Starting phenix.real_space_refine on Thu Jul 31 03:06:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6o5b_0626/07_2025/6o5b_0626.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o5b_0626/07_2025/6o5b_0626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6o5b_0626/07_2025/6o5b_0626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o5b_0626/07_2025/6o5b_0626.map" model { file = "/net/cci-nas-00/data/ceres_data/6o5b_0626/07_2025/6o5b_0626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o5b_0626/07_2025/6o5b_0626.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 40 5.16 5 C 8472 2.51 5 N 2279 2.21 5 O 2377 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13169 Number of models: 1 Model: "" Number of chains: 13 Chain: "J" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 723 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 6, 'TRANS': 84} Chain: "K" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 723 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 6, 'TRANS': 84} Chain: "E" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2226 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain: "F" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "C" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2211 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain: "D" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "A" Number of atoms: 2254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2254 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "B" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "L" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 723 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 6, 'TRANS': 84} Chain: "I" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 723 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 6, 'TRANS': 84} Chain: "G" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2069 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 9, 'TRANS': 240} Chain breaks: 1 Chain: "H" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 373 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.20, per 1000 atoms: 0.62 Number of scatterers: 13169 At special positions: 0 Unit cell: (103.32, 150.36, 136.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 40 16.00 O 2377 8.00 N 2279 7.00 C 8472 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: 2.72 Conformation dependent library (CDL) restraints added in 1.6 seconds 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 17 sheets defined 53.8% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'J' and resid 107 through 112 Processing helix chain 'J' and resid 140 through 147 removed outlier: 4.519A pdb=" N ASP J 147 " --> pdb=" O LEU J 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 119 removed outlier: 3.675A pdb=" N ARG K 113 " --> pdb=" O GLY K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 145 Processing helix chain 'E' and resid 107 through 119 removed outlier: 3.822A pdb=" N ARG E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 144 Processing helix chain 'E' and resid 169 through 190 removed outlier: 4.643A pdb=" N LEU E 176 " --> pdb=" O ASN E 172 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU E 182 " --> pdb=" O ASP E 178 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU E 190 " --> pdb=" O LEU E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 253 removed outlier: 3.733A pdb=" N GLU E 200 " --> pdb=" O GLN E 196 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU E 208 " --> pdb=" O ILE E 204 " (cutoff:3.500A) Proline residue: E 216 - end of helix removed outlier: 4.317A pdb=" N LYS E 219 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL E 220 " --> pdb=" O PRO E 216 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE E 224 " --> pdb=" O VAL E 220 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE E 247 " --> pdb=" O MET E 243 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE E 249 " --> pdb=" O THR E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 285 removed outlier: 3.986A pdb=" N THR E 267 " --> pdb=" O MET E 263 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR E 268 " --> pdb=" O GLU E 264 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA E 275 " --> pdb=" O THR E 271 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR E 279 " --> pdb=" O ALA E 275 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE E 282 " --> pdb=" O MET E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 310 removed outlier: 3.912A pdb=" N ARG E 297 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLN E 298 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS E 309 " --> pdb=" O LYS E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 328 removed outlier: 3.662A pdb=" N TYR E 317 " --> pdb=" O ASP E 313 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU E 320 " --> pdb=" O LYS E 316 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA E 325 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN E 326 " --> pdb=" O ASP E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 335 Processing helix chain 'F' and resid 65 through 96 removed outlier: 3.732A pdb=" N PHE F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE F 73 " --> pdb=" O ARG F 69 " (cutoff:3.500A) Proline residue: F 76 - end of helix removed outlier: 4.103A pdb=" N SER F 85 " --> pdb=" O GLY F 81 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN F 87 " --> pdb=" O LEU F 83 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N PHE F 88 " --> pdb=" O ILE F 84 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA F 89 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA F 90 " --> pdb=" O LYS F 86 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU F 91 " --> pdb=" O ASN F 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 94 removed outlier: 3.550A pdb=" N ARG C 94 " --> pdb=" O PRO C 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 91 through 94' Processing helix chain 'C' and resid 107 through 119 removed outlier: 3.691A pdb=" N PHE C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU C 118 " --> pdb=" O GLN C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 178 through 190 removed outlier: 3.537A pdb=" N THR C 188 " --> pdb=" O GLN C 184 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 214 removed outlier: 3.503A pdb=" N HIS C 195 " --> pdb=" O CYS C 191 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE C 204 " --> pdb=" O GLU C 200 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 257 removed outlier: 3.661A pdb=" N ARG C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU C 223 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS C 230 " --> pdb=" O ARG C 226 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU C 250 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TRP C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TRP C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 284 removed outlier: 4.235A pdb=" N VAL C 266 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA C 275 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE C 282 " --> pdb=" O MET C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 311 removed outlier: 3.682A pdb=" N LYS C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER C 310 " --> pdb=" O GLY C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 335 removed outlier: 3.799A pdb=" N ASN C 318 " --> pdb=" O LEU C 314 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP C 322 " --> pdb=" O ASN C 318 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA C 323 " --> pdb=" O GLN C 319 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN C 326 " --> pdb=" O ASP C 322 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET C 329 " --> pdb=" O ALA C 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 96 removed outlier: 3.947A pdb=" N ARG D 69 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE D 75 " --> pdb=" O PHE D 71 " (cutoff:3.500A) Proline residue: D 76 - end of helix removed outlier: 3.643A pdb=" N SER D 85 " --> pdb=" O GLY D 81 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE D 88 " --> pdb=" O ILE D 84 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU D 91 " --> pdb=" O ASN D 87 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLU D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP D 96 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 118 removed outlier: 3.607A pdb=" N ARG A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 145 removed outlier: 3.601A pdb=" N LEU A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 174 removed outlier: 3.591A pdb=" N ALA A 174 " --> pdb=" O GLU A 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 171 through 174' Processing helix chain 'A' and resid 175 through 192 removed outlier: 3.827A pdb=" N THR A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 192 " --> pdb=" O THR A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 215 removed outlier: 3.908A pdb=" N LEU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 226 removed outlier: 3.898A pdb=" N ARG A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 256 removed outlier: 3.634A pdb=" N THR A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU A 250 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 253 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 285 removed outlier: 3.699A pdb=" N THR A 267 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 282 " --> pdb=" O MET A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 310 removed outlier: 3.796A pdb=" N ARG A 295 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 340 removed outlier: 3.653A pdb=" N ALA A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Proline residue: A 337 - end of helix Processing helix chain 'B' and resid 66 through 71 removed outlier: 3.657A pdb=" N PHE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 96 removed outlier: 4.057A pdb=" N PHE B 77 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 119 removed outlier: 3.701A pdb=" N GLN L 116 " --> pdb=" O LEU L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 145 Processing helix chain 'I' and resid 107 through 117 removed outlier: 3.571A pdb=" N PHE I 111 " --> pdb=" O SER I 107 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU I 115 " --> pdb=" O PHE I 111 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN I 116 " --> pdb=" O LEU I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 144 Processing helix chain 'G' and resid 107 through 117 removed outlier: 3.549A pdb=" N PHE G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 145 Processing helix chain 'G' and resid 179 through 189 Processing helix chain 'G' and resid 192 through 257 removed outlier: 4.001A pdb=" N LEU G 197 " --> pdb=" O GLU G 193 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG G 201 " --> pdb=" O LEU G 197 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU G 202 " --> pdb=" O ASN G 198 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS G 211 " --> pdb=" O LEU G 207 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA G 215 " --> pdb=" O LYS G 211 " (cutoff:3.500A) Proline residue: G 216 - end of helix removed outlier: 4.196A pdb=" N VAL G 220 " --> pdb=" O PRO G 216 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU G 223 " --> pdb=" O LYS G 219 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL G 235 " --> pdb=" O ARG G 231 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY G 238 " --> pdb=" O LEU G 234 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE G 247 " --> pdb=" O MET G 243 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY G 248 " --> pdb=" O ALA G 244 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU G 253 " --> pdb=" O ILE G 249 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR G 254 " --> pdb=" O LEU G 250 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP G 255 " --> pdb=" O ALA G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 262 Processing helix chain 'G' and resid 263 through 286 removed outlier: 3.901A pdb=" N THR G 271 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET G 278 " --> pdb=" O SER G 274 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE G 282 " --> pdb=" O MET G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 305 removed outlier: 3.551A pdb=" N ARG G 295 " --> pdb=" O TYR G 291 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP G 296 " --> pdb=" O PRO G 292 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU G 300 " --> pdb=" O ASP G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 310 removed outlier: 3.673A pdb=" N LYS G 309 " --> pdb=" O LYS G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 334 removed outlier: 3.787A pdb=" N GLN G 319 " --> pdb=" O GLU G 315 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP G 322 " --> pdb=" O ASN G 318 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA G 325 " --> pdb=" O LYS G 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 75 removed outlier: 3.783A pdb=" N ARG H 69 " --> pdb=" O PHE H 65 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE H 73 " --> pdb=" O ARG H 69 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL H 74 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE H 75 " --> pdb=" O PHE H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 93 removed outlier: 3.661A pdb=" N GLY H 81 " --> pdb=" O PHE H 77 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE H 84 " --> pdb=" O VAL H 80 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER H 85 " --> pdb=" O GLY H 81 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS H 86 " --> pdb=" O THR H 82 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU H 91 " --> pdb=" O ASN H 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 76 through 80 Processing sheet with id=AA2, first strand: chain 'J' and resid 125 through 128 removed outlier: 3.610A pdb=" N PHE J 149 " --> pdb=" O VAL J 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 134 through 135 removed outlier: 6.427A pdb=" N ARG J 134 " --> pdb=" O GLN I 98 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU I 95 " --> pdb=" O LEU I 90 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU I 90 " --> pdb=" O GLU I 95 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL I 78 " --> pdb=" O VAL I 85 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR I 76 " --> pdb=" O SER I 87 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 76 through 80 Processing sheet with id=AA5, first strand: chain 'K' and resid 126 through 128 removed outlier: 3.674A pdb=" N PHE K 149 " --> pdb=" O VAL K 160 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL K 160 " --> pdb=" O PHE K 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 76 through 80 removed outlier: 3.910A pdb=" N ARG G 134 " --> pdb=" O ARG E 96 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 125 through 127 Processing sheet with id=AA8, first strand: chain 'E' and resid 134 through 135 removed outlier: 6.569A pdb=" N ARG E 134 " --> pdb=" O GLN C 98 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N THR C 100 " --> pdb=" O ARG E 134 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 125 through 128 removed outlier: 3.578A pdb=" N ILE C 153 " --> pdb=" O LEU C 156 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 134 through 135 removed outlier: 3.784A pdb=" N THR A 76 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 126 through 128 Processing sheet with id=AB3, first strand: chain 'L' and resid 78 through 80 removed outlier: 3.533A pdb=" N VAL L 78 " --> pdb=" O VAL L 85 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 87 through 90 removed outlier: 3.664A pdb=" N GLU L 95 " --> pdb=" O LEU L 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 125 through 128 Processing sheet with id=AB6, first strand: chain 'I' and resid 126 through 128 removed outlier: 3.556A pdb=" N ALA I 126 " --> pdb=" O VAL I 152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 86 through 88 removed outlier: 3.707A pdb=" N ILE G 86 " --> pdb=" O PHE G 99 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 125 through 128 644 hydrogen bonds defined for protein. 1830 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: 3.58 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4172 1.34 - 1.46: 2547 1.46 - 1.58: 6639 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 13426 Sorted by residual: bond pdb=" N ILE J 153 " pdb=" CA ILE J 153 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.29e-02 6.01e+03 7.22e+00 bond pdb=" N ILE C 153 " pdb=" CA ILE C 153 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.24e-02 6.50e+03 7.09e+00 bond pdb=" CA PRO C 162 " pdb=" C PRO C 162 " ideal model delta sigma weight residual 1.517 1.539 -0.022 9.30e-03 1.16e+04 5.78e+00 bond pdb=" N LEU G 101 " pdb=" CA LEU G 101 " ideal model delta sigma weight residual 1.457 1.485 -0.029 1.24e-02 6.50e+03 5.39e+00 bond pdb=" N ILE E 153 " pdb=" CA ILE E 153 " ideal model delta sigma weight residual 1.460 1.492 -0.033 1.42e-02 4.96e+03 5.25e+00 ... (remaining 13421 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 17513 2.52 - 5.04: 529 5.04 - 7.56: 111 7.56 - 10.08: 35 10.08 - 12.61: 2 Bond angle restraints: 18190 Sorted by residual: angle pdb=" C ARG C 161 " pdb=" N PRO C 162 " pdb=" CA PRO C 162 " ideal model delta sigma weight residual 120.38 129.92 -9.54 1.03e+00 9.43e-01 8.58e+01 angle pdb=" N ASP J 155 " pdb=" CA ASP J 155 " pdb=" C ASP J 155 " ideal model delta sigma weight residual 113.16 123.39 -10.23 1.24e+00 6.50e-01 6.81e+01 angle pdb=" N ILE B 49 " pdb=" CA ILE B 49 " pdb=" C ILE B 49 " ideal model delta sigma weight residual 113.71 107.23 6.48 9.50e-01 1.11e+00 4.65e+01 angle pdb=" N ILE H 49 " pdb=" CA ILE H 49 " pdb=" C ILE H 49 " ideal model delta sigma weight residual 112.96 106.70 6.26 1.00e+00 1.00e+00 3.92e+01 angle pdb=" N ASP C 155 " pdb=" CA ASP C 155 " pdb=" C ASP C 155 " ideal model delta sigma weight residual 112.90 119.73 -6.83 1.31e+00 5.83e-01 2.72e+01 ... (remaining 18185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.25: 7617 15.25 - 30.51: 434 30.51 - 45.76: 126 45.76 - 61.02: 6 61.02 - 76.27: 11 Dihedral angle restraints: 8194 sinusoidal: 3419 harmonic: 4775 Sorted by residual: dihedral pdb=" CA MET B 63 " pdb=" C MET B 63 " pdb=" N SER B 64 " pdb=" CA SER B 64 " ideal model delta harmonic sigma weight residual 180.00 150.54 29.46 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ILE G 153 " pdb=" C ILE G 153 " pdb=" N ASN G 154 " pdb=" CA ASN G 154 " ideal model delta harmonic sigma weight residual 180.00 -151.81 -28.19 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA LEU C 253 " pdb=" C LEU C 253 " pdb=" N THR C 254 " pdb=" CA THR C 254 " ideal model delta harmonic sigma weight residual 180.00 -152.60 -27.40 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 8191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1505 0.062 - 0.125: 465 0.125 - 0.187: 97 0.187 - 0.249: 23 0.249 - 0.311: 3 Chirality restraints: 2093 Sorted by residual: chirality pdb=" CA ASP J 155 " pdb=" N ASP J 155 " pdb=" C ASP J 155 " pdb=" CB ASP J 155 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CB ILE E 122 " pdb=" CA ILE E 122 " pdb=" CG1 ILE E 122 " pdb=" CG2 ILE E 122 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CB THR D 82 " pdb=" CA THR D 82 " pdb=" OG1 THR D 82 " pdb=" CG2 THR D 82 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 2090 not shown) Planarity restraints: 2309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 161 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.31e+00 pdb=" C ARG C 161 " 0.053 2.00e-02 2.50e+03 pdb=" O ARG C 161 " -0.020 2.00e-02 2.50e+03 pdb=" N PRO C 162 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS G 102 " 0.048 5.00e-02 4.00e+02 7.23e-02 8.37e+00 pdb=" N PRO G 103 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO G 103 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 103 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 90 " 0.042 5.00e-02 4.00e+02 6.38e-02 6.51e+00 pdb=" N PRO J 91 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO J 91 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO J 91 " 0.035 5.00e-02 4.00e+02 ... (remaining 2306 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3811 2.83 - 3.34: 11556 3.34 - 3.86: 20186 3.86 - 4.38: 22074 4.38 - 4.90: 38001 Nonbonded interactions: 95628 Sorted by model distance: nonbonded pdb=" O GLN E 185 " pdb=" OG1 THR E 189 " model vdw 2.307 3.040 nonbonded pdb=" NH1 ARG E 221 " pdb=" OH TYR E 317 " model vdw 2.378 3.120 nonbonded pdb=" OG SER E 138 " pdb=" NE2 GLN C 114 " model vdw 2.387 3.120 nonbonded pdb=" O TYR G 281 " pdb=" OG1 THR G 285 " model vdw 2.393 3.040 nonbonded pdb=" OE1 GLN C 196 " pdb=" NE2 GLN G 184 " model vdw 2.398 3.120 ... (remaining 95623 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 75 through 164 or resid 177 through 336)) selection = (chain 'C' and (resid 75 through 164 or resid 177 through 336)) selection = (chain 'E' and (resid 75 through 164 or resid 177 through 336)) selection = (chain 'G' and resid 75 through 336) } ncs_group { reference = (chain 'B' and resid 48 through 95) selection = (chain 'D' and resid 48 through 95) selection = (chain 'F' and resid 48 through 95) selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 1.590 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: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 29.940 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 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:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 13426 Z= 0.288 Angle : 1.128 12.605 18190 Z= 0.614 Chirality : 0.064 0.311 2093 Planarity : 0.007 0.072 2309 Dihedral : 11.132 76.271 5098 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.41 % Allowed : 6.26 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.17), residues: 1594 helix: -2.99 (0.12), residues: 840 sheet: -0.94 (0.37), residues: 175 loop : -2.80 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP E 255 HIS 0.008 0.002 HIS H 95 PHE 0.030 0.003 PHE I 149 TYR 0.027 0.002 TYR G 79 ARG 0.013 0.001 ARG C 297 Details of bonding type rmsd hydrogen bonds : bond 0.15037 ( 644) hydrogen bonds : angle 6.44168 ( 1830) covalent geometry : bond 0.00655 (13426) covalent geometry : angle 1.12833 (18190) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 335 time to evaluate : 1.450 Fit side-chains REVERT: J 105 SER cc_start: 0.6994 (p) cc_final: 0.6772 (p) REVERT: J 133 VAL cc_start: 0.8541 (m) cc_final: 0.8329 (m) REVERT: E 104 ILE cc_start: 0.7994 (pt) cc_final: 0.7638 (mp) REVERT: E 243 MET cc_start: 0.8082 (tpt) cc_final: 0.7788 (tpp) REVERT: C 148 ASP cc_start: 0.8022 (p0) cc_final: 0.7746 (m-30) REVERT: A 161 ARG cc_start: 0.7858 (ppp80) cc_final: 0.7604 (mtt90) REVERT: A 165 ARG cc_start: 0.7133 (tpt170) cc_final: 0.6830 (mtm-85) REVERT: A 177 ASN cc_start: 0.8106 (t160) cc_final: 0.7588 (p0) REVERT: A 278 MET cc_start: 0.8349 (mtt) cc_final: 0.8116 (mtm) REVERT: B 83 LEU cc_start: 0.8030 (tp) cc_final: 0.7695 (mp) REVERT: L 115 LEU cc_start: 0.6485 (mt) cc_final: 0.6272 (mp) REVERT: I 120 ARG cc_start: 0.7935 (pmm150) cc_final: 0.7539 (mtt90) outliers start: 6 outliers final: 1 residues processed: 340 average time/residue: 0.3276 time to fit residues: 147.1263 Evaluate side-chains 173 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 142 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 116 GLN E 159 HIS E 184 GLN E 194 GLN F 95 HIS C 81 ASN C 114 GLN A 98 GLN A 177 ASN ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 196 GLN H 95 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.111685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.099405 restraints weight = 34745.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.101137 restraints weight = 19144.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.102286 restraints weight = 12535.929| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13426 Z= 0.141 Angle : 0.670 8.535 18190 Z= 0.344 Chirality : 0.045 0.172 2093 Planarity : 0.005 0.060 2309 Dihedral : 5.641 25.187 1812 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.68 % Allowed : 13.34 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.20), residues: 1594 helix: -1.28 (0.16), residues: 845 sheet: -0.39 (0.39), residues: 165 loop : -2.26 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 255 HIS 0.007 0.001 HIS H 95 PHE 0.024 0.002 PHE L 111 TYR 0.015 0.001 TYR K 79 ARG 0.006 0.000 ARG C 96 Details of bonding type rmsd hydrogen bonds : bond 0.04633 ( 644) hydrogen bonds : angle 4.67226 ( 1830) covalent geometry : bond 0.00315 (13426) covalent geometry : angle 0.67027 (18190) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 194 time to evaluate : 1.406 Fit side-chains REVERT: J 164 LYS cc_start: 0.2250 (mttp) cc_final: 0.1720 (mtpt) REVERT: E 104 ILE cc_start: 0.7970 (pt) cc_final: 0.7645 (mp) REVERT: C 164 LYS cc_start: 0.7702 (pmtt) cc_final: 0.6967 (ptmm) REVERT: C 278 MET cc_start: 0.8383 (mtm) cc_final: 0.8183 (mtp) REVERT: A 165 ARG cc_start: 0.7037 (tpt170) cc_final: 0.6795 (mtm-85) REVERT: A 177 ASN cc_start: 0.8021 (t0) cc_final: 0.7569 (p0) REVERT: B 83 LEU cc_start: 0.8090 (tp) cc_final: 0.7820 (mp) REVERT: L 122 ILE cc_start: 0.4686 (OUTLIER) cc_final: 0.4353 (tt) REVERT: L 158 TYR cc_start: 0.5632 (m-80) cc_final: 0.5357 (m-80) REVERT: I 120 ARG cc_start: 0.7864 (pmm150) cc_final: 0.7412 (mtt90) outliers start: 39 outliers final: 20 residues processed: 225 average time/residue: 0.2571 time to fit residues: 82.4761 Evaluate side-chains 173 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 290 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 99 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 116 GLN ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.108336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.095877 restraints weight = 35881.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.097580 restraints weight = 20075.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.098730 restraints weight = 13285.311| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 13426 Z= 0.208 Angle : 0.714 9.445 18190 Z= 0.359 Chirality : 0.047 0.214 2093 Planarity : 0.006 0.081 2309 Dihedral : 5.551 25.880 1812 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 4.75 % Allowed : 13.76 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.21), residues: 1594 helix: -0.64 (0.18), residues: 847 sheet: -0.02 (0.40), residues: 162 loop : -2.09 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 255 HIS 0.006 0.001 HIS E 304 PHE 0.019 0.002 PHE L 111 TYR 0.018 0.002 TYR C 258 ARG 0.007 0.001 ARG J 161 Details of bonding type rmsd hydrogen bonds : bond 0.04694 ( 644) hydrogen bonds : angle 4.59310 ( 1830) covalent geometry : bond 0.00494 (13426) covalent geometry : angle 0.71406 (18190) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 156 time to evaluate : 1.593 Fit side-chains revert: symmetry clash REVERT: J 118 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7298 (tp30) REVERT: E 104 ILE cc_start: 0.8090 (pt) cc_final: 0.7766 (mp) REVERT: E 284 MET cc_start: 0.7504 (tpp) cc_final: 0.7036 (mtt) REVERT: E 339 GLN cc_start: 0.7158 (OUTLIER) cc_final: 0.6922 (tm-30) REVERT: F 91 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7148 (pp) REVERT: C 164 LYS cc_start: 0.7873 (pmtt) cc_final: 0.7017 (ptmm) REVERT: A 165 ARG cc_start: 0.7172 (tpt170) cc_final: 0.6800 (mtm-85) REVERT: A 177 ASN cc_start: 0.8046 (t0) cc_final: 0.7526 (p0) REVERT: A 242 TYR cc_start: 0.7865 (t80) cc_final: 0.7647 (t80) REVERT: A 263 MET cc_start: 0.6987 (mmm) cc_final: 0.6784 (tpp) REVERT: B 83 LEU cc_start: 0.8153 (tp) cc_final: 0.7942 (mp) REVERT: L 158 TYR cc_start: 0.5608 (m-80) cc_final: 0.5307 (m-80) REVERT: I 120 ARG cc_start: 0.7932 (pmm150) cc_final: 0.7433 (mtt90) REVERT: G 120 ARG cc_start: 0.7524 (mmt180) cc_final: 0.7318 (mmp80) outliers start: 69 outliers final: 35 residues processed: 206 average time/residue: 0.2603 time to fit residues: 78.9861 Evaluate side-chains 181 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 339 GLN Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 84 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 72 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 138 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 143 optimal weight: 8.9990 chunk 152 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.110821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.098535 restraints weight = 34729.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.100263 restraints weight = 19322.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.101411 restraints weight = 12709.056| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13426 Z= 0.126 Angle : 0.630 9.779 18190 Z= 0.313 Chirality : 0.044 0.267 2093 Planarity : 0.005 0.060 2309 Dihedral : 5.031 23.713 1811 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.58 % Allowed : 16.16 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.21), residues: 1594 helix: -0.12 (0.18), residues: 851 sheet: 0.18 (0.40), residues: 166 loop : -1.87 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 256 HIS 0.006 0.001 HIS C 159 PHE 0.022 0.001 PHE L 111 TYR 0.016 0.001 TYR C 268 ARG 0.006 0.000 ARG J 161 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 644) hydrogen bonds : angle 4.21564 ( 1830) covalent geometry : bond 0.00283 (13426) covalent geometry : angle 0.63015 (18190) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 167 time to evaluate : 1.431 Fit side-chains revert: symmetry clash REVERT: J 118 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7395 (tp30) REVERT: J 164 LYS cc_start: 0.2573 (mttp) cc_final: 0.1732 (mtpt) REVERT: E 104 ILE cc_start: 0.8065 (pt) cc_final: 0.7740 (mp) REVERT: E 182 LEU cc_start: 0.8319 (tp) cc_final: 0.8100 (mt) REVERT: E 284 MET cc_start: 0.7383 (tpp) cc_final: 0.7060 (mtt) REVERT: E 339 GLN cc_start: 0.7009 (OUTLIER) cc_final: 0.6804 (tp40) REVERT: F 91 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.7117 (pp) REVERT: C 164 LYS cc_start: 0.7763 (pmtt) cc_final: 0.7032 (ptmm) REVERT: A 165 ARG cc_start: 0.7109 (tpt170) cc_final: 0.6803 (mtm-85) REVERT: A 177 ASN cc_start: 0.7913 (t0) cc_final: 0.7426 (p0) REVERT: B 83 LEU cc_start: 0.8134 (tp) cc_final: 0.7914 (mp) REVERT: I 120 ARG cc_start: 0.7970 (pmm150) cc_final: 0.7402 (mtt90) REVERT: G 153 ILE cc_start: 0.5650 (OUTLIER) cc_final: 0.5387 (mt) outliers start: 52 outliers final: 31 residues processed: 201 average time/residue: 0.2460 time to fit residues: 71.8052 Evaluate side-chains 185 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 339 GLN Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 107 SER Chi-restraints excluded: chain L residue 153 ILE Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 84 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 16 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 172 ASN ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.109719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.097407 restraints weight = 35374.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.099124 restraints weight = 19700.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.100264 restraints weight = 12915.377| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13426 Z= 0.154 Angle : 0.640 7.957 18190 Z= 0.320 Chirality : 0.045 0.277 2093 Planarity : 0.005 0.061 2309 Dihedral : 4.971 24.009 1811 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.47 % Allowed : 16.30 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.21), residues: 1594 helix: 0.09 (0.18), residues: 851 sheet: 0.11 (0.39), residues: 176 loop : -1.80 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 256 HIS 0.005 0.001 HIS C 159 PHE 0.022 0.001 PHE L 111 TYR 0.016 0.001 TYR C 299 ARG 0.003 0.000 ARG C 297 Details of bonding type rmsd hydrogen bonds : bond 0.04000 ( 644) hydrogen bonds : angle 4.22394 ( 1830) covalent geometry : bond 0.00365 (13426) covalent geometry : angle 0.64024 (18190) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 149 time to evaluate : 2.246 Fit side-chains REVERT: J 118 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7540 (tp30) REVERT: E 104 ILE cc_start: 0.8075 (pt) cc_final: 0.7746 (mp) REVERT: E 284 MET cc_start: 0.7411 (tpp) cc_final: 0.6992 (mtt) REVERT: E 339 GLN cc_start: 0.7019 (OUTLIER) cc_final: 0.6791 (tp40) REVERT: F 91 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.7117 (pp) REVERT: C 164 LYS cc_start: 0.7822 (pmtt) cc_final: 0.7068 (ptmm) REVERT: A 165 ARG cc_start: 0.7102 (tpt170) cc_final: 0.6772 (mtm-85) REVERT: A 177 ASN cc_start: 0.7916 (t0) cc_final: 0.7410 (p0) REVERT: B 83 LEU cc_start: 0.8145 (tp) cc_final: 0.7929 (mp) REVERT: I 120 ARG cc_start: 0.8023 (pmm150) cc_final: 0.7422 (mtt90) REVERT: G 153 ILE cc_start: 0.5681 (OUTLIER) cc_final: 0.5422 (mt) outliers start: 65 outliers final: 47 residues processed: 193 average time/residue: 0.2699 time to fit residues: 78.8752 Evaluate side-chains 198 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 148 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 339 GLN Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 107 SER Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 84 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 12 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 130 optimal weight: 0.0020 chunk 156 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.109348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.097014 restraints weight = 35821.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.098726 restraints weight = 19893.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.099864 restraints weight = 13058.323| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13426 Z= 0.152 Angle : 0.640 8.366 18190 Z= 0.320 Chirality : 0.045 0.266 2093 Planarity : 0.004 0.062 2309 Dihedral : 4.896 23.310 1811 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.13 % Allowed : 17.33 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.22), residues: 1594 helix: 0.28 (0.18), residues: 847 sheet: 0.22 (0.39), residues: 176 loop : -1.69 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 256 HIS 0.005 0.001 HIS C 159 PHE 0.020 0.001 PHE L 149 TYR 0.013 0.001 TYR C 258 ARG 0.006 0.000 ARG J 161 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 644) hydrogen bonds : angle 4.17471 ( 1830) covalent geometry : bond 0.00361 (13426) covalent geometry : angle 0.64035 (18190) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 144 time to evaluate : 1.459 Fit side-chains REVERT: J 118 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7588 (tp30) REVERT: K 106 ASP cc_start: 0.6558 (m-30) cc_final: 0.6350 (m-30) REVERT: E 104 ILE cc_start: 0.8072 (pt) cc_final: 0.7739 (mp) REVERT: E 284 MET cc_start: 0.7456 (tpp) cc_final: 0.7023 (mtt) REVERT: E 339 GLN cc_start: 0.7047 (OUTLIER) cc_final: 0.6782 (tp40) REVERT: C 164 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7011 (ptmm) REVERT: A 165 ARG cc_start: 0.7091 (tpt170) cc_final: 0.6796 (mtm-85) REVERT: A 177 ASN cc_start: 0.7927 (t0) cc_final: 0.7437 (p0) REVERT: B 83 LEU cc_start: 0.8116 (tp) cc_final: 0.7907 (mp) REVERT: L 158 TYR cc_start: 0.5691 (m-80) cc_final: 0.5368 (m-80) REVERT: I 120 ARG cc_start: 0.8038 (pmm150) cc_final: 0.7422 (mtt90) REVERT: G 153 ILE cc_start: 0.5701 (OUTLIER) cc_final: 0.5441 (mt) outliers start: 60 outliers final: 48 residues processed: 184 average time/residue: 0.2281 time to fit residues: 62.3883 Evaluate side-chains 192 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 141 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 339 GLN Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 107 SER Chi-restraints excluded: chain L residue 153 ILE Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 84 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 16 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 133 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.108554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.096209 restraints weight = 35704.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.097912 restraints weight = 19981.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.099045 restraints weight = 13121.824| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13426 Z= 0.166 Angle : 0.653 8.234 18190 Z= 0.326 Chirality : 0.046 0.261 2093 Planarity : 0.005 0.062 2309 Dihedral : 4.923 23.802 1811 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.68 % Allowed : 17.47 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.22), residues: 1594 helix: 0.33 (0.18), residues: 851 sheet: 0.24 (0.39), residues: 176 loop : -1.67 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 256 HIS 0.005 0.001 HIS C 159 PHE 0.020 0.002 PHE L 149 TYR 0.014 0.001 TYR C 258 ARG 0.006 0.000 ARG J 161 Details of bonding type rmsd hydrogen bonds : bond 0.04054 ( 644) hydrogen bonds : angle 4.21349 ( 1830) covalent geometry : bond 0.00396 (13426) covalent geometry : angle 0.65310 (18190) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 142 time to evaluate : 2.130 Fit side-chains REVERT: J 95 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7985 (pm20) REVERT: J 118 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7693 (tp30) REVERT: K 106 ASP cc_start: 0.6517 (m-30) cc_final: 0.6315 (m-30) REVERT: E 104 ILE cc_start: 0.8076 (pt) cc_final: 0.7745 (mp) REVERT: E 143 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8826 (tt) REVERT: E 284 MET cc_start: 0.7486 (tpp) cc_final: 0.7057 (mtt) REVERT: E 320 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8383 (tt) REVERT: E 339 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6933 (tm-30) REVERT: C 164 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7019 (ptmm) REVERT: A 165 ARG cc_start: 0.7034 (tpt170) cc_final: 0.6778 (mtm-85) REVERT: A 177 ASN cc_start: 0.7920 (t0) cc_final: 0.7477 (p0) REVERT: B 83 LEU cc_start: 0.8160 (tp) cc_final: 0.7860 (mp) REVERT: L 158 TYR cc_start: 0.5540 (m-80) cc_final: 0.5195 (m-80) REVERT: I 120 ARG cc_start: 0.8037 (pmm150) cc_final: 0.7425 (mtt90) REVERT: G 94 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6500 (ptt-90) REVERT: G 153 ILE cc_start: 0.5840 (OUTLIER) cc_final: 0.5564 (mt) REVERT: G 284 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.8091 (mtp) outliers start: 68 outliers final: 52 residues processed: 189 average time/residue: 0.2725 time to fit residues: 76.5125 Evaluate side-chains 197 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 137 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 339 GLN Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 107 SER Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 94 ARG Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 84 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 146 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 136 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 44 optimal weight: 0.3980 chunk 115 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.111516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.099182 restraints weight = 35612.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.100923 restraints weight = 19704.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.102083 restraints weight = 12880.977| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13426 Z= 0.112 Angle : 0.607 8.416 18190 Z= 0.300 Chirality : 0.043 0.265 2093 Planarity : 0.004 0.066 2309 Dihedral : 4.544 22.229 1811 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.23 % Allowed : 19.12 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.22), residues: 1594 helix: 0.69 (0.19), residues: 846 sheet: 0.36 (0.40), residues: 175 loop : -1.59 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 260 HIS 0.005 0.001 HIS C 159 PHE 0.023 0.001 PHE L 149 TYR 0.013 0.001 TYR A 242 ARG 0.007 0.000 ARG K 134 Details of bonding type rmsd hydrogen bonds : bond 0.03511 ( 644) hydrogen bonds : angle 3.87957 ( 1830) covalent geometry : bond 0.00247 (13426) covalent geometry : angle 0.60654 (18190) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 155 time to evaluate : 1.886 Fit side-chains revert: symmetry clash REVERT: J 118 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7600 (tp30) REVERT: J 133 VAL cc_start: 0.8518 (OUTLIER) cc_final: 0.8299 (m) REVERT: E 104 ILE cc_start: 0.8069 (pt) cc_final: 0.7737 (mp) REVERT: E 284 MET cc_start: 0.7458 (tpp) cc_final: 0.7059 (mtt) REVERT: E 320 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8471 (tt) REVERT: C 164 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7009 (ptmm) REVERT: C 258 TYR cc_start: 0.7040 (OUTLIER) cc_final: 0.4757 (t80) REVERT: A 177 ASN cc_start: 0.7873 (t0) cc_final: 0.7440 (p0) REVERT: B 83 LEU cc_start: 0.8137 (tp) cc_final: 0.7890 (mp) REVERT: L 158 TYR cc_start: 0.5457 (m-80) cc_final: 0.5086 (m-80) REVERT: I 120 ARG cc_start: 0.7981 (pmm150) cc_final: 0.7349 (mtt90) REVERT: G 138 SER cc_start: 0.8049 (m) cc_final: 0.7634 (p) REVERT: G 153 ILE cc_start: 0.5634 (OUTLIER) cc_final: 0.5344 (mt) outliers start: 47 outliers final: 34 residues processed: 190 average time/residue: 0.2412 time to fit residues: 67.5313 Evaluate side-chains 179 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 140 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 153 ILE Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 84 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 67 optimal weight: 0.3980 chunk 4 optimal weight: 0.0770 overall best weight: 2.0944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.110063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.097727 restraints weight = 35558.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.099444 restraints weight = 19685.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.100580 restraints weight = 12935.291| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13426 Z= 0.142 Angle : 0.637 8.569 18190 Z= 0.317 Chirality : 0.045 0.259 2093 Planarity : 0.005 0.099 2309 Dihedral : 4.591 22.567 1811 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.03 % Allowed : 20.15 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.22), residues: 1594 helix: 0.73 (0.19), residues: 848 sheet: 0.39 (0.40), residues: 175 loop : -1.53 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 256 HIS 0.005 0.001 HIS C 159 PHE 0.022 0.001 PHE L 149 TYR 0.011 0.001 TYR C 258 ARG 0.005 0.000 ARG K 134 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 644) hydrogen bonds : angle 3.94544 ( 1830) covalent geometry : bond 0.00337 (13426) covalent geometry : angle 0.63664 (18190) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 139 time to evaluate : 1.919 Fit side-chains revert: symmetry clash REVERT: J 118 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7695 (tp30) REVERT: E 104 ILE cc_start: 0.8078 (pt) cc_final: 0.7739 (mp) REVERT: E 284 MET cc_start: 0.7491 (tpp) cc_final: 0.7041 (mtt) REVERT: E 320 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8339 (tt) REVERT: C 164 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.6993 (ptmm) REVERT: C 258 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.4761 (t80) REVERT: C 308 LYS cc_start: 0.7597 (tmtt) cc_final: 0.7017 (ttmt) REVERT: A 177 ASN cc_start: 0.7880 (t0) cc_final: 0.7453 (p0) REVERT: B 83 LEU cc_start: 0.8076 (tp) cc_final: 0.7828 (mp) REVERT: I 120 ARG cc_start: 0.8016 (pmm150) cc_final: 0.7384 (mtt90) REVERT: G 138 SER cc_start: 0.8022 (OUTLIER) cc_final: 0.7589 (p) REVERT: G 153 ILE cc_start: 0.5659 (OUTLIER) cc_final: 0.5378 (mt) REVERT: G 284 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.8032 (mtp) outliers start: 44 outliers final: 34 residues processed: 171 average time/residue: 0.2663 time to fit residues: 68.0879 Evaluate side-chains 174 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain H residue 84 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 37 optimal weight: 0.1980 chunk 139 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 GLN ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.107476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.095016 restraints weight = 35659.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.096738 restraints weight = 19663.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.097893 restraints weight = 12881.644| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13426 Z= 0.210 Angle : 0.714 10.088 18190 Z= 0.356 Chirality : 0.047 0.246 2093 Planarity : 0.005 0.095 2309 Dihedral : 4.965 23.763 1811 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.30 % Allowed : 20.08 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.22), residues: 1594 helix: 0.54 (0.18), residues: 847 sheet: 0.31 (0.40), residues: 175 loop : -1.58 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 237 HIS 0.005 0.001 HIS C 159 PHE 0.021 0.002 PHE L 149 TYR 0.018 0.002 TYR C 258 ARG 0.006 0.000 ARG K 134 Details of bonding type rmsd hydrogen bonds : bond 0.04301 ( 644) hydrogen bonds : angle 4.27085 ( 1830) covalent geometry : bond 0.00507 (13426) covalent geometry : angle 0.71362 (18190) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 140 time to evaluate : 1.416 Fit side-chains REVERT: J 118 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7734 (tp30) REVERT: E 104 ILE cc_start: 0.8051 (pt) cc_final: 0.7681 (mp) REVERT: E 320 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8428 (tt) REVERT: C 164 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.6971 (ptmm) REVERT: C 258 TYR cc_start: 0.7224 (OUTLIER) cc_final: 0.5016 (t80) REVERT: A 165 ARG cc_start: 0.7070 (tpt170) cc_final: 0.6795 (mtm-85) REVERT: A 177 ASN cc_start: 0.7913 (t0) cc_final: 0.7481 (p0) REVERT: A 263 MET cc_start: 0.6800 (ptp) cc_final: 0.6586 (ptt) REVERT: B 83 LEU cc_start: 0.8108 (tp) cc_final: 0.7868 (mp) REVERT: I 120 ARG cc_start: 0.8068 (pmm150) cc_final: 0.7429 (mtt90) REVERT: G 94 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6438 (ptt-90) REVERT: G 153 ILE cc_start: 0.5820 (OUTLIER) cc_final: 0.5523 (mt) REVERT: G 284 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8216 (mtp) outliers start: 48 outliers final: 38 residues processed: 171 average time/residue: 0.2488 time to fit residues: 62.8373 Evaluate side-chains 180 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 136 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain G residue 94 ARG Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain H residue 84 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 71 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 154 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.108754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.096489 restraints weight = 35741.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.098186 restraints weight = 19833.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.099298 restraints weight = 13061.407| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13426 Z= 0.147 Angle : 0.656 9.291 18190 Z= 0.326 Chirality : 0.045 0.253 2093 Planarity : 0.005 0.093 2309 Dihedral : 4.794 23.501 1811 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.23 % Allowed : 20.08 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.22), residues: 1594 helix: 0.71 (0.18), residues: 845 sheet: 0.35 (0.40), residues: 175 loop : -1.55 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 256 HIS 0.005 0.001 HIS C 159 PHE 0.026 0.001 PHE L 149 TYR 0.012 0.001 TYR C 258 ARG 0.005 0.000 ARG K 134 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 644) hydrogen bonds : angle 4.06651 ( 1830) covalent geometry : bond 0.00348 (13426) covalent geometry : angle 0.65553 (18190) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4488.05 seconds wall clock time: 81 minutes 17.36 seconds (4877.36 seconds total)