT: V 73 GLN cc_start: 0.8462 (pp30) cc_final: 0.8163 (pp30) REVERT: V 235 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8721 (tm-30) REVERT: V 251 TYR cc_start: 0.9132 (t80) cc_final: 0.8757 (t80) REVERT: V 278 LYS cc_start: 0.9440 (mttp) cc_final: 0.8754 (mttm) REVERT: V 279 HIS cc_start: 0.8755 (m90) cc_final: 0.8549 (m-70) REVERT: V 285 ASP cc_start: 0.8608 (t70) cc_final: 0.8273 (t70) REVERT: T 79 GLU cc_start: 0.9329 (tp30) cc_final: 0.8766 (pt0) REVERT: T 82 PHE cc_start: 0.8833 (t80) cc_final: 0.8579 (t80) REVERT: T 86 LYS cc_start: 0.8319 (mttt) cc_final: 0.8091 (mmmt) REVERT: T 158 GLN cc_start: 0.8744 (pp30) cc_final: 0.8413 (tp-100) REVERT: T 226 TRP cc_start: 0.7716 (m-10) cc_final: 0.7132 (m-10) REVERT: Z 406 TRP cc_start: 0.5772 (p-90) cc_final: 0.4694 (t-100) REVERT: Z 455 ILE cc_start: 0.2028 (mm) cc_final: 0.1725 (tp) REVERT: Z 736 LEU cc_start: 0.5486 (tt) cc_final: 0.5140 (mt) REVERT: Z 815 MET cc_start: 0.6294 (ppp) cc_final: 0.5888 (ppp) REVERT: N 15 GLU cc_start: 0.7964 (mp0) cc_final: 0.7447 (mp0) REVERT: N 26 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8913 (mp0) REVERT: N 89 PHE cc_start: 0.8165 (t80) cc_final: 0.7777 (t80) REVERT: N 90 ASP cc_start: 0.8086 (m-30) cc_final: 0.7798 (m-30) REVERT: N 267 GLN cc_start: 0.7735 (tp40) cc_final: 0.7114 (tp40) REVERT: N 270 LEU cc_start: 0.8482 (tp) cc_final: 0.7683 (mt) REVERT: N 271 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8190 (mm-30) REVERT: N 339 MET cc_start: 0.6472 (mmm) cc_final: 0.5751 (mmp) REVERT: N 412 TYR cc_start: 0.7203 (m-80) cc_final: 0.6585 (m-80) REVERT: N 436 ASP cc_start: 0.7645 (m-30) cc_final: 0.7376 (t70) REVERT: N 450 ILE cc_start: 0.8598 (tt) cc_final: 0.8287 (tp) REVERT: N 570 ARG cc_start: 0.9158 (mmp-170) cc_final: 0.8772 (mmp-170) REVERT: N 580 ASN cc_start: 0.8431 (t0) cc_final: 0.8161 (t0) REVERT: N 682 PHE cc_start: 0.8489 (m-80) cc_final: 0.7924 (m-80) REVERT: N 707 ASN cc_start: 0.8499 (m-40) cc_final: 0.8138 (t0) REVERT: N 773 MET cc_start: 0.7304 (tpt) cc_final: 0.7103 (tpp) REVERT: N 875 LEU cc_start: 0.8774 (mt) cc_final: 0.8277 (mt) REVERT: S 40 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8535 (pt0) REVERT: S 47 THR cc_start: 0.8738 (t) cc_final: 0.8519 (t) REVERT: S 58 LYS cc_start: 0.4682 (mtmt) cc_final: 0.3999 (ttmt) REVERT: S 147 TRP cc_start: 0.7034 (t-100) cc_final: 0.6425 (m100) REVERT: S 269 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8540 (mt-10) REVERT: S 297 ILE cc_start: 0.8754 (mt) cc_final: 0.8536 (mt) REVERT: S 422 MET cc_start: 0.8332 (mmp) cc_final: 0.8105 (mmp) REVERT: S 437 ASN cc_start: 0.9204 (t0) cc_final: 0.8745 (t0) REVERT: P 245 TYR cc_start: 0.7317 (t80) cc_final: 0.7073 (t80) REVERT: P 356 TYR cc_start: 0.7043 (m-10) cc_final: 0.6757 (m-80) REVERT: Q 133 LEU cc_start: 0.8614 (tp) cc_final: 0.8407 (tp) REVERT: Q 210 CYS cc_start: 0.4465 (m) cc_final: 0.3945 (m) REVERT: Q 424 ASP cc_start: 0.9021 (m-30) cc_final: 0.8816 (m-30) REVERT: Q 434 TYR cc_start: 0.7646 (m-10) cc_final: 0.7416 (m-80) REVERT: R 40 ILE cc_start: 0.6719 (pt) cc_final: 0.6460 (tp) REVERT: R 59 MET cc_start: 0.6873 (mmp) cc_final: 0.6517 (mmp) REVERT: R 333 MET cc_start: 0.8771 (mmm) cc_final: 0.8358 (mmm) REVERT: R 405 LYS cc_start: 0.8826 (mmmt) cc_final: 0.8390 (mmtt) REVERT: U 1 MET cc_start: 0.5723 (mtm) cc_final: 0.5380 (mtm) REVERT: U 17 SER cc_start: 0.9284 (m) cc_final: 0.8976 (t) REVERT: U 78 GLU cc_start: 0.9045 (pt0) cc_final: 0.8711 (pt0) REVERT: U 137 TYR cc_start: 0.7679 (m-80) cc_final: 0.7114 (m-80) REVERT: U 229 LEU cc_start: 0.9189 (mm) cc_final: 0.8974 (mm) REVERT: U 247 ILE cc_start: 0.9179 (tp) cc_final: 0.8787 (tp) REVERT: U 251 ASN cc_start: 0.9142 (m-40) cc_final: 0.8886 (m-40) REVERT: U 268 LYS cc_start: 0.9137 (mmtm) cc_final: 0.8615 (mmtm) REVERT: O 64 ASN cc_start: 0.9108 (m-40) cc_final: 0.8646 (m110) REVERT: O 77 SER cc_start: 0.8806 (m) cc_final: 0.8528 (p) REVERT: O 289 GLN cc_start: 0.8371 (tp-100) cc_final: 0.7768 (tp-100) REVERT: O 372 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7492 (pm20) outliers start: 2 outliers final: 1 residues processed: 919 average time/residue: 0.2497 time to fit residues: 378.2820 Evaluate side-chains 725 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 723 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 169 optimal weight: 50.0000 chunk 455 optimal weight: 20.0000 chunk 214 optimal weight: 20.0000 chunk 423 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 328 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 106 optimal weight: 30.0000 chunk 159 optimal weight: 30.0000 chunk 387 optimal weight: 9.9990 overall best weight: 4.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 106 GLN W 107 HIS V 195 HIS T 83 ASN T 116 GLN T 123 HIS Z 26 ASN Z 243 GLN Z 532 HIS Z 539 ASN ** Z 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 256 GLN N 375 HIS ** N 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 407 ASN Q 16 ASN ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 287 GLN U 216 ASN U 230 GLN U 256 ASN U 260 ASN ** U 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 GLN ** O 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 282 GLN ** O 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.156697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.130145 restraints weight = 166758.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.132484 restraints weight = 121519.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.133822 restraints weight = 89545.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.135232 restraints weight = 74155.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.135936 restraints weight = 62033.943| |-----------------------------------------------------------------------------| r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.9019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 41662 Z= 0.173 Angle : 0.714 13.630 56279 Z= 0.377 Chirality : 0.042 0.278 6447 Planarity : 0.005 0.091 7202 Dihedral : 5.451 42.660 5504 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.03 % Favored : 94.66 % Rotamer: Outliers : 0.02 % Allowed : 1.31 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.04 % 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: -0.61 (0.11), residues: 5108 helix: 0.28 (0.09), residues: 3336 sheet: -1.03 (0.32), residues: 235 loop : -1.68 (0.15), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG W 122 TYR 0.031 0.002 TYR S 475 PHE 0.033 0.002 PHE N 682 TRP 0.033 0.003 TRP T 151 HIS 0.009 0.002 HIS V 195 Details of bonding type rmsd covalent geometry : bond 0.00369 (41662) covalent geometry : angle 0.71428 (56279) hydrogen bonds : bond 0.04446 ( 2182) hydrogen bonds : angle 4.96128 ( 6453) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 896 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 92 GLN cc_start: 0.8723 (mp10) cc_final: 0.8240 (mp10) REVERT: V 34 LEU cc_start: 0.9664 (tp) cc_final: 0.9068 (tp) REVERT: V 50 MET cc_start: 0.8480 (mmm) cc_final: 0.7958 (tpp) REVERT: V 53 MET cc_start: 0.7522 (mtm) cc_final: 0.7138 (mtm) REVERT: V 73 GLN cc_start: 0.8667 (pp30) cc_final: 0.8131 (pp30) REVERT: V 91 MET cc_start: 0.8575 (mmp) cc_final: 0.8236 (mmp) REVERT: V 235 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8711 (tm-30) REVERT: V 251 TYR cc_start: 0.9120 (t80) cc_final: 0.8793 (t80) REVERT: V 278 LYS cc_start: 0.9434 (mttp) cc_final: 0.8725 (mttm) REVERT: V 279 HIS cc_start: 0.8716 (m90) cc_final: 0.8487 (m-70) REVERT: V 285 ASP cc_start: 0.8605 (t70) cc_final: 0.8299 (t70) REVERT: T 127 GLN cc_start: 0.4776 (tp40) cc_final: 0.4392 (tm-30) REVERT: T 153 MET cc_start: 0.4568 (mpp) cc_final: 0.4262 (mpp) REVERT: T 158 GLN cc_start: 0.8557 (pp30) cc_final: 0.8060 (tp40) REVERT: T 226 TRP cc_start: 0.7713 (m-10) cc_final: 0.7222 (m-10) REVERT: Z 276 ASN cc_start: 0.6754 (t0) cc_final: 0.6399 (p0) REVERT: Z 428 TRP cc_start: 0.3337 (t60) cc_final: 0.1350 (m100) REVERT: Z 815 MET cc_start: 0.6358 (ppp) cc_final: 0.6019 (ppp) REVERT: N 46 ILE cc_start: 0.4568 (mt) cc_final: 0.4256 (mt) REVERT: N 64 ILE cc_start: 0.7492 (mp) cc_final: 0.7262 (mp) REVERT: N 89 PHE cc_start: 0.8055 (t80) cc_final: 0.7561 (t80) REVERT: N 90 ASP cc_start: 0.7872 (m-30) cc_final: 0.7560 (m-30) REVERT: N 210 SER cc_start: 0.7812 (t) cc_final: 0.7593 (p) REVERT: N 270 LEU cc_start: 0.8353 (tp) cc_final: 0.7633 (tp) REVERT: N 271 GLU cc_start: 0.8682 (mm-30) cc_final: 0.7958 (mm-30) REVERT: N 339 MET cc_start: 0.6290 (mmm) cc_final: 0.5405 (mmp) REVERT: N 386 MET cc_start: 0.7631 (ppp) cc_final: 0.7158 (ppp) REVERT: N 408 LEU cc_start: 0.8788 (tp) cc_final: 0.8109 (mt) REVERT: N 412 TYR cc_start: 0.7086 (m-80) cc_final: 0.6495 (m-80) REVERT: N 450 ILE cc_start: 0.8578 (tt) cc_final: 0.8317 (tp) REVERT: N 513 ILE cc_start: 0.9564 (mt) cc_final: 0.9278 (mm) REVERT: N 580 ASN cc_start: 0.8385 (t0) cc_final: 0.8145 (t0) REVERT: N 707 ASN cc_start: 0.8511 (m-40) cc_final: 0.8248 (t0) REVERT: N 773 MET cc_start: 0.7028 (tpt) cc_final: 0.6801 (tpp) REVERT: N 875 LEU cc_start: 0.8863 (mt) cc_final: 0.8399 (mt) REVERT: S 40 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8511 (pt0) REVERT: S 47 THR cc_start: 0.8698 (t) cc_final: 0.8468 (t) REVERT: S 58 LYS cc_start: 0.4370 (mtmt) cc_final: 0.3764 (ttmt) REVERT: S 147 TRP cc_start: 0.7147 (t-100) cc_final: 0.6608 (m100) REVERT: S 269 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8638 (mt-10) REVERT: S 280 ASN cc_start: 0.8337 (m-40) cc_final: 0.7619 (t0) REVERT: S 297 ILE cc_start: 0.8806 (mt) cc_final: 0.8573 (mt) REVERT: S 422 MET cc_start: 0.8500 (mmp) cc_final: 0.8229 (mmp) REVERT: P 98 GLN cc_start: 0.8888 (mt0) cc_final: 0.8493 (mt0) REVERT: P 135 GLU cc_start: 0.9058 (pm20) cc_final: 0.8574 (pm20) REVERT: P 356 TYR cc_start: 0.6827 (m-10) cc_final: 0.6527 (m-80) REVERT: Q 187 LYS cc_start: 0.8737 (mmtt) cc_final: 0.8440 (pttt) REVERT: Q 210 CYS cc_start: 0.4959 (m) cc_final: 0.4486 (m) REVERT: R 40 ILE cc_start: 0.6771 (pt) cc_final: 0.6497 (tp) REVERT: R 206 ARG cc_start: 0.8684 (mtt90) cc_final: 0.8183 (mtt-85) REVERT: R 229 LYS cc_start: 0.9063 (ptpp) cc_final: 0.8843 (pttm) REVERT: R 319 CYS cc_start: 0.7806 (m) cc_final: 0.7341 (t) REVERT: R 333 MET cc_start: 0.8872 (mmm) cc_final: 0.8513 (mmm) REVERT: R 405 LYS cc_start: 0.8816 (mmmt) cc_final: 0.8376 (mmtt) REVERT: U 1 MET cc_start: 0.5590 (mtm) cc_final: 0.5085 (mtm) REVERT: U 17 SER cc_start: 0.9323 (m) cc_final: 0.8989 (t) REVERT: U 78 GLU cc_start: 0.8878 (pt0) cc_final: 0.8591 (pt0) REVERT: U 83 ILE cc_start: 0.8982 (mm) cc_final: 0.8637 (mm) REVERT: U 137 TYR cc_start: 0.7479 (m-80) cc_final: 0.7102 (m-80) REVERT: U 174 LEU cc_start: 0.9159 (mt) cc_final: 0.8875 (pp) REVERT: U 229 LEU cc_start: 0.9337 (mm) cc_final: 0.8974 (mm) REVERT: U 247 ILE cc_start: 0.9182 (tp) cc_final: 0.8772 (tp) REVERT: U 251 ASN cc_start: 0.9171 (m-40) cc_final: 0.8945 (m-40) REVERT: O 64 ASN cc_start: 0.9013 (m-40) cc_final: 0.8647 (m-40) REVERT: O 289 GLN cc_start: 0.8332 (tp-100) cc_final: 0.7657 (tp-100) outliers start: 1 outliers final: 1 residues processed: 897 average time/residue: 0.2466 time to fit residues: 366.0580 Evaluate side-chains 731 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 730 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 301 optimal weight: 9.9990 chunk 412 optimal weight: 8.9990 chunk 139 optimal weight: 50.0000 chunk 322 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 5 optimal weight: 30.0000 chunk 259 optimal weight: 20.0000 chunk 466 optimal weight: 7.9990 chunk 271 optimal weight: 0.0000 chunk 488 optimal weight: 20.0000 chunk 311 optimal weight: 1.9990 overall best weight: 4.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 217 HIS ** V 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 123 HIS Z 26 ASN Z 215 ASN Z 243 GLN ** Z 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 256 GLN ** N 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 287 GLN U 156 HIS U 230 GLN U 256 ASN U 260 ASN ** U 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 105 GLN ** O 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 282 GLN ** O 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.156333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.130340 restraints weight = 169380.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.132370 restraints weight = 124359.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.133880 restraints weight = 92658.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.134678 restraints weight = 72825.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.135641 restraints weight = 63612.747| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.9311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 41662 Z= 0.173 Angle : 0.715 13.097 56279 Z= 0.379 Chirality : 0.043 0.337 6447 Planarity : 0.005 0.094 7202 Dihedral : 5.428 42.625 5504 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.21 % Favored : 94.48 % Rotamer: Outliers : 0.02 % Allowed : 0.70 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.04 % 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: -0.67 (0.11), residues: 5108 helix: 0.22 (0.09), residues: 3336 sheet: -1.18 (0.34), residues: 209 loop : -1.64 (0.15), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG V 254 TYR 0.034 0.002 TYR S 272 PHE 0.068 0.002 PHE Q 335 TRP 0.031 0.002 TRP S 54 HIS 0.007 0.001 HIS P 425 Details of bonding type rmsd covalent geometry : bond 0.00369 (41662) covalent geometry : angle 0.71514 (56279) hydrogen bonds : bond 0.04362 ( 2182) hydrogen bonds : angle 5.00469 ( 6453) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 911 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 1 MET cc_start: 0.2946 (ttt) cc_final: 0.2636 (ttt) REVERT: W 79 THR cc_start: 0.8016 (t) cc_final: 0.7586 (t) REVERT: W 92 GLN cc_start: 0.8761 (mp10) cc_final: 0.8334 (mp10) REVERT: V 34 LEU cc_start: 0.9637 (tp) cc_final: 0.9110 (tp) REVERT: V 50 MET cc_start: 0.8345 (mmm) cc_final: 0.8011 (tpp) REVERT: V 53 MET cc_start: 0.7584 (mtm) cc_final: 0.7156 (mtm) REVERT: V 71 MET cc_start: 0.8335 (ttm) cc_final: 0.8086 (ttm) REVERT: V 73 GLN cc_start: 0.8714 (pp30) cc_final: 0.8444 (pp30) REVERT: V 91 MET cc_start: 0.8713 (mmp) cc_final: 0.8404 (mmp) REVERT: V 157 ARG cc_start: 0.8606 (ttt180) cc_final: 0.8279 (tpt-90) REVERT: V 235 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8777 (tm-30) REVERT: V 253 LYS cc_start: 0.9167 (tptp) cc_final: 0.8931 (pttt) REVERT: V 278 LYS cc_start: 0.9449 (mttp) cc_final: 0.8697 (mttm) REVERT: V 279 HIS cc_start: 0.8711 (m90) cc_final: 0.8449 (m-70) REVERT: V 285 ASP cc_start: 0.8600 (t70) cc_final: 0.7595 (t70) REVERT: V 289 GLU cc_start: 0.8543 (pt0) cc_final: 0.7977 (pt0) REVERT: T 127 GLN cc_start: 0.4844 (tp40) cc_final: 0.4456 (tm-30) REVERT: T 153 MET cc_start: 0.4492 (mpp) cc_final: 0.4192 (mpp) REVERT: T 158 GLN cc_start: 0.8552 (pp30) cc_final: 0.8073 (tp40) REVERT: T 161 TRP cc_start: 0.7690 (t60) cc_final: 0.6897 (t60) REVERT: T 162 ASP cc_start: 0.8476 (m-30) cc_final: 0.8215 (m-30) REVERT: T 264 MET cc_start: 0.7274 (mmm) cc_final: 0.6976 (mmt) REVERT: Z 171 LYS cc_start: 0.5391 (mttt) cc_final: 0.5118 (mmtt) REVERT: Z 406 TRP cc_start: 0.5319 (p-90) cc_final: 0.4592 (t-100) REVERT: Z 428 TRP cc_start: 0.2656 (t60) cc_final: 0.0966 (m100) REVERT: Z 776 VAL cc_start: 0.7116 (m) cc_final: 0.6746 (m) REVERT: Z 945 ILE cc_start: 0.6375 (tp) cc_final: 0.5856 (tp) REVERT: N 26 GLU cc_start: 0.9143 (mp0) cc_final: 0.8931 (mp0) REVERT: N 46 ILE cc_start: 0.4803 (mt) cc_final: 0.4529 (mt) REVERT: N 64 ILE cc_start: 0.7490 (mp) cc_final: 0.7071 (mp) REVERT: N 89 PHE cc_start: 0.8093 (t80) cc_final: 0.7576 (t80) REVERT: N 210 SER cc_start: 0.7878 (t) cc_final: 0.7605 (p) REVERT: N 270 LEU cc_start: 0.8365 (tp) cc_final: 0.7735 (mt) REVERT: N 271 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8382 (mm-30) REVERT: N 339 MET cc_start: 0.6309 (mmm) cc_final: 0.5205 (mmp) REVERT: N 386 MET cc_start: 0.7618 (ppp) cc_final: 0.7134 (ppp) REVERT: N 408 LEU cc_start: 0.8891 (tp) cc_final: 0.8230 (mt) REVERT: N 412 TYR cc_start: 0.7230 (m-80) cc_final: 0.6644 (m-80) REVERT: N 450 ILE cc_start: 0.8625 (tt) cc_final: 0.8343 (tp) REVERT: N 513 ILE cc_start: 0.9563 (mt) cc_final: 0.9293 (mm) REVERT: N 580 ASN cc_start: 0.8434 (t0) cc_final: 0.8155 (t0) REVERT: N 679 ASN cc_start: 0.9279 (m-40) cc_final: 0.9065 (m-40) REVERT: N 707 ASN cc_start: 0.8515 (m-40) cc_final: 0.8040 (t0) REVERT: N 787 MET cc_start: 0.7351 (ppp) cc_final: 0.7099 (ppp) REVERT: S 40 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8440 (pt0) REVERT: S 47 THR cc_start: 0.8590 (t) cc_final: 0.8340 (t) REVERT: S 58 LYS cc_start: 0.4428 (mtmt) cc_final: 0.3836 (ttmt) REVERT: S 147 TRP cc_start: 0.7166 (t-100) cc_final: 0.6730 (m100) REVERT: S 214 MET cc_start: 0.7761 (tmm) cc_final: 0.7473 (tmm) REVERT: S 269 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8513 (mt-10) REVERT: S 280 ASN cc_start: 0.8388 (m-40) cc_final: 0.7664 (t0) REVERT: S 297 ILE cc_start: 0.8728 (mt) cc_final: 0.8501 (mt) REVERT: P 13 TYR cc_start: 0.8413 (m-10) cc_final: 0.7966 (t80) REVERT: P 42 LEU cc_start: 0.8874 (mt) cc_final: 0.8363 (tp) REVERT: P 98 GLN cc_start: 0.8740 (mt0) cc_final: 0.8419 (mt0) REVERT: P 135 GLU cc_start: 0.9028 (pm20) cc_final: 0.8685 (pm20) REVERT: P 173 MET cc_start: 0.8721 (ppp) cc_final: 0.8367 (ppp) REVERT: Q 95 LYS cc_start: 0.6666 (mptt) cc_final: 0.6354 (mptt) REVERT: Q 98 LYS cc_start: 0.9124 (tptp) cc_final: 0.8839 (tptp) REVERT: Q 210 CYS cc_start: 0.4878 (m) cc_final: 0.4400 (m) REVERT: Q 257 LYS cc_start: 0.7984 (pttm) cc_final: 0.7219 (pttt) REVERT: Q 335 PHE cc_start: 0.6535 (m-80) cc_final: 0.5927 (m-80) REVERT: Q 434 TYR cc_start: 0.8241 (m-80) cc_final: 0.6695 (m-80) REVERT: R 28 GLU cc_start: 0.8546 (pp20) cc_final: 0.7822 (pp20) REVERT: R 40 ILE cc_start: 0.6754 (pt) cc_final: 0.6502 (tp) REVERT: R 185 LEU cc_start: 0.8498 (mp) cc_final: 0.7847 (mt) REVERT: R 206 ARG cc_start: 0.8749 (mtt90) cc_final: 0.8334 (mtt-85) REVERT: R 213 TYR cc_start: 0.8918 (m-10) cc_final: 0.8520 (m-10) REVERT: R 287 GLN cc_start: 0.8743 (tt0) cc_final: 0.8409 (tt0) REVERT: R 319 CYS cc_start: 0.7950 (m) cc_final: 0.7500 (t) REVERT: R 320 LYS cc_start: 0.8631 (mmtt) cc_final: 0.8415 (mmtm) REVERT: R 333 MET cc_start: 0.8884 (mmm) cc_final: 0.8607 (mmm) REVERT: R 349 SER cc_start: 0.8612 (t) cc_final: 0.8131 (t) REVERT: R 353 MET cc_start: 0.6983 (pmm) cc_final: 0.5685 (pmm) REVERT: R 405 LYS cc_start: 0.8806 (mmmt) cc_final: 0.8360 (mmtt) REVERT: U 1 MET cc_start: 0.5661 (mtm) cc_final: 0.5144 (mtm) REVERT: U 7 LYS cc_start: 0.8357 (tptt) cc_final: 0.8135 (tptt) REVERT: U 17 SER cc_start: 0.9345 (m) cc_final: 0.9077 (t) REVERT: U 83 ILE cc_start: 0.9032 (mm) cc_final: 0.8737 (mm) REVERT: U 137 TYR cc_start: 0.7448 (m-80) cc_final: 0.7119 (m-80) REVERT: U 161 ILE cc_start: 0.9001 (mm) cc_final: 0.8613 (mm) REVERT: U 229 LEU cc_start: 0.9289 (mm) cc_final: 0.8927 (mm) REVERT: U 247 ILE cc_start: 0.9249 (tp) cc_final: 0.8852 (tp) REVERT: U 251 ASN cc_start: 0.9130 (m-40) cc_final: 0.8885 (m-40) REVERT: O 64 ASN cc_start: 0.9080 (m-40) cc_final: 0.8715 (m-40) REVERT: O 154 GLU cc_start: 0.9061 (tp30) cc_final: 0.8779 (tp30) REVERT: O 289 GLN cc_start: 0.8344 (tp-100) cc_final: 0.7635 (tp-100) REVERT: O 325 GLU cc_start: 0.7404 (tm-30) cc_final: 0.6888 (tm-30) REVERT: O 373 TRP cc_start: 0.8214 (t60) cc_final: 0.7765 (t60) outliers start: 1 outliers final: 1 residues processed: 912 average time/residue: 0.2493 time to fit residues: 377.7008 Evaluate side-chains 724 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 723 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 257 optimal weight: 20.0000 chunk 278 optimal weight: 20.0000 chunk 124 optimal weight: 0.0970 chunk 408 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 283 optimal weight: 8.9990 chunk 332 optimal weight: 9.9990 chunk 122 optimal weight: 30.0000 chunk 144 optimal weight: 30.0000 chunk 464 optimal weight: 10.0000 overall best weight: 6.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 220 GLN T 48 ASN ** T 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 123 HIS Z 26 ASN ** Z 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 243 GLN ** Z 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 256 GLN N 375 HIS ** N 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 115 GLN U 230 GLN U 260 ASN ** U 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 282 GLN O 318 HIS ** O 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.153529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.127271 restraints weight = 169707.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.129174 restraints weight = 124996.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.130269 restraints weight = 93723.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.131744 restraints weight = 77087.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.132432 restraints weight = 64586.665| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.9762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 41662 Z= 0.211 Angle : 0.783 10.644 56279 Z= 0.414 Chirality : 0.045 0.290 6447 Planarity : 0.005 0.113 7202 Dihedral : 5.756 51.541 5504 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.97 % Favored : 93.75 % Rotamer: Outliers : 0.02 % Allowed : 0.52 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.01 (0.11), residues: 5108 helix: -0.06 (0.09), residues: 3350 sheet: -1.07 (0.33), residues: 216 loop : -1.78 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 58 TYR 0.033 0.003 TYR V 251 PHE 0.054 0.003 PHE Q 335 TRP 0.032 0.003 TRP S 54 HIS 0.013 0.002 HIS P 425 Details of bonding type rmsd covalent geometry : bond 0.00446 (41662) covalent geometry : angle 0.78318 (56279) hydrogen bonds : bond 0.04758 ( 2182) hydrogen bonds : angle 5.22660 ( 6453) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 888 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 92 GLN cc_start: 0.8704 (mp10) cc_final: 0.8273 (mp10) REVERT: V 50 MET cc_start: 0.8327 (mmm) cc_final: 0.7902 (tpp) REVERT: V 53 MET cc_start: 0.7676 (mtm) cc_final: 0.7250 (mtm) REVERT: V 73 GLN cc_start: 0.8428 (pp30) cc_final: 0.8196 (pp30) REVERT: V 92 MET cc_start: 0.8885 (mpp) cc_final: 0.8464 (mpp) REVERT: V 157 ARG cc_start: 0.8729 (ttt180) cc_final: 0.8507 (tpt-90) REVERT: V 235 GLU cc_start: 0.9092 (tm-30) cc_final: 0.8819 (tm-30) REVERT: V 251 TYR cc_start: 0.9040 (t80) cc_final: 0.8784 (t80) REVERT: V 279 HIS cc_start: 0.8541 (m90) cc_final: 0.8339 (m-70) REVERT: V 285 ASP cc_start: 0.8658 (t70) cc_final: 0.7608 (t70) REVERT: V 289 GLU cc_start: 0.8564 (pt0) cc_final: 0.8036 (pt0) REVERT: T 61 ILE cc_start: 0.7684 (mm) cc_final: 0.7447 (tt) REVERT: T 127 GLN cc_start: 0.4998 (tp40) cc_final: 0.4613 (tm-30) REVERT: T 153 MET cc_start: 0.4496 (mpp) cc_final: 0.4140 (mpp) REVERT: T 158 GLN cc_start: 0.8621 (pp30) cc_final: 0.8112 (tp40) REVERT: T 161 TRP cc_start: 0.7737 (t60) cc_final: 0.6933 (t60) REVERT: T 162 ASP cc_start: 0.8372 (m-30) cc_final: 0.8077 (m-30) REVERT: T 262 LYS cc_start: 0.9154 (ptpp) cc_final: 0.8945 (ptpp) REVERT: Z 9 GLN cc_start: 0.3929 (mm110) cc_final: 0.3035 (tp-100) REVERT: Z 428 TRP cc_start: 0.2163 (t60) cc_final: 0.0976 (m100) REVERT: Z 775 MET cc_start: 0.4687 (tmm) cc_final: 0.4466 (tmm) REVERT: Z 776 VAL cc_start: 0.7082 (m) cc_final: 0.6785 (m) REVERT: N 46 ILE cc_start: 0.4602 (mt) cc_final: 0.4357 (mt) REVERT: N 89 PHE cc_start: 0.8118 (t80) cc_final: 0.7564 (t80) REVERT: N 166 ILE cc_start: 0.7365 (mm) cc_final: 0.7029 (mm) REVERT: N 210 SER cc_start: 0.7957 (t) cc_final: 0.7655 (p) REVERT: N 271 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8227 (mm-30) REVERT: N 339 MET cc_start: 0.6019 (mmm) cc_final: 0.5356 (mmp) REVERT: N 386 MET cc_start: 0.7676 (ppp) cc_final: 0.7153 (ppp) REVERT: N 408 LEU cc_start: 0.8884 (tp) cc_final: 0.8212 (mt) REVERT: N 412 TYR cc_start: 0.7235 (m-80) cc_final: 0.6695 (m-80) REVERT: N 707 ASN cc_start: 0.8368 (m-40) cc_final: 0.8027 (t0) REVERT: N 735 MET cc_start: 0.8182 (mmp) cc_final: 0.7933 (mmp) REVERT: N 773 MET cc_start: 0.6687 (tpp) cc_final: 0.6111 (tpp) REVERT: N 787 MET cc_start: 0.7309 (ppp) cc_final: 0.6938 (ppp) REVERT: S 147 TRP cc_start: 0.7173 (t-100) cc_final: 0.6738 (m100) REVERT: S 214 MET cc_start: 0.7587 (tmm) cc_final: 0.7287 (tmm) REVERT: S 269 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8591 (mt-10) REVERT: P 13 TYR cc_start: 0.8446 (m-10) cc_final: 0.7974 (t80) REVERT: P 42 LEU cc_start: 0.8890 (mt) cc_final: 0.8413 (tp) REVERT: P 98 GLN cc_start: 0.8738 (mt0) cc_final: 0.8498 (mt0) REVERT: P 135 GLU cc_start: 0.9008 (pm20) cc_final: 0.8785 (pm20) REVERT: P 173 MET cc_start: 0.8645 (ppp) cc_final: 0.8315 (ppp) REVERT: P 356 TYR cc_start: 0.6171 (m-80) cc_final: 0.5239 (m-80) REVERT: Q 68 MET cc_start: 0.1755 (ptt) cc_final: 0.1445 (ptt) REVERT: Q 95 LYS cc_start: 0.6697 (mptt) cc_final: 0.6346 (mptt) REVERT: Q 98 LYS cc_start: 0.9189 (tptp) cc_final: 0.8872 (tptp) REVERT: Q 210 CYS cc_start: 0.4932 (m) cc_final: 0.4449 (m) REVERT: Q 257 LYS cc_start: 0.8024 (pttm) cc_final: 0.7297 (pttt) REVERT: R 40 ILE cc_start: 0.6862 (pt) cc_final: 0.6581 (tp) REVERT: R 192 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8882 (mm-30) REVERT: R 213 TYR cc_start: 0.8939 (m-10) cc_final: 0.8585 (m-10) REVERT: R 272 ASP cc_start: 0.9017 (m-30) cc_final: 0.8815 (m-30) REVERT: R 319 CYS cc_start: 0.8130 (m) cc_final: 0.7782 (t) REVERT: R 320 LYS cc_start: 0.8686 (mmtt) cc_final: 0.8445 (mmtm) REVERT: R 333 MET cc_start: 0.8940 (mmm) cc_final: 0.8715 (mmm) REVERT: R 349 SER cc_start: 0.8582 (t) cc_final: 0.8045 (t) REVERT: R 353 MET cc_start: 0.6865 (pmm) cc_final: 0.6076 (pmm) REVERT: R 405 LYS cc_start: 0.8823 (mmmt) cc_final: 0.8280 (mmtt) REVERT: R 408 ASP cc_start: 0.8153 (t70) cc_final: 0.7927 (t70) REVERT: U 17 SER cc_start: 0.9340 (m) cc_final: 0.9075 (t) REVERT: U 74 GLU cc_start: 0.8071 (mp0) cc_final: 0.7762 (pm20) REVERT: U 135 ASP cc_start: 0.7397 (m-30) cc_final: 0.7075 (m-30) REVERT: U 137 TYR cc_start: 0.7442 (m-80) cc_final: 0.7067 (m-80) REVERT: U 174 LEU cc_start: 0.9244 (mt) cc_final: 0.8987 (pp) REVERT: U 229 LEU cc_start: 0.9314 (mm) cc_final: 0.8963 (mm) REVERT: U 247 ILE cc_start: 0.9264 (tp) cc_final: 0.8866 (tp) REVERT: U 251 ASN cc_start: 0.9128 (m-40) cc_final: 0.8902 (m-40) REVERT: U 261 LEU cc_start: 0.9268 (mp) cc_final: 0.9044 (mp) REVERT: U 268 LYS cc_start: 0.8516 (tppt) cc_final: 0.8016 (tppt) REVERT: O 64 ASN cc_start: 0.8980 (m-40) cc_final: 0.8639 (m110) REVERT: O 154 GLU cc_start: 0.9158 (tp30) cc_final: 0.8902 (tp30) REVERT: O 289 GLN cc_start: 0.8280 (tp-100) cc_final: 0.7621 (tp-100) REVERT: O 373 TRP cc_start: 0.8162 (t60) cc_final: 0.7857 (t60) outliers start: 1 outliers final: 1 residues processed: 889 average time/residue: 0.2557 time to fit residues: 377.7387 Evaluate side-chains 728 residues out of total 4574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 727 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 229 optimal weight: 9.9990 chunk 247 optimal weight: 4.9990 chunk 104 optimal weight: 40.0000 chunk 312 optimal weight: 20.0000 chunk 439 optimal weight: 3.9990 chunk 383 optimal weight: 8.9990 chunk 498 optimal weight: 9.9990 chunk 474 optimal weight: 0.1980 chunk 261 optimal weight: 0.0570 chunk 211 optimal weight: 6.9990 chunk 492 optimal weight: 3.9990 overall best weight: 2.6504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 12 ASN V 64 ASN ** V 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 26 ASN Z 156 HIS Z 243 GLN ** Z 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 256 GLN ** N 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 525 ASN ** N 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 177 ASN ** S 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 323 ASN U 115 GLN U 117 ASN U 230 GLN U 256 ASN U 260 ASN ** U 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 282 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.157377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.130836 restraints weight = 167234.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.132893 restraints weight = 125434.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.134300 restraints weight = 94205.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.134686 restraints weight = 76772.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.136118 restraints weight = 69738.629| |-----------------------------------------------------------------------------| r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.9817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 41662 Z= 0.145 Angle : 0.717 11.318 56279 Z= 0.376 Chirality : 0.043 0.290 6447 Planarity : 0.004 0.064 7202 Dihedral : 5.514 53.998 5504 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.01 % Favored : 94.71 % Rotamer: Outliers : 0.07 % Allowed : 0.33 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.76 (0.11), residues: 5108 helix: 0.13 (0.09), residues: 3337 sheet: -0.99 (0.33), residues: 223 loop : -1.65 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG P 395 TYR 0.034 0.002 TYR O 98 PHE 0.042 0.002 PHE Q 335 TRP 0.028 0.002 TRP N 742 HIS 0.017 0.001 HIS P 425 Details of bonding type rmsd covalent geometry : bond 0.00312 (41662) covalent geometry : angle 0.71712 (56279) hydrogen bonds : bond 0.04335 ( 2182) hydrogen bonds : angle 4.97339 ( 6453) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10488.68 seconds wall clock time: 180 minutes 52.30 seconds (10852.30 seconds total)