Starting phenix.real_space_refine on Thu Sep 26 11:47:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o5b_0626/09_2024/6o5b_0626.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o5b_0626/09_2024/6o5b_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o5b_0626/09_2024/6o5b_0626.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o5b_0626/09_2024/6o5b_0626.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o5b_0626/09_2024/6o5b_0626.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o5b_0626/09_2024/6o5b_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-5461/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: 8.14, 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 1.7 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: 1.20 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: 3.35 Time building geometry restraints manager: 3.32 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: 1.880 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: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 29.460 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.580 ------------------------------------------------------------------------------- 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= 0.416 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 *********************** 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 fitting. rotamer outliers: 6 poor density : 335 time to evaluate : 1.659 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: 0.3304 time to fit residues: 148.3529 Evaluate side-chains 173 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 1.503 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 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= 0.205 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 *********************** 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 fitting. rotamer outliers: 39 poor density : 194 time to evaluate : 1.628 Fit side-chains REVERT: J 164 LYS cc_start: 0.2246 (mttp) cc_final: 0.1719 (mtpt) REVERT: E 104 ILE cc_start: 0.7975 (pt) cc_final: 0.7644 (mp) REVERT: C 164 LYS cc_start: 0.7669 (pmtt) cc_final: 0.6962 (ptmm) REVERT: A 165 ARG cc_start: 0.6990 (tpt170) cc_final: 0.6785 (mtm-85) REVERT: A 177 ASN cc_start: 0.7962 (t0) cc_final: 0.7554 (p0) REVERT: B 83 LEU cc_start: 0.8081 (tp) cc_final: 0.7805 (mp) REVERT: L 122 ILE cc_start: 0.4745 (OUTLIER) cc_final: 0.4417 (tt) REVERT: L 158 TYR cc_start: 0.5657 (m-80) cc_final: 0.5400 (m-80) REVERT: I 120 ARG cc_start: 0.7850 (pmm150) cc_final: 0.7425 (mtt90) outliers start: 39 outliers final: 20 residues processed: 225 average time/residue: 0.2602 time to fit residues: 83.6548 Evaluate side-chains 173 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 1.411 ------------------------------------------------------------------------------- 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 79 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 118 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 13426 Z= 0.336 Angle : 0.726 9.689 18190 Z= 0.365 Chirality : 0.048 0.216 2093 Planarity : 0.006 0.080 2309 Dihedral : 5.590 26.115 1812 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 4.88 % Allowed : 13.69 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.74 (0.21), residues: 1594 helix: -0.67 (0.18), residues: 847 sheet: -0.02 (0.40), residues: 162 loop : -2.10 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 255 HIS 0.006 0.001 HIS E 304 PHE 0.019 0.002 PHE L 111 TYR 0.019 0.002 TYR C 258 ARG 0.007 0.001 ARG J 161 *********************** 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 227 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 156 time to evaluate : 1.554 Fit side-chains revert: symmetry clash REVERT: J 118 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7308 (tp30) REVERT: E 104 ILE cc_start: 0.8090 (pt) cc_final: 0.7772 (mp) REVERT: E 284 MET cc_start: 0.7484 (tpp) cc_final: 0.7029 (mtt) REVERT: E 339 GLN cc_start: 0.7202 (OUTLIER) cc_final: 0.6887 (tm-30) REVERT: F 91 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7077 (pp) REVERT: C 164 LYS cc_start: 0.7848 (pmtt) cc_final: 0.7020 (ptmm) REVERT: A 165 ARG cc_start: 0.7088 (tpt170) cc_final: 0.6788 (mtm-85) REVERT: A 177 ASN cc_start: 0.8001 (t0) cc_final: 0.7513 (p0) REVERT: A 242 TYR cc_start: 0.7870 (t80) cc_final: 0.7649 (t80) REVERT: A 263 MET cc_start: 0.7093 (mmm) cc_final: 0.6883 (tpp) REVERT: B 83 LEU cc_start: 0.8149 (tp) cc_final: 0.7929 (mp) REVERT: L 158 TYR cc_start: 0.5635 (m-80) cc_final: 0.5349 (m-80) REVERT: I 120 ARG cc_start: 0.7923 (pmm150) cc_final: 0.7461 (mtt90) REVERT: G 120 ARG cc_start: 0.7496 (mmt180) cc_final: 0.7293 (mmp80) outliers start: 71 outliers final: 37 residues processed: 207 average time/residue: 0.2438 time to fit residues: 73.5904 Evaluate side-chains 183 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 144 time to evaluate : 1.661 ------------------------------------------------------------------------------- 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 133 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 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 78 LEU 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 141 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 114 GLN ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 13426 Z= 0.370 Angle : 0.740 10.906 18190 Z= 0.372 Chirality : 0.049 0.290 2093 Planarity : 0.005 0.061 2309 Dihedral : 5.590 24.939 1811 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 5.09 % Allowed : 15.61 % Favored : 79.30 % 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: -1.50 (0.21), residues: 1594 helix: -0.44 (0.18), residues: 849 sheet: -0.13 (0.39), residues: 176 loop : -2.02 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 256 HIS 0.006 0.002 HIS E 304 PHE 0.020 0.002 PHE L 111 TYR 0.019 0.002 TYR C 258 ARG 0.007 0.001 ARG J 161 *********************** 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 224 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 150 time to evaluate : 1.557 Fit side-chains revert: symmetry clash REVERT: J 118 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7455 (tp30) REVERT: K 94 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.5950 (mtm180) REVERT: E 104 ILE cc_start: 0.8104 (pt) cc_final: 0.7770 (mp) REVERT: E 339 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6634 (tm-30) REVERT: C 164 LYS cc_start: 0.7826 (pmtt) cc_final: 0.7018 (ptmm) REVERT: A 165 ARG cc_start: 0.7055 (tpt170) cc_final: 0.6773 (mtm-85) REVERT: A 177 ASN cc_start: 0.8009 (t0) cc_final: 0.7559 (p0) REVERT: B 83 LEU cc_start: 0.8160 (tp) cc_final: 0.7931 (mp) REVERT: I 120 ARG cc_start: 0.8067 (pmm150) cc_final: 0.7513 (mtt90) REVERT: G 153 ILE cc_start: 0.5754 (OUTLIER) cc_final: 0.5496 (mt) outliers start: 74 outliers final: 50 residues processed: 202 average time/residue: 0.2371 time to fit residues: 70.3918 Evaluate side-chains 192 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 139 time to evaluate : 1.549 ------------------------------------------------------------------------------- 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 110 VAL Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 94 ARG Chi-restraints excluded: chain K residue 104 ILE 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 290 VAL 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 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 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 B residue 65 PHE 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 95 GLU Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 157 THR 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 78 LEU Chi-restraints excluded: chain H residue 82 THR 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 86 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 0.0050 chunk 136 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 overall best weight: 4.0002 ------------------------------------------------------------------------------- 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** A 114 GLN ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 13426 Z= 0.339 Angle : 0.708 10.613 18190 Z= 0.355 Chirality : 0.047 0.256 2093 Planarity : 0.005 0.062 2309 Dihedral : 5.497 26.812 1811 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 5.43 % Allowed : 16.99 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.28 (0.21), residues: 1594 helix: -0.25 (0.18), residues: 850 sheet: -0.07 (0.39), residues: 175 loop : -1.92 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 256 HIS 0.005 0.001 HIS C 159 PHE 0.021 0.002 PHE L 111 TYR 0.017 0.002 TYR C 258 ARG 0.004 0.000 ARG C 297 *********************** 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 223 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 144 time to evaluate : 1.653 Fit side-chains revert: symmetry clash REVERT: J 118 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7006 (tp30) REVERT: K 94 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6143 (mtm180) REVERT: E 104 ILE cc_start: 0.8105 (pt) cc_final: 0.7771 (mp) REVERT: E 143 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8779 (tt) REVERT: E 339 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6617 (tm-30) REVERT: C 164 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7030 (ptmm) REVERT: C 192 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8932 (mm) REVERT: C 258 TYR cc_start: 0.7183 (OUTLIER) cc_final: 0.5195 (t80) REVERT: C 295 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8081 (ptt-90) REVERT: A 165 ARG cc_start: 0.7024 (tpt170) cc_final: 0.6772 (mtm-85) REVERT: A 177 ASN cc_start: 0.8010 (t0) cc_final: 0.7606 (p0) REVERT: B 83 LEU cc_start: 0.8166 (tp) cc_final: 0.7849 (mp) REVERT: I 120 ARG cc_start: 0.8062 (pmm150) cc_final: 0.7493 (mmt-90) REVERT: G 153 ILE cc_start: 0.5951 (OUTLIER) cc_final: 0.5703 (mt) outliers start: 79 outliers final: 54 residues processed: 199 average time/residue: 0.2463 time to fit residues: 71.0198 Evaluate side-chains 202 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 140 time to evaluate : 1.507 ------------------------------------------------------------------------------- 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 80 GLN Chi-restraints excluded: chain K residue 94 ARG Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 131 ASP 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 290 VAL 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 94 GLU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 125 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 192 ILE Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 295 ARG 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 70 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 A residue 284 MET Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 61 VAL 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 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 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 136 optimal weight: 20.0000 chunk 29 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 0.0870 chunk 12 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3518 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= 0.199 Angle : 0.630 7.739 18190 Z= 0.314 Chirality : 0.044 0.268 2093 Planarity : 0.005 0.066 2309 Dihedral : 5.037 24.522 1811 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.26 % Allowed : 18.64 % Favored : 77.10 % 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: -0.85 (0.22), residues: 1594 helix: 0.13 (0.18), residues: 851 sheet: 0.12 (0.40), residues: 175 loop : -1.79 (0.27), residues: 568 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 0.012 0.001 TYR C 268 ARG 0.005 0.000 ARG J 161 *********************** 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 202 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 140 time to evaluate : 1.576 Fit side-chains revert: symmetry clash REVERT: J 95 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7459 (pm20) REVERT: J 118 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7402 (tp30) REVERT: K 94 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.5973 (mtm180) REVERT: E 104 ILE cc_start: 0.8081 (pt) cc_final: 0.7731 (mp) REVERT: E 284 MET cc_start: 0.7474 (tpp) cc_final: 0.7072 (mtt) REVERT: C 164 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7017 (ptmm) REVERT: C 258 TYR cc_start: 0.7150 (OUTLIER) cc_final: 0.4998 (t80) REVERT: C 295 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8031 (ptt-90) REVERT: A 165 ARG cc_start: 0.7010 (tpt170) cc_final: 0.6730 (mtm-85) REVERT: A 177 ASN cc_start: 0.7891 (t0) cc_final: 0.7567 (p0) REVERT: B 83 LEU cc_start: 0.8166 (tp) cc_final: 0.7931 (mp) REVERT: I 120 ARG cc_start: 0.8015 (pmm150) cc_final: 0.7447 (mmt-90) REVERT: G 94 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6543 (ptt-90) REVERT: G 153 ILE cc_start: 0.5782 (OUTLIER) cc_final: 0.5490 (mt) REVERT: G 284 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.8004 (mtp) outliers start: 62 outliers final: 41 residues processed: 185 average time/residue: 0.2503 time to fit residues: 67.1333 Evaluate side-chains 186 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 137 time to evaluate : 1.383 ------------------------------------------------------------------------------- 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 133 VAL Chi-restraints excluded: chain K residue 80 GLN Chi-restraints excluded: chain K residue 94 ARG Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K 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 331 LEU 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 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 258 TYR Chi-restraints excluded: chain C residue 295 ARG 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 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 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 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 284 MET Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain H residue 70 VAL 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 17 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 85 optimal weight: 0.0970 chunk 127 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 overall best weight: 3.2184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13426 Z= 0.286 Angle : 0.673 9.163 18190 Z= 0.337 Chirality : 0.046 0.261 2093 Planarity : 0.005 0.065 2309 Dihedral : 5.102 25.355 1811 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 4.61 % Allowed : 18.78 % 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: -0.81 (0.22), residues: 1594 helix: 0.18 (0.18), residues: 849 sheet: 0.16 (0.40), residues: 175 loop : -1.79 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 256 HIS 0.007 0.001 HIS E 341 PHE 0.020 0.002 PHE L 149 TYR 0.016 0.001 TYR C 258 ARG 0.005 0.000 ARG J 161 *********************** 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 203 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 136 time to evaluate : 1.773 Fit side-chains REVERT: J 95 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7496 (pm20) REVERT: J 118 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7502 (tp30) REVERT: K 94 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6065 (mtm180) REVERT: E 104 ILE cc_start: 0.8096 (pt) cc_final: 0.7748 (mp) REVERT: E 320 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8374 (tt) REVERT: C 164 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7010 (ptmm) REVERT: C 258 TYR cc_start: 0.7239 (OUTLIER) cc_final: 0.5030 (t80) REVERT: C 295 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8061 (ptt-90) REVERT: A 165 ARG cc_start: 0.7004 (tpt170) cc_final: 0.6729 (mtm-85) REVERT: A 177 ASN cc_start: 0.7924 (t0) cc_final: 0.7592 (p0) REVERT: B 83 LEU cc_start: 0.8169 (tp) cc_final: 0.7849 (mp) REVERT: I 120 ARG cc_start: 0.8071 (pmm150) cc_final: 0.7483 (mmt-90) REVERT: G 94 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6398 (ptt-90) REVERT: G 153 ILE cc_start: 0.5811 (OUTLIER) cc_final: 0.5525 (mt) REVERT: H 67 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7517 (tt) outliers start: 67 outliers final: 51 residues processed: 184 average time/residue: 0.2599 time to fit residues: 69.7867 Evaluate side-chains 194 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 134 time to evaluate : 1.582 ------------------------------------------------------------------------------- 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 80 GLN Chi-restraints excluded: chain K residue 94 ARG Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K 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 217 LEU Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 258 TYR 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 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 258 TYR Chi-restraints excluded: chain C residue 295 ARG 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 70 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 A residue 235 VAL Chi-restraints excluded: chain B residue 61 VAL 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 284 MET Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 70 VAL 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 60 optimal weight: 0.0170 chunk 90 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 14 optimal weight: 0.0770 chunk 118 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 116 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 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 : 0.002 0.038 13426 Z= 0.158 Angle : 0.606 8.039 18190 Z= 0.301 Chirality : 0.043 0.272 2093 Planarity : 0.004 0.069 2309 Dihedral : 4.627 23.296 1811 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.30 % Allowed : 20.29 % Favored : 76.41 % 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: -0.36 (0.22), residues: 1594 helix: 0.62 (0.19), residues: 845 sheet: 0.17 (0.43), residues: 165 loop : -1.61 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 237 HIS 0.005 0.001 HIS C 159 PHE 0.024 0.001 PHE L 149 TYR 0.011 0.001 TYR A 242 ARG 0.005 0.000 ARG J 161 *********************** 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 208 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 160 time to evaluate : 1.640 Fit side-chains REVERT: J 95 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7400 (pm20) REVERT: J 118 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7361 (tp30) REVERT: E 104 ILE cc_start: 0.8083 (pt) cc_final: 0.7738 (mp) REVERT: E 284 MET cc_start: 0.7453 (tpp) cc_final: 0.7032 (mtt) REVERT: E 320 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8473 (tt) REVERT: C 164 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.6989 (ptmm) REVERT: C 258 TYR cc_start: 0.7071 (OUTLIER) cc_final: 0.4798 (t80) REVERT: A 165 ARG cc_start: 0.6911 (tpt170) cc_final: 0.6684 (mtm-85) REVERT: A 177 ASN cc_start: 0.7843 (t0) cc_final: 0.7454 (p0) REVERT: B 83 LEU cc_start: 0.8168 (tp) cc_final: 0.7937 (mp) REVERT: L 158 TYR cc_start: 0.5646 (m-80) cc_final: 0.5330 (m-80) REVERT: I 120 ARG cc_start: 0.8022 (pmm150) cc_final: 0.7443 (mtt90) REVERT: G 94 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6431 (ptt-90) REVERT: G 153 ILE cc_start: 0.5916 (OUTLIER) cc_final: 0.5643 (mt) outliers start: 48 outliers final: 35 residues processed: 192 average time/residue: 0.2430 time to fit residues: 68.0611 Evaluate side-chains 187 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 146 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 95 GLU 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 K residue 138 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 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 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 284 MET 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 A residue 235 VAL Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 138 SER Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain G residue 94 ARG 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 82 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 116 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13426 Z= 0.288 Angle : 0.675 8.121 18190 Z= 0.336 Chirality : 0.046 0.259 2093 Planarity : 0.005 0.065 2309 Dihedral : 4.843 24.270 1811 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.23 % Allowed : 20.98 % Favored : 75.79 % 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: -0.41 (0.22), residues: 1594 helix: 0.52 (0.19), residues: 849 sheet: 0.31 (0.42), residues: 175 loop : -1.63 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 256 HIS 0.005 0.001 HIS E 341 PHE 0.022 0.002 PHE L 149 TYR 0.015 0.002 TYR C 258 ARG 0.005 0.000 ARG J 161 *********************** 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 193 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 146 time to evaluate : 1.494 Fit side-chains REVERT: J 95 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7454 (pm20) REVERT: J 118 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7522 (tp30) REVERT: E 104 ILE cc_start: 0.8108 (pt) cc_final: 0.7748 (mp) REVERT: E 320 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8369 (tt) REVERT: E 339 GLN cc_start: 0.7021 (tm-30) cc_final: 0.6685 (tm-30) REVERT: C 164 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7055 (ptmm) REVERT: C 258 TYR cc_start: 0.7052 (OUTLIER) cc_final: 0.4945 (t80) REVERT: A 165 ARG cc_start: 0.6998 (tpt170) cc_final: 0.6733 (mtm-85) REVERT: A 177 ASN cc_start: 0.7893 (t0) cc_final: 0.7485 (p0) REVERT: B 83 LEU cc_start: 0.8123 (tp) cc_final: 0.7857 (mp) REVERT: L 158 TYR cc_start: 0.5723 (m-80) cc_final: 0.5424 (m-80) REVERT: I 120 ARG cc_start: 0.8068 (pmm150) cc_final: 0.7455 (mmt-90) REVERT: G 94 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6454 (ptt-90) REVERT: G 153 ILE cc_start: 0.5814 (OUTLIER) cc_final: 0.5538 (mt) outliers start: 47 outliers final: 38 residues processed: 177 average time/residue: 0.2437 time to fit residues: 63.2818 Evaluate side-chains 184 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 140 time to evaluate : 1.552 ------------------------------------------------------------------------------- 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 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 K residue 138 SER Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 320 LEU 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 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 67 LEU 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 L residue 90 LEU 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 94 ARG 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 82 THR 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 149 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 156 optimal weight: 0.7980 chunk 143 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13426 Z= 0.242 Angle : 0.655 8.087 18190 Z= 0.326 Chirality : 0.045 0.260 2093 Planarity : 0.004 0.067 2309 Dihedral : 4.823 24.682 1811 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.65 % Allowed : 20.98 % Favored : 75.38 % 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: -0.34 (0.22), residues: 1594 helix: 0.60 (0.18), residues: 848 sheet: 0.29 (0.41), residues: 175 loop : -1.61 (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 0.024 0.002 PHE L 149 TYR 0.013 0.001 TYR C 258 ARG 0.004 0.000 ARG J 161 ********************** 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 197 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 144 time to evaluate : 1.705 Fit side-chains REVERT: J 95 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7513 (pm20) REVERT: J 118 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7491 (tp30) REVERT: E 104 ILE cc_start: 0.8090 (pt) cc_final: 0.7726 (mp) REVERT: E 320 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8340 (tt) REVERT: E 339 GLN cc_start: 0.7033 (tm-30) cc_final: 0.6637 (tm-30) REVERT: C 164 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7005 (ptmm) REVERT: C 258 TYR cc_start: 0.7142 (OUTLIER) cc_final: 0.5038 (t80) REVERT: A 165 ARG cc_start: 0.6989 (tpt170) cc_final: 0.6703 (mtm-85) REVERT: A 177 ASN cc_start: 0.7888 (t0) cc_final: 0.7487 (p0) REVERT: B 83 LEU cc_start: 0.8165 (tp) cc_final: 0.7847 (mp) REVERT: L 158 TYR cc_start: 0.5612 (m-80) cc_final: 0.5265 (m-80) REVERT: I 120 ARG cc_start: 0.8059 (pmm150) cc_final: 0.7448 (mmt-90) REVERT: G 94 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6457 (ptt-90) REVERT: G 153 ILE cc_start: 0.5858 (OUTLIER) cc_final: 0.5570 (mt) outliers start: 53 outliers final: 43 residues processed: 182 average time/residue: 0.2432 time to fit residues: 64.7086 Evaluate side-chains 190 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 141 time to evaluate : 1.539 ------------------------------------------------------------------------------- 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 133 VAL Chi-restraints excluded: chain K residue 80 GLN 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 K residue 138 SER Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 320 LEU 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 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 67 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 78 VAL 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 160 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain B residue 61 VAL 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 153 ILE Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain H residue 82 THR 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 132 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 124 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.110195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.097868 restraints weight = 35342.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.099586 restraints weight = 19724.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.100737 restraints weight = 13008.129| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13426 Z= 0.182 Angle : 0.627 8.066 18190 Z= 0.311 Chirality : 0.044 0.265 2093 Planarity : 0.004 0.069 2309 Dihedral : 4.617 23.665 1811 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.30 % Allowed : 21.39 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.13 (0.22), residues: 1594 helix: 0.82 (0.19), residues: 845 sheet: 0.35 (0.41), residues: 175 loop : -1.58 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 256 HIS 0.005 0.001 HIS C 159 PHE 0.026 0.001 PHE L 149 TYR 0.011 0.001 TYR E 268 ARG 0.004 0.000 ARG J 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2649.13 seconds wall clock time: 47 minutes 54.81 seconds (2874.81 seconds total)