Starting phenix.real_space_refine on Fri Mar 6 02:05:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qo2_53254/03_2026/9qo2_53254.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qo2_53254/03_2026/9qo2_53254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qo2_53254/03_2026/9qo2_53254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qo2_53254/03_2026/9qo2_53254.map" model { file = "/net/cci-nas-00/data/ceres_data/9qo2_53254/03_2026/9qo2_53254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qo2_53254/03_2026/9qo2_53254.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.031 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 6 5.49 5 S 145 5.16 5 C 16833 2.51 5 N 4531 2.21 5 O 4976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26494 Number of models: 1 Model: "" Number of chains: 16 Chain: "B" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3305 Classifications: {'peptide': 404} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 393} Chain breaks: 1 Chain: "C" Number of atoms: 2809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2809 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 12, 'TRANS': 337} Chain breaks: 1 Chain: "D" Number of atoms: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3067 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 9, 'TRANS': 371} Chain: "E" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 713 Classifications: {'peptide': 90} Link IDs: {'TRANS': 89} Chain breaks: 1 Chain: "F" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 790 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 96} Chain: "G" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1694 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 4, 'TRANS': 209} Chain: "H" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1359 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 4583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 4583 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PTRANS': 10, 'TRANS': 614} Chain breaks: 12 Unresolved non-hydrogen bonds: 575 Unresolved non-hydrogen angles: 701 Unresolved non-hydrogen dihedrals: 491 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 27, 'HIS:plan': 3, 'TYR:plan': 10, 'ASN:plan1': 5, 'ASP:plan': 14, 'PHE:plan': 3, 'GLN:plan1': 6, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 352 Chain: "J" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 661 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain breaks: 1 Chain: "L" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1021 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2561 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 310} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 614 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 6, 'TRANS': 64} Chain: "P" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 179 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "A" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3099 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 11, 'TRANS': 394} Chain breaks: 3 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 6, 'ARG:plan': 5, 'HIS:plan': 3, 'ASP:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 91 Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18684 SG CYS J 75 46.636 69.409 67.991 1.00177.26 S ATOM 18851 SG CYS J 94 47.739 70.052 71.910 1.00174.19 S ATOM 18497 SG CYS J 42 44.872 62.170 79.182 1.00167.71 S ATOM 18755 SG CYS J 83 42.736 64.168 82.049 1.00171.71 S ATOM 18583 SG CYS J 53 39.057 62.712 84.347 1.00179.32 S ATOM 18606 SG CYS J 56 35.577 62.404 85.721 1.00182.09 S ATOM 18634 SG CYS J 68 36.318 61.149 82.197 1.00182.65 S Time building chain proxies: 5.68, per 1000 atoms: 0.21 Number of scatterers: 26494 At special positions: 0 Unit cell: (120.96, 198.72, 186.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 145 16.00 P 6 15.00 O 4976 8.00 N 4531 7.00 C 16833 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS M 240 " - pdb=" SG CYS M 266 " distance=2.03 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: 2.37 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J 201 " pdb="ZN ZN J 201 " - pdb=" ND1 HIS J 77 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 94 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 75 " pdb=" ZN J 202 " pdb="ZN ZN J 202 " - pdb=" SG CYS J 83 " pdb="ZN ZN J 202 " - pdb=" ND1 HIS J 80 " pdb="ZN ZN J 202 " - pdb=" SG CYS J 42 " pdb=" ZN J 203 " pdb="ZN ZN J 203 " - pdb=" ND1 HIS J 82 " pdb="ZN ZN J 203 " - pdb=" SG CYS J 56 " pdb="ZN ZN J 203 " - pdb=" SG CYS J 53 " pdb="ZN ZN J 203 " - pdb=" SG CYS J 68 " Number of angles added : 3 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6484 Finding SS restraints... Secondary structure from input PDB file: 173 helices and 13 sheets defined 69.1% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'B' and resid 35 through 42 Processing helix chain 'B' and resid 50 through 61 removed outlier: 4.302A pdb=" N PHE B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 82 removed outlier: 3.817A pdb=" N LEU B 82 " --> pdb=" O ILE B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 93 Processing helix chain 'B' and resid 95 through 100 removed outlier: 4.095A pdb=" N TYR B 98 " --> pdb=" O LEU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 119 Processing helix chain 'B' and resid 126 through 140 removed outlier: 4.214A pdb=" N GLU B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 162 removed outlier: 3.850A pdb=" N TRP B 148 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 172 Processing helix chain 'B' and resid 175 through 181 Processing helix chain 'B' and resid 193 through 208 removed outlier: 3.618A pdb=" N ILE B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 222 Processing helix chain 'B' and resid 230 through 249 Processing helix chain 'B' and resid 252 through 269 removed outlier: 3.889A pdb=" N THR B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 removed outlier: 3.726A pdb=" N CYS B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 322 through 333 removed outlier: 3.717A pdb=" N PHE B 326 " --> pdb=" O ASP B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 346 Processing helix chain 'B' and resid 347 through 363 Processing helix chain 'B' and resid 371 through 379 Processing helix chain 'B' and resid 381 through 395 Processing helix chain 'B' and resid 419 through 439 Processing helix chain 'C' and resid 53 through 65 removed outlier: 3.587A pdb=" N LYS C 65 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 89 removed outlier: 4.539A pdb=" N ASN C 89 " --> pdb=" O ILE C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 removed outlier: 3.818A pdb=" N TYR C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA C 96 " --> pdb=" O HIS C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 116 through 119 removed outlier: 3.688A pdb=" N ARG C 119 " --> pdb=" O GLN C 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 116 through 119' Processing helix chain 'C' and resid 120 through 131 removed outlier: 3.744A pdb=" N LEU C 124 " --> pdb=" O GLY C 120 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS C 125 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN C 126 " --> pdb=" O GLY C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 153 removed outlier: 4.228A pdb=" N ASP C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 162 Proline residue: C 160 - end of helix Processing helix chain 'C' and resid 177 through 195 removed outlier: 4.004A pdb=" N PHE C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY C 189 " --> pdb=" O TYR C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 210 removed outlier: 3.776A pdb=" N ALA C 201 " --> pdb=" O ASN C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 236 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.686A pdb=" N LEU C 256 " --> pdb=" O PHE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 269 removed outlier: 3.858A pdb=" N THR C 269 " --> pdb=" O GLN C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 282 Processing helix chain 'C' and resid 282 through 289 Processing helix chain 'C' and resid 293 through 310 Processing helix chain 'C' and resid 319 through 326 Processing helix chain 'C' and resid 330 through 345 removed outlier: 3.736A pdb=" N ALA C 334 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 399 removed outlier: 3.804A pdb=" N VAL C 399 " --> pdb=" O GLN C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 407 Processing helix chain 'D' and resid 24 through 36 Processing helix chain 'D' and resid 39 through 52 removed outlier: 4.434A pdb=" N GLU D 43 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 73 removed outlier: 3.765A pdb=" N ASP D 68 " --> pdb=" O GLN D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 80 through 93 removed outlier: 3.609A pdb=" N HIS D 86 " --> pdb=" O LYS D 82 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 96 No H-bonds generated for 'chain 'D' and resid 94 through 96' Processing helix chain 'D' and resid 100 through 117 removed outlier: 3.529A pdb=" N ALA D 104 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 128 removed outlier: 3.927A pdb=" N ALA D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 157 Processing helix chain 'D' and resid 160 through 175 removed outlier: 3.761A pdb=" N ALA D 164 " --> pdb=" O ASP D 160 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU D 174 " --> pdb=" O ARG D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 198 removed outlier: 3.626A pdb=" N GLN D 184 " --> pdb=" O ASN D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 212 removed outlier: 3.528A pdb=" N ALA D 204 " --> pdb=" O LYS D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 236 removed outlier: 4.116A pdb=" N LEU D 223 " --> pdb=" O GLU D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 252 removed outlier: 3.800A pdb=" N SER D 243 " --> pdb=" O GLY D 239 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP D 252 " --> pdb=" O THR D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 258 removed outlier: 3.818A pdb=" N GLN D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 269 removed outlier: 3.890A pdb=" N LEU D 269 " --> pdb=" O GLU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 278 Processing helix chain 'D' and resid 279 through 283 removed outlier: 3.729A pdb=" N ALA D 283 " --> pdb=" O GLU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 291 removed outlier: 3.978A pdb=" N ALA D 291 " --> pdb=" O HIS D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 313 Processing helix chain 'D' and resid 321 through 328 Processing helix chain 'D' and resid 331 through 345 removed outlier: 3.552A pdb=" N ALA D 335 " --> pdb=" O PRO D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 392 removed outlier: 3.560A pdb=" N ALA D 392 " --> pdb=" O ILE D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 401 removed outlier: 3.567A pdb=" N THR D 396 " --> pdb=" O ALA D 392 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 241 removed outlier: 3.619A pdb=" N GLU E 239 " --> pdb=" O ARG E 235 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU E 240 " --> pdb=" O LYS E 236 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU E 241 " --> pdb=" O LEU E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 251 Processing helix chain 'E' and resid 254 through 257 Processing helix chain 'E' and resid 258 through 283 removed outlier: 3.989A pdb=" N GLY E 283 " --> pdb=" O GLN E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 329 Processing helix chain 'F' and resid 217 through 248 removed outlier: 3.643A pdb=" N ARG F 234 " --> pdb=" O MET F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 266 removed outlier: 4.027A pdb=" N LEU F 257 " --> pdb=" O ASN F 253 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS F 265 " --> pdb=" O TYR F 261 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N CYS F 266 " --> pdb=" O ALA F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 312 removed outlier: 4.020A pdb=" N VAL F 311 " --> pdb=" O ASN F 307 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU F 312 " --> pdb=" O LYS F 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 19 Processing helix chain 'G' and resid 26 through 35 Processing helix chain 'G' and resid 49 through 55 removed outlier: 3.555A pdb=" N LEU G 55 " --> pdb=" O ASN G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 73 removed outlier: 4.239A pdb=" N LEU G 64 " --> pdb=" O ASN G 60 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN G 65 " --> pdb=" O ALA G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 81 Processing helix chain 'G' and resid 89 through 108 removed outlier: 3.904A pdb=" N ARG G 107 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET G 108 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 121 Processing helix chain 'G' and resid 124 through 138 removed outlier: 3.596A pdb=" N LEU G 128 " --> pdb=" O ASN G 124 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR G 138 " --> pdb=" O GLU G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 165 No H-bonds generated for 'chain 'G' and resid 163 through 165' Processing helix chain 'G' and resid 166 through 222 removed outlier: 3.692A pdb=" N ILE G 170 " --> pdb=" O ASP G 166 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA G 222 " --> pdb=" O LYS G 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 27 Processing helix chain 'H' and resid 33 through 47 removed outlier: 3.529A pdb=" N TYR H 37 " --> pdb=" O THR H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 60 Processing helix chain 'H' and resid 61 through 68 Processing helix chain 'H' and resid 69 through 84 removed outlier: 3.850A pdb=" N VAL H 77 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY H 78 " --> pdb=" O ILE H 74 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN H 83 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG H 84 " --> pdb=" O ARG H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 94 removed outlier: 3.971A pdb=" N ASN H 94 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 124 Processing helix chain 'H' and resid 130 through 137 Processing helix chain 'H' and resid 140 through 148 removed outlier: 3.650A pdb=" N ILE H 148 " --> pdb=" O ALA H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 152 Processing helix chain 'H' and resid 196 through 209 Processing helix chain 'I' and resid 19 through 32 removed outlier: 4.429A pdb=" N ASP I 23 " --> pdb=" O GLN I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 55 Processing helix chain 'I' and resid 88 through 104 Processing helix chain 'I' and resid 105 through 106 No H-bonds generated for 'chain 'I' and resid 105 through 106' Processing helix chain 'I' and resid 115 through 115 No H-bonds generated for 'chain 'I' and resid 115 through 115' Processing helix chain 'I' and resid 116 through 139 removed outlier: 3.709A pdb=" N THR I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR I 139 " --> pdb=" O GLY I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 149 removed outlier: 4.784A pdb=" N TRP I 144 " --> pdb=" O ASN I 141 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N VAL I 145 " --> pdb=" O ARG I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 193 Proline residue: I 174 - end of helix Processing helix chain 'I' and resid 199 through 210 removed outlier: 3.511A pdb=" N GLY I 203 " --> pdb=" O ARG I 199 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU I 210 " --> pdb=" O GLN I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 249 removed outlier: 3.685A pdb=" N PHE I 232 " --> pdb=" O TYR I 228 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR I 249 " --> pdb=" O THR I 245 " (cutoff:3.500A) Processing helix chain 'I' and resid 260 through 279 removed outlier: 4.089A pdb=" N LEU I 279 " --> pdb=" O VAL I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 312 removed outlier: 5.645A pdb=" N GLU I 301 " --> pdb=" O GLU I 297 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ILE I 302 " --> pdb=" O LYS I 298 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS I 304 " --> pdb=" O LEU I 300 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN I 308 " --> pdb=" O HIS I 304 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN I 309 " --> pdb=" O THR I 305 " (cutoff:3.500A) Processing helix chain 'I' and resid 316 through 327 removed outlier: 3.536A pdb=" N GLY I 320 " --> pdb=" O ASN I 316 " (cutoff:3.500A) Processing helix chain 'I' and resid 330 through 356 removed outlier: 4.033A pdb=" N GLY I 334 " --> pdb=" O GLN I 330 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY I 356 " --> pdb=" O ILE I 352 " (cutoff:3.500A) Processing helix chain 'I' and resid 363 through 385 Processing helix chain 'I' and resid 388 through 405 removed outlier: 3.711A pdb=" N ASN I 405 " --> pdb=" O ARG I 401 " (cutoff:3.500A) Processing helix chain 'I' and resid 406 through 412 Processing helix chain 'I' and resid 417 through 430 removed outlier: 3.526A pdb=" N LEU I 422 " --> pdb=" O SER I 418 " (cutoff:3.500A) Processing helix chain 'I' and resid 438 through 454 Processing helix chain 'I' and resid 458 through 476 removed outlier: 4.026A pdb=" N PHE I 462 " --> pdb=" O ASP I 458 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N HIS I 476 " --> pdb=" O LYS I 472 " (cutoff:3.500A) Processing helix chain 'I' and resid 481 through 496 Processing helix chain 'I' and resid 497 through 502 removed outlier: 4.023A pdb=" N THR I 501 " --> pdb=" O GLY I 497 " (cutoff:3.500A) Processing helix chain 'I' and resid 504 through 528 removed outlier: 3.789A pdb=" N PHE I 508 " --> pdb=" O LEU I 504 " (cutoff:3.500A) Processing helix chain 'I' and resid 559 through 574 Processing helix chain 'I' and resid 611 through 615 Processing helix chain 'I' and resid 622 through 629 Processing helix chain 'I' and resid 632 through 646 removed outlier: 4.231A pdb=" N GLN I 638 " --> pdb=" O ASP I 634 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU I 643 " --> pdb=" O VAL I 639 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 723 Processing helix chain 'I' and resid 726 through 739 removed outlier: 3.772A pdb=" N THR I 736 " --> pdb=" O GLY I 732 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN I 737 " --> pdb=" O GLU I 733 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU I 738 " --> pdb=" O VAL I 734 " (cutoff:3.500A) Processing helix chain 'I' and resid 745 through 750 Processing helix chain 'J' and resid 53 through 59 removed outlier: 3.641A pdb=" N ASN J 59 " --> pdb=" O GLU J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 89 Processing helix chain 'L' and resid 17 through 22 removed outlier: 4.040A pdb=" N ALA L 21 " --> pdb=" O ASP L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 33 removed outlier: 3.772A pdb=" N ASP L 33 " --> pdb=" O THR L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 65 removed outlier: 3.928A pdb=" N LYS L 57 " --> pdb=" O ALA L 53 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS L 65 " --> pdb=" O TRP L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 93 removed outlier: 3.658A pdb=" N LEU L 93 " --> pdb=" O ASP L 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 89 through 93' Processing helix chain 'L' and resid 98 through 111 removed outlier: 4.441A pdb=" N GLU L 102 " --> pdb=" O GLY L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 128 removed outlier: 3.774A pdb=" N ASP L 117 " --> pdb=" O LYS L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 140 Processing helix chain 'L' and resid 149 through 157 Processing helix chain 'M' and resid 101 through 110 Processing helix chain 'M' and resid 113 through 122 removed outlier: 4.240A pdb=" N GLY M 122 " --> pdb=" O LEU M 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 124 through 132 removed outlier: 3.746A pdb=" N SER M 132 " --> pdb=" O TYR M 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 148 through 159 removed outlier: 3.837A pdb=" N GLY M 159 " --> pdb=" O LEU M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 203 Processing helix chain 'M' and resid 219 through 229 removed outlier: 4.368A pdb=" N ASN M 229 " --> pdb=" O THR M 225 " (cutoff:3.500A) Processing helix chain 'M' and resid 244 through 255 removed outlier: 3.576A pdb=" N LEU M 248 " --> pdb=" O SER M 244 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N CYS M 255 " --> pdb=" O LEU M 251 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 281 Processing helix chain 'M' and resid 298 through 309 removed outlier: 3.608A pdb=" N CYS M 309 " --> pdb=" O LEU M 305 " (cutoff:3.500A) Processing helix chain 'M' and resid 326 through 331 removed outlier: 3.950A pdb=" N GLU M 330 " --> pdb=" O ASP M 326 " (cutoff:3.500A) Processing helix chain 'M' and resid 332 through 334 No H-bonds generated for 'chain 'M' and resid 332 through 334' Processing helix chain 'M' and resid 351 through 359 removed outlier: 4.069A pdb=" N LEU M 354 " --> pdb=" O GLU M 351 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE M 359 " --> pdb=" O LEU M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 375 through 383 Processing helix chain 'N' and resid 25 through 30 removed outlier: 3.571A pdb=" N LYS N 30 " --> pdb=" O LYS N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 39 through 47 removed outlier: 3.971A pdb=" N GLY N 47 " --> pdb=" O TRP N 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 48 removed outlier: 3.594A pdb=" N TYR A 47 " --> pdb=" O ASP A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 50 No H-bonds generated for 'chain 'A' and resid 49 through 50' Processing helix chain 'A' and resid 51 through 53 No H-bonds generated for 'chain 'A' and resid 51 through 53' Processing helix chain 'A' and resid 54 through 67 removed outlier: 4.154A pdb=" N GLU A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 83 removed outlier: 3.614A pdb=" N GLN A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 106 removed outlier: 3.652A pdb=" N TYR A 91 " --> pdb=" O ASN A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 155 removed outlier: 3.548A pdb=" N ASN A 155 " --> pdb=" O ASN A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 175 removed outlier: 3.676A pdb=" N CYS A 175 " --> pdb=" O HIS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 187 removed outlier: 3.958A pdb=" N ARG A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 213 removed outlier: 3.626A pdb=" N ASN A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 226 removed outlier: 3.616A pdb=" N GLU A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 260 removed outlier: 3.862A pdb=" N ALA A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 272 removed outlier: 3.912A pdb=" N LEU A 272 " --> pdb=" O LYS A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 301 removed outlier: 3.894A pdb=" N ALA A 290 " --> pdb=" O PRO A 286 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 removed outlier: 3.635A pdb=" N VAL A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 322 removed outlier: 3.531A pdb=" N LYS A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N PHE A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 335 removed outlier: 3.756A pdb=" N ARG A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 354 removed outlier: 3.923A pdb=" N CYS A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASP A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A 354 " --> pdb=" O ASP A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 379 removed outlier: 3.567A pdb=" N LEU A 365 " --> pdb=" O HIS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 393 Processing helix chain 'A' and resid 396 through 410 removed outlier: 3.585A pdb=" N GLN A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 462 removed outlier: 3.668A pdb=" N ASN A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 368 through 370 removed outlier: 7.374A pdb=" N VAL A 382 " --> pdb=" O GLY B 400 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ILE B 402 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA A 384 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL A 382 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU C 315 " --> pdb=" O PHE C 360 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N THR H 126 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ILE C 351 " --> pdb=" O THR H 126 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE H 128 " --> pdb=" O ILE C 351 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN H 154 " --> pdb=" O LEU H 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 318 through 320 Processing sheet with id=AA3, first strand: chain 'G' and resid 110 through 112 removed outlier: 6.684A pdb=" N GLN G 142 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 535 through 541 removed outlier: 3.871A pdb=" N SER I 536 " --> pdb=" O TRP J 27 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA J 29 " --> pdb=" O SER I 536 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN I 538 " --> pdb=" O ALA J 29 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA J 31 " --> pdb=" O GLN I 538 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL J 30 " --> pdb=" O LEU I 582 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 679 through 681 removed outlier: 6.456A pdb=" N THR I 600 " --> pdb=" O LEU I 680 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 620 through 621 removed outlier: 3.783A pdb=" N TYR I 620 " --> pdb=" O ILE I 669 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE I 669 " --> pdb=" O TYR I 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'J' and resid 70 through 71 removed outlier: 3.645A pdb=" N PHE J 79 " --> pdb=" O ALA J 71 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 314 through 316 removed outlier: 7.054A pdb=" N LEU M 288 " --> pdb=" O ASP M 316 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU M 261 " --> pdb=" O ASN M 289 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU M 211 " --> pdb=" O ASN M 236 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N MET M 186 " --> pdb=" O SER M 212 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU M 140 " --> pdb=" O ARG M 164 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU M 416 " --> pdb=" O THR M 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 216 through 217 removed outlier: 7.158A pdb=" N LEU M 216 " --> pdb=" O SER M 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'M' and resid 339 through 341 Processing sheet with id=AB2, first strand: chain 'M' and resid 408 through 409 Processing sheet with id=AB3, first strand: chain 'N' and resid 7 through 8 removed outlier: 3.848A pdb=" N TYR N 19 " --> pdb=" O TYR N 12 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TYR N 12 " --> pdb=" O TYR N 19 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 7 through 8 1571 hydrogen bonds defined for protein. 4605 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: 5.46 Time building geometry restraints manager: 3.12 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: 8696 1.34 - 1.46: 5427 1.46 - 1.58: 12603 1.58 - 1.70: 7 1.70 - 1.81: 219 Bond restraints: 26952 Sorted by residual: bond pdb=" O14 IHP B 501 " pdb=" P4 IHP B 501 " ideal model delta sigma weight residual 1.671 1.599 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" O12 IHP B 501 " pdb=" P2 IHP B 501 " ideal model delta sigma weight residual 1.675 1.605 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" O15 IHP B 501 " pdb=" P5 IHP B 501 " ideal model delta sigma weight residual 1.675 1.605 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" O16 IHP B 501 " pdb=" P6 IHP B 501 " ideal model delta sigma weight residual 1.672 1.605 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C5 IHP B 501 " pdb=" O15 IHP B 501 " ideal model delta sigma weight residual 1.389 1.442 -0.053 2.00e-02 2.50e+03 6.96e+00 ... (remaining 26947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 35863 1.96 - 3.92: 539 3.92 - 5.88: 73 5.88 - 7.85: 4 7.85 - 9.81: 5 Bond angle restraints: 36484 Sorted by residual: angle pdb=" N VAL B 439 " pdb=" CA VAL B 439 " pdb=" C VAL B 439 " ideal model delta sigma weight residual 110.21 105.04 5.17 1.13e+00 7.83e-01 2.09e+01 angle pdb=" N GLU B 163 " pdb=" CA GLU B 163 " pdb=" CB GLU B 163 " ideal model delta sigma weight residual 114.17 109.53 4.64 1.14e+00 7.69e-01 1.66e+01 angle pdb=" C GLU A 92 " pdb=" N GLU A 93 " pdb=" CA GLU A 93 " ideal model delta sigma weight residual 120.28 115.26 5.02 1.34e+00 5.57e-01 1.41e+01 angle pdb=" C PHE I 172 " pdb=" N ARG I 173 " pdb=" CA ARG I 173 " ideal model delta sigma weight residual 121.80 112.93 8.87 2.44e+00 1.68e-01 1.32e+01 angle pdb=" N VAL A 37 " pdb=" CA VAL A 37 " pdb=" C VAL A 37 " ideal model delta sigma weight residual 113.20 109.89 3.31 9.60e-01 1.09e+00 1.19e+01 ... (remaining 36479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 14891 17.93 - 35.86: 1217 35.86 - 53.79: 201 53.79 - 71.73: 53 71.73 - 89.66: 27 Dihedral angle restraints: 16389 sinusoidal: 6454 harmonic: 9935 Sorted by residual: dihedral pdb=" CA GLN G 147 " pdb=" C GLN G 147 " pdb=" N ARG G 148 " pdb=" CA ARG G 148 " ideal model delta harmonic sigma weight residual 180.00 155.97 24.03 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA GLY M 239 " pdb=" C GLY M 239 " pdb=" N CYS M 240 " pdb=" CA CYS M 240 " ideal model delta harmonic sigma weight residual -180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA LYS B 93 " pdb=" C LYS B 93 " pdb=" N GLN B 94 " pdb=" CA GLN B 94 " ideal model delta harmonic sigma weight residual 180.00 159.56 20.44 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 16386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3539 0.049 - 0.098: 559 0.098 - 0.148: 100 0.148 - 0.197: 6 0.197 - 0.246: 3 Chirality restraints: 4207 Sorted by residual: chirality pdb=" C1 IHP B 501 " pdb=" C2 IHP B 501 " pdb=" C6 IHP B 501 " pdb=" O11 IHP B 501 " both_signs ideal model delta sigma weight residual False 2.32 2.56 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C3 IHP B 501 " pdb=" C2 IHP B 501 " pdb=" C4 IHP B 501 " pdb=" O13 IHP B 501 " both_signs ideal model delta sigma weight residual False -2.34 -2.58 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CG LEU D 127 " pdb=" CB LEU D 127 " pdb=" CD1 LEU D 127 " pdb=" CD2 LEU D 127 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 4204 not shown) Planarity restraints: 4645 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP I 169 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.02e+00 pdb=" C ASP I 169 " -0.042 2.00e-02 2.50e+03 pdb=" O ASP I 169 " 0.016 2.00e-02 2.50e+03 pdb=" N CYS I 170 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 155 " 0.019 2.00e-02 2.50e+03 1.56e-02 4.89e+00 pdb=" CG TYR D 155 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR D 155 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR D 155 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR D 155 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 155 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR D 155 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 155 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG I 168 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.35e+00 pdb=" C ARG I 168 " -0.036 2.00e-02 2.50e+03 pdb=" O ARG I 168 " 0.013 2.00e-02 2.50e+03 pdb=" N ASP I 169 " 0.012 2.00e-02 2.50e+03 ... (remaining 4642 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 247 2.55 - 3.14: 23014 3.14 - 3.72: 40568 3.72 - 4.31: 51671 4.31 - 4.90: 85284 Nonbonded interactions: 200784 Sorted by model distance: nonbonded pdb=" OD1 ASP C 163 " pdb=" OH TYR C 192 " model vdw 1.961 3.040 nonbonded pdb=" O GLY A 53 " pdb=" OH TYR A 211 " model vdw 1.973 3.040 nonbonded pdb=" O25 IHP B 501 " pdb=" O44 IHP B 501 " model vdw 2.044 3.040 nonbonded pdb=" O21 IHP B 501 " pdb=" O32 IHP B 501 " model vdw 2.051 3.040 nonbonded pdb=" OG SER N 39 " pdb=" OE1 GLU N 42 " model vdw 2.059 3.040 ... (remaining 200779 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 27.280 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 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 : 0.003 0.072 26963 Z= 0.161 Angle : 0.615 9.807 36489 Z= 0.339 Chirality : 0.038 0.246 4207 Planarity : 0.004 0.063 4645 Dihedral : 14.068 89.658 9902 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.83 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.15), residues: 3290 helix: 1.24 (0.11), residues: 2088 sheet: -1.50 (0.53), residues: 105 loop : -2.03 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 91 TYR 0.038 0.002 TYR D 155 PHE 0.035 0.002 PHE C 78 TRP 0.028 0.001 TRP D 395 HIS 0.011 0.001 HIS D 307 Details of bonding type rmsd covalent geometry : bond 0.00329 (26952) covalent geometry : angle 0.61434 (36484) SS BOND : bond 0.00019 ( 1) SS BOND : angle 2.30267 ( 2) hydrogen bonds : bond 0.13830 ( 1569) hydrogen bonds : angle 5.79291 ( 4605) metal coordination : bond 0.00777 ( 10) metal coordination : angle 2.48997 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1226 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1226 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 GLN cc_start: 0.8237 (mp10) cc_final: 0.7957 (mp10) REVERT: B 75 MET cc_start: 0.7505 (ppp) cc_final: 0.7031 (ppp) REVERT: B 76 ILE cc_start: 0.8405 (mt) cc_final: 0.7764 (mt) REVERT: B 100 ARG cc_start: 0.7193 (ttp-110) cc_final: 0.6695 (ttp-110) REVERT: B 109 GLU cc_start: 0.7627 (tp30) cc_final: 0.7014 (tp30) REVERT: B 127 LEU cc_start: 0.8763 (mt) cc_final: 0.8326 (mp) REVERT: B 133 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8340 (mt-10) REVERT: B 149 PHE cc_start: 0.7854 (t80) cc_final: 0.7444 (t80) REVERT: B 152 ASN cc_start: 0.7982 (t0) cc_final: 0.7616 (t0) REVERT: B 161 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7371 (tm-30) REVERT: B 176 HIS cc_start: 0.7014 (m170) cc_final: 0.6533 (m170) REVERT: B 201 GLU cc_start: 0.8169 (pp20) cc_final: 0.7643 (pp20) REVERT: B 226 SER cc_start: 0.8301 (m) cc_final: 0.8039 (p) REVERT: B 234 MET cc_start: 0.7507 (mmm) cc_final: 0.6983 (mmm) REVERT: B 247 ARG cc_start: 0.8217 (ttm170) cc_final: 0.7761 (ttm170) REVERT: B 252 GLU cc_start: 0.7986 (tp30) cc_final: 0.7622 (tp30) REVERT: B 253 LYS cc_start: 0.8157 (mmtp) cc_final: 0.7587 (mtmm) REVERT: B 257 ASP cc_start: 0.8513 (m-30) cc_final: 0.7897 (m-30) REVERT: B 260 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7779 (mm-30) REVERT: B 266 ASP cc_start: 0.8456 (t0) cc_final: 0.8251 (t0) REVERT: B 297 GLN cc_start: 0.7878 (mt0) cc_final: 0.7670 (mt0) REVERT: B 307 GLU cc_start: 0.8080 (mp0) cc_final: 0.7731 (mp0) REVERT: B 318 TYR cc_start: 0.8806 (t80) cc_final: 0.8581 (t80) REVERT: B 322 ASP cc_start: 0.8457 (t0) cc_final: 0.8181 (t0) REVERT: B 325 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7394 (mm-30) REVERT: B 327 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7886 (mm-30) REVERT: B 328 LYS cc_start: 0.9041 (ttpp) cc_final: 0.8704 (ttmm) REVERT: B 338 MET cc_start: 0.7185 (tpt) cc_final: 0.6284 (tpt) REVERT: B 345 GLU cc_start: 0.8041 (tt0) cc_final: 0.7778 (tt0) REVERT: B 350 LEU cc_start: 0.8660 (mm) cc_final: 0.8344 (mp) REVERT: B 361 LYS cc_start: 0.8673 (tptp) cc_final: 0.8361 (tptp) REVERT: B 368 ARG cc_start: 0.8289 (mtp-110) cc_final: 0.8087 (mtp-110) REVERT: B 391 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7428 (tm-30) REVERT: B 401 ARG cc_start: 0.8380 (mtm180) cc_final: 0.8161 (mtm180) REVERT: B 406 ASN cc_start: 0.8643 (m-40) cc_final: 0.8306 (m110) REVERT: B 407 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7392 (mm-40) REVERT: B 408 LEU cc_start: 0.7940 (pp) cc_final: 0.7705 (pt) REVERT: B 411 LEU cc_start: 0.8200 (mp) cc_final: 0.7979 (mp) REVERT: B 415 LYS cc_start: 0.8426 (tttp) cc_final: 0.8148 (tttp) REVERT: B 433 SER cc_start: 0.9285 (m) cc_final: 0.9019 (p) REVERT: B 436 GLN cc_start: 0.8381 (mm-40) cc_final: 0.8057 (tp40) REVERT: C 82 GLN cc_start: 0.8329 (mt0) cc_final: 0.8028 (mt0) REVERT: C 100 PHE cc_start: 0.7382 (t80) cc_final: 0.6786 (t80) REVERT: C 104 CYS cc_start: 0.8549 (m) cc_final: 0.8092 (m) REVERT: C 115 LYS cc_start: 0.8742 (mttt) cc_final: 0.8529 (mttt) REVERT: C 116 GLN cc_start: 0.8504 (mt0) cc_final: 0.7801 (mp10) REVERT: C 126 GLN cc_start: 0.8135 (mt0) cc_final: 0.7752 (mp10) REVERT: C 129 ASP cc_start: 0.7673 (m-30) cc_final: 0.7298 (m-30) REVERT: C 130 LYS cc_start: 0.8546 (mmmt) cc_final: 0.8303 (mmmt) REVERT: C 136 ASN cc_start: 0.8991 (p0) cc_final: 0.8680 (p0) REVERT: C 147 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7892 (tm-30) REVERT: C 219 ILE cc_start: 0.8199 (mt) cc_final: 0.7851 (mm) REVERT: C 244 TYR cc_start: 0.7780 (p90) cc_final: 0.7066 (p90) REVERT: C 247 GLN cc_start: 0.8002 (pp30) cc_final: 0.7423 (tm-30) REVERT: C 258 ASN cc_start: 0.8123 (p0) cc_final: 0.7920 (p0) REVERT: C 271 ASN cc_start: 0.8161 (t0) cc_final: 0.7783 (t0) REVERT: C 280 ASN cc_start: 0.8610 (m-40) cc_final: 0.8331 (m110) REVERT: C 290 ASN cc_start: 0.8814 (m110) cc_final: 0.8573 (m110) REVERT: C 291 ASN cc_start: 0.8465 (m110) cc_final: 0.8241 (m110) REVERT: C 304 LYS cc_start: 0.8787 (mttp) cc_final: 0.8412 (mmtm) REVERT: C 320 GLN cc_start: 0.8353 (tp-100) cc_final: 0.7987 (tp40) REVERT: C 351 ILE cc_start: 0.8252 (mp) cc_final: 0.7961 (mp) REVERT: C 375 ASN cc_start: 0.8240 (m-40) cc_final: 0.7990 (m-40) REVERT: C 383 CYS cc_start: 0.8228 (t) cc_final: 0.7885 (p) REVERT: C 384 ILE cc_start: 0.8058 (mt) cc_final: 0.7765 (mt) REVERT: C 393 MET cc_start: 0.7510 (tpp) cc_final: 0.7081 (tpp) REVERT: C 405 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8199 (tm-30) REVERT: C 406 LYS cc_start: 0.8952 (mttp) cc_final: 0.8457 (mttp) REVERT: D 32 LYS cc_start: 0.8713 (ttmm) cc_final: 0.8511 (ttmm) REVERT: D 50 GLU cc_start: 0.8373 (pt0) cc_final: 0.7938 (pt0) REVERT: D 53 VAL cc_start: 0.7689 (m) cc_final: 0.7293 (p) REVERT: D 56 ASN cc_start: 0.8122 (p0) cc_final: 0.7230 (t0) REVERT: D 66 LEU cc_start: 0.7714 (tp) cc_final: 0.7466 (tp) REVERT: D 90 GLU cc_start: 0.7696 (tp30) cc_final: 0.6592 (tp30) REVERT: D 91 LYS cc_start: 0.8284 (mmpt) cc_final: 0.7492 (mmpt) REVERT: D 116 LYS cc_start: 0.8471 (ttpp) cc_final: 0.8201 (ttpp) REVERT: D 141 VAL cc_start: 0.8492 (p) cc_final: 0.8044 (t) REVERT: D 144 LYS cc_start: 0.8163 (mtmt) cc_final: 0.7676 (mtmt) REVERT: D 145 LEU cc_start: 0.8186 (tp) cc_final: 0.7691 (mm) REVERT: D 146 GLU cc_start: 0.7903 (tp30) cc_final: 0.7223 (tp30) REVERT: D 149 LEU cc_start: 0.8038 (mt) cc_final: 0.7568 (mt) REVERT: D 150 LYS cc_start: 0.8575 (ttmm) cc_final: 0.8267 (ttmm) REVERT: D 160 ASP cc_start: 0.7981 (t0) cc_final: 0.7545 (t0) REVERT: D 203 GLU cc_start: 0.7911 (mp0) cc_final: 0.7646 (mp0) REVERT: D 226 LEU cc_start: 0.8784 (tp) cc_final: 0.8501 (tp) REVERT: D 230 LEU cc_start: 0.8530 (tp) cc_final: 0.8299 (tp) REVERT: D 241 GLN cc_start: 0.8037 (tp40) cc_final: 0.7272 (tp40) REVERT: D 266 LYS cc_start: 0.8897 (mttt) cc_final: 0.8598 (mttt) REVERT: D 268 TYR cc_start: 0.8666 (t80) cc_final: 0.8464 (t80) REVERT: D 301 ASP cc_start: 0.7350 (m-30) cc_final: 0.6926 (m-30) REVERT: D 306 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7656 (mt-10) REVERT: D 321 PHE cc_start: 0.8942 (m-80) cc_final: 0.8605 (m-80) REVERT: D 323 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7082 (mt-10) REVERT: D 324 LEU cc_start: 0.8817 (tp) cc_final: 0.8536 (tp) REVERT: D 329 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7246 (mm-30) REVERT: D 336 GLU cc_start: 0.8521 (tt0) cc_final: 0.8140 (tt0) REVERT: D 342 MET cc_start: 0.8448 (ttp) cc_final: 0.8227 (ttm) REVERT: D 354 GLN cc_start: 0.8382 (tt0) cc_final: 0.8114 (tt0) REVERT: D 358 ILE cc_start: 0.8587 (mt) cc_final: 0.8236 (mm) REVERT: D 380 GLN cc_start: 0.8359 (mm110) cc_final: 0.8087 (mm-40) REVERT: D 385 LEU cc_start: 0.8873 (tp) cc_final: 0.8627 (tp) REVERT: D 387 LYS cc_start: 0.9092 (tttt) cc_final: 0.8882 (tttt) REVERT: E 252 SER cc_start: 0.8491 (m) cc_final: 0.8276 (m) REVERT: E 258 ASN cc_start: 0.8442 (m-40) cc_final: 0.8130 (m-40) REVERT: E 262 THR cc_start: 0.9175 (m) cc_final: 0.8890 (p) REVERT: E 265 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8228 (mm-40) REVERT: E 305 ARG cc_start: 0.8172 (mtp-110) cc_final: 0.7505 (mtp-110) REVERT: E 308 CYS cc_start: 0.8804 (m) cc_final: 0.8379 (m) REVERT: E 309 LYS cc_start: 0.8816 (tttt) cc_final: 0.8280 (tttt) REVERT: E 313 GLU cc_start: 0.8370 (tp30) cc_final: 0.7809 (tp30) REVERT: E 321 GLN cc_start: 0.8863 (mm110) cc_final: 0.8588 (mm110) REVERT: E 330 GLN cc_start: 0.8313 (mm-40) cc_final: 0.8071 (mm-40) REVERT: F 240 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7437 (mt-10) REVERT: F 241 TYR cc_start: 0.8578 (t80) cc_final: 0.8321 (t80) REVERT: F 270 LEU cc_start: 0.8763 (tp) cc_final: 0.8496 (tp) REVERT: F 278 ASP cc_start: 0.8219 (m-30) cc_final: 0.7785 (m-30) REVERT: F 283 CYS cc_start: 0.8997 (m) cc_final: 0.8541 (m) REVERT: F 301 THR cc_start: 0.8516 (m) cc_final: 0.8276 (p) REVERT: G 14 GLN cc_start: 0.7989 (mt0) cc_final: 0.7665 (mt0) REVERT: G 36 GLU cc_start: 0.7983 (pt0) cc_final: 0.7646 (pt0) REVERT: G 45 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7113 (tp30) REVERT: G 48 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6898 (mt-10) REVERT: G 65 GLN cc_start: 0.8066 (tp-100) cc_final: 0.7322 (tp-100) REVERT: G 66 LEU cc_start: 0.8737 (tt) cc_final: 0.8478 (tt) REVERT: G 67 LEU cc_start: 0.9091 (tp) cc_final: 0.8828 (tp) REVERT: G 74 THR cc_start: 0.8336 (p) cc_final: 0.7606 (p) REVERT: G 93 GLN cc_start: 0.8527 (pt0) cc_final: 0.8291 (pt0) REVERT: G 97 LYS cc_start: 0.8791 (mttt) cc_final: 0.8278 (mmtp) REVERT: G 99 LEU cc_start: 0.8774 (mt) cc_final: 0.8518 (mt) REVERT: G 125 LEU cc_start: 0.8582 (mt) cc_final: 0.8107 (mt) REVERT: G 129 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7806 (mt-10) REVERT: G 133 ILE cc_start: 0.8331 (mm) cc_final: 0.8064 (mm) REVERT: G 145 LEU cc_start: 0.8326 (tt) cc_final: 0.8101 (tt) REVERT: G 150 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8176 (mm-40) REVERT: G 155 ASP cc_start: 0.8430 (m-30) cc_final: 0.8179 (m-30) REVERT: G 169 ASN cc_start: 0.8516 (m110) cc_final: 0.8290 (m-40) REVERT: G 181 CYS cc_start: 0.8337 (m) cc_final: 0.7998 (m) REVERT: G 184 VAL cc_start: 0.8936 (t) cc_final: 0.8513 (p) REVERT: G 193 LEU cc_start: 0.8969 (tp) cc_final: 0.8757 (tp) REVERT: G 197 GLN cc_start: 0.8426 (tm-30) cc_final: 0.8087 (tm-30) REVERT: G 202 HIS cc_start: 0.8276 (t70) cc_final: 0.7916 (t70) REVERT: G 206 GLN cc_start: 0.7867 (tt0) cc_final: 0.7536 (tt0) REVERT: H 17 LEU cc_start: 0.8395 (tp) cc_final: 0.7968 (tp) REVERT: H 18 ASP cc_start: 0.7749 (m-30) cc_final: 0.7401 (m-30) REVERT: H 21 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7874 (mt-10) REVERT: H 22 ASN cc_start: 0.8561 (m-40) cc_final: 0.7808 (m-40) REVERT: H 23 GLN cc_start: 0.8578 (tt0) cc_final: 0.8155 (tt0) REVERT: H 26 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7376 (mp0) REVERT: H 58 LYS cc_start: 0.8526 (ttmt) cc_final: 0.8260 (ttmt) REVERT: H 125 TYR cc_start: 0.8085 (m-80) cc_final: 0.7735 (m-80) REVERT: I 22 ASP cc_start: 0.7727 (p0) cc_final: 0.7226 (p0) REVERT: I 91 ARG cc_start: 0.6640 (mpp80) cc_final: 0.6392 (mtm-85) REVERT: I 95 PHE cc_start: 0.6745 (t80) cc_final: 0.6472 (t80) REVERT: I 121 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8554 (tm-30) REVERT: I 243 PHE cc_start: 0.8090 (t80) cc_final: 0.7556 (t80) REVERT: I 247 GLU cc_start: 0.7080 (mp0) cc_final: 0.6712 (mp0) REVERT: I 262 LYS cc_start: 0.8457 (pttp) cc_final: 0.8242 (pttp) REVERT: I 287 LEU cc_start: 0.8633 (tp) cc_final: 0.8394 (tp) REVERT: I 312 ASP cc_start: 0.8528 (p0) cc_final: 0.8233 (p0) REVERT: I 322 MET cc_start: 0.8115 (ttm) cc_final: 0.7770 (ttm) REVERT: I 374 HIS cc_start: 0.8723 (t-90) cc_final: 0.8432 (t-170) REVERT: I 404 ASN cc_start: 0.8145 (m-40) cc_final: 0.7667 (m-40) REVERT: I 464 LYS cc_start: 0.8472 (tptm) cc_final: 0.8087 (tptm) REVERT: I 468 LYS cc_start: 0.8741 (tppt) cc_final: 0.8140 (tppt) REVERT: I 503 LYS cc_start: 0.8442 (ttmm) cc_final: 0.8086 (ttmm) REVERT: I 522 LYS cc_start: 0.8479 (tppp) cc_final: 0.8079 (tppp) REVERT: I 561 ARG cc_start: 0.7916 (mtt-85) cc_final: 0.7610 (mtt-85) REVERT: I 563 TYR cc_start: 0.8798 (t80) cc_final: 0.8351 (t80) REVERT: I 578 LYS cc_start: 0.8245 (pttp) cc_final: 0.7880 (pttp) REVERT: I 589 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6513 (mt-10) REVERT: I 607 GLN cc_start: 0.7861 (mp10) cc_final: 0.7658 (mp10) REVERT: I 638 GLN cc_start: 0.8647 (mp10) cc_final: 0.8303 (mp10) REVERT: I 721 MET cc_start: 0.8479 (mtm) cc_final: 0.8225 (mtm) REVERT: L 47 LEU cc_start: 0.5189 (mp) cc_final: 0.4893 (tt) REVERT: L 57 LYS cc_start: 0.8430 (ptpt) cc_final: 0.8203 (ptpt) REVERT: L 113 LYS cc_start: 0.9038 (pttm) cc_final: 0.8807 (pttm) REVERT: L 126 MET cc_start: 0.8241 (mmp) cc_final: 0.7935 (mmp) REVERT: M 155 LEU cc_start: 0.8588 (mp) cc_final: 0.8375 (mp) REVERT: M 323 LEU cc_start: 0.8779 (mp) cc_final: 0.8140 (pp) REVERT: M 335 ASN cc_start: 0.7679 (p0) cc_final: 0.7358 (p0) REVERT: M 368 PHE cc_start: 0.8960 (m-10) cc_final: 0.8748 (m-10) REVERT: N 23 MET cc_start: 0.6586 (ttm) cc_final: 0.6358 (ttm) REVERT: P 43 PHE cc_start: 0.8607 (p90) cc_final: 0.8170 (p90) REVERT: P 44 PHE cc_start: 0.7685 (t80) cc_final: 0.7437 (t80) REVERT: P 51 PHE cc_start: 0.9098 (m-80) cc_final: 0.8694 (m-80) REVERT: P 52 ASP cc_start: 0.7291 (t0) cc_final: 0.6747 (t0) REVERT: A 73 GLU cc_start: 0.8305 (mp0) cc_final: 0.8077 (mp0) REVERT: A 77 MET cc_start: 0.8751 (mtt) cc_final: 0.8536 (mtt) REVERT: A 81 PHE cc_start: 0.8427 (m-80) cc_final: 0.8006 (m-80) REVERT: A 90 MET cc_start: 0.8065 (tpt) cc_final: 0.7548 (tpt) REVERT: A 98 LEU cc_start: 0.9167 (mm) cc_final: 0.8833 (mm) REVERT: A 130 TRP cc_start: 0.6859 (t60) cc_final: 0.6486 (t60) REVERT: A 165 HIS cc_start: 0.8749 (m-70) cc_final: 0.8085 (m90) REVERT: A 172 TYR cc_start: 0.7819 (m-80) cc_final: 0.7602 (m-80) REVERT: A 196 LYS cc_start: 0.8903 (mptt) cc_final: 0.8647 (mptt) REVERT: A 226 GLU cc_start: 0.7702 (pt0) cc_final: 0.7178 (tm-30) REVERT: A 257 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7556 (mt-10) REVERT: A 262 LYS cc_start: 0.8736 (ttpp) cc_final: 0.8193 (ttpt) REVERT: A 301 PHE cc_start: 0.7962 (m-10) cc_final: 0.7525 (m-80) REVERT: A 302 ASP cc_start: 0.7235 (p0) cc_final: 0.6836 (p0) REVERT: A 321 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7821 (mt-10) REVERT: A 333 PHE cc_start: 0.8376 (t80) cc_final: 0.8176 (t80) REVERT: A 348 MET cc_start: 0.7446 (tmm) cc_final: 0.7231 (tmm) REVERT: A 378 PHE cc_start: 0.8581 (t80) cc_final: 0.8338 (t80) REVERT: A 379 SER cc_start: 0.8586 (t) cc_final: 0.8299 (p) REVERT: A 386 MET cc_start: 0.8597 (mtp) cc_final: 0.8394 (mtp) REVERT: A 388 ARG cc_start: 0.8193 (mtp180) cc_final: 0.7975 (mtm-85) REVERT: A 402 ASP cc_start: 0.7830 (t0) cc_final: 0.7415 (t0) REVERT: A 405 THR cc_start: 0.8268 (m) cc_final: 0.7974 (p) REVERT: A 406 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7929 (mm-40) REVERT: A 437 GLU cc_start: 0.8248 (tp30) cc_final: 0.7955 (tp30) REVERT: A 449 ARG cc_start: 0.8281 (mtm-85) cc_final: 0.7947 (mtm180) REVERT: A 451 LYS cc_start: 0.8551 (mtmt) cc_final: 0.7716 (mtmt) outliers start: 0 outliers final: 0 residues processed: 1226 average time/residue: 0.1679 time to fit residues: 319.9202 Evaluate side-chains 1155 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1155 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 10.0000 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS C 282 HIS D 75 ASN ** D 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 HIS E 248 ASN ** E 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 HIS F 284 ASN G 98 HIS ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 602 GLN L 64 HIS ** M 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 ASN A 309 ASN A 447 GLN A 465 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.136351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.109950 restraints weight = 60996.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.113819 restraints weight = 30929.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.116324 restraints weight = 18894.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.117994 restraints weight = 13094.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.119174 restraints weight = 9989.719| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26963 Z= 0.157 Angle : 0.662 12.874 36489 Z= 0.347 Chirality : 0.043 0.239 4207 Planarity : 0.004 0.047 4645 Dihedral : 5.124 54.549 3635 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.02 % Favored : 94.95 % Rotamer: Outliers : 2.37 % Allowed : 12.27 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.15), residues: 3290 helix: 1.54 (0.11), residues: 2121 sheet: -1.00 (0.49), residues: 124 loop : -1.89 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 46 TYR 0.037 0.002 TYR A 211 PHE 0.025 0.002 PHE C 252 TRP 0.028 0.002 TRP D 395 HIS 0.008 0.001 HIS D 307 Details of bonding type rmsd covalent geometry : bond 0.00328 (26952) covalent geometry : angle 0.66169 (36484) SS BOND : bond 0.00902 ( 1) SS BOND : angle 1.47896 ( 2) hydrogen bonds : bond 0.05399 ( 1569) hydrogen bonds : angle 4.57434 ( 4605) metal coordination : bond 0.00711 ( 10) metal coordination : angle 1.50974 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1271 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 1204 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 GLN cc_start: 0.8401 (mp10) cc_final: 0.7973 (mp10) REVERT: B 56 LYS cc_start: 0.8933 (mptt) cc_final: 0.8432 (mptt) REVERT: B 61 GLU cc_start: 0.7633 (pp20) cc_final: 0.7402 (pp20) REVERT: B 72 LEU cc_start: 0.8742 (mt) cc_final: 0.7950 (mt) REVERT: B 75 MET cc_start: 0.7807 (ppp) cc_final: 0.7215 (ppp) REVERT: B 76 ILE cc_start: 0.8497 (mt) cc_final: 0.7971 (mt) REVERT: B 109 GLU cc_start: 0.7965 (tp30) cc_final: 0.7333 (tp30) REVERT: B 124 GLN cc_start: 0.8191 (tt0) cc_final: 0.7593 (tt0) REVERT: B 127 LEU cc_start: 0.8716 (mt) cc_final: 0.8344 (mt) REVERT: B 149 PHE cc_start: 0.7995 (t80) cc_final: 0.7614 (t80) REVERT: B 152 ASN cc_start: 0.8121 (t0) cc_final: 0.7605 (t0) REVERT: B 161 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7316 (tm-30) REVERT: B 176 HIS cc_start: 0.7444 (m170) cc_final: 0.6455 (m170) REVERT: B 201 GLU cc_start: 0.8205 (pp20) cc_final: 0.7727 (pp20) REVERT: B 226 SER cc_start: 0.8443 (m) cc_final: 0.8194 (p) REVERT: B 234 MET cc_start: 0.7825 (mmm) cc_final: 0.7424 (mmm) REVERT: B 247 ARG cc_start: 0.8159 (ttm170) cc_final: 0.7649 (ttm170) REVERT: B 248 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7709 (tm-30) REVERT: B 252 GLU cc_start: 0.8234 (tp30) cc_final: 0.7929 (tp30) REVERT: B 253 LYS cc_start: 0.7980 (mmtp) cc_final: 0.7299 (mtmm) REVERT: B 257 ASP cc_start: 0.8481 (m-30) cc_final: 0.7853 (m-30) REVERT: B 260 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7829 (mm-30) REVERT: B 300 LYS cc_start: 0.8639 (ttpp) cc_final: 0.8101 (ttpp) REVERT: B 307 GLU cc_start: 0.8272 (mp0) cc_final: 0.8043 (mp0) REVERT: B 318 TYR cc_start: 0.8779 (t80) cc_final: 0.8532 (t80) REVERT: B 322 ASP cc_start: 0.8370 (t0) cc_final: 0.8040 (t0) REVERT: B 325 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7489 (mm-30) REVERT: B 328 LYS cc_start: 0.9102 (ttpp) cc_final: 0.8805 (ttmm) REVERT: B 338 MET cc_start: 0.7277 (tpt) cc_final: 0.6300 (tpt) REVERT: B 345 GLU cc_start: 0.8240 (tt0) cc_final: 0.7868 (tt0) REVERT: B 352 ARG cc_start: 0.7779 (ttm170) cc_final: 0.7544 (ttm170) REVERT: B 361 LYS cc_start: 0.8727 (tptp) cc_final: 0.8375 (tptp) REVERT: B 368 ARG cc_start: 0.8367 (mtp-110) cc_final: 0.8084 (mtp-110) REVERT: B 391 GLN cc_start: 0.8151 (tm-30) cc_final: 0.7596 (tm-30) REVERT: B 407 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7439 (mm-40) REVERT: B 410 GLU cc_start: 0.7623 (pp20) cc_final: 0.7162 (pp20) REVERT: B 411 LEU cc_start: 0.8185 (mp) cc_final: 0.7730 (mp) REVERT: B 415 LYS cc_start: 0.8447 (tttp) cc_final: 0.8173 (tttp) REVERT: B 429 ASN cc_start: 0.8900 (m110) cc_final: 0.8675 (m110) REVERT: B 433 SER cc_start: 0.9236 (m) cc_final: 0.8924 (p) REVERT: C 78 PHE cc_start: 0.8735 (t80) cc_final: 0.8430 (t80) REVERT: C 82 GLN cc_start: 0.8457 (mt0) cc_final: 0.8044 (mt0) REVERT: C 104 CYS cc_start: 0.8674 (m) cc_final: 0.8261 (m) REVERT: C 106 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8083 (mm-40) REVERT: C 116 GLN cc_start: 0.8546 (mt0) cc_final: 0.7913 (mp10) REVERT: C 126 GLN cc_start: 0.8343 (mt0) cc_final: 0.7619 (mm-40) REVERT: C 129 ASP cc_start: 0.7657 (m-30) cc_final: 0.7250 (m-30) REVERT: C 136 ASN cc_start: 0.8929 (p0) cc_final: 0.8346 (p0) REVERT: C 147 GLN cc_start: 0.8300 (tm-30) cc_final: 0.7984 (tm-30) REVERT: C 164 VAL cc_start: 0.8425 (p) cc_final: 0.8108 (m) REVERT: C 190 MET cc_start: 0.7799 (ttm) cc_final: 0.7527 (tpp) REVERT: C 219 ILE cc_start: 0.7988 (mt) cc_final: 0.7630 (mm) REVERT: C 244 TYR cc_start: 0.7954 (p90) cc_final: 0.7381 (p90) REVERT: C 247 GLN cc_start: 0.7995 (pp30) cc_final: 0.7378 (tm-30) REVERT: C 271 ASN cc_start: 0.7899 (t0) cc_final: 0.7112 (t0) REVERT: C 291 ASN cc_start: 0.8464 (m110) cc_final: 0.8066 (m110) REVERT: C 292 MET cc_start: 0.7929 (tmm) cc_final: 0.7674 (tmm) REVERT: C 304 LYS cc_start: 0.8819 (mttp) cc_final: 0.8426 (mmtp) REVERT: C 320 GLN cc_start: 0.8303 (tp-100) cc_final: 0.7914 (tp40) REVERT: C 354 LYS cc_start: 0.8540 (ttpp) cc_final: 0.7876 (tmmt) REVERT: C 366 LYS cc_start: 0.8686 (mmmm) cc_final: 0.8423 (mtpp) REVERT: C 380 MET cc_start: 0.8379 (mtt) cc_final: 0.7407 (mmm) REVERT: C 383 CYS cc_start: 0.8319 (t) cc_final: 0.7800 (p) REVERT: C 384 ILE cc_start: 0.8171 (mt) cc_final: 0.7865 (mt) REVERT: C 385 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7270 (tm-30) REVERT: C 393 MET cc_start: 0.7493 (tpp) cc_final: 0.7120 (tpp) REVERT: C 405 GLN cc_start: 0.8539 (tm-30) cc_final: 0.8206 (tm-30) REVERT: C 406 LYS cc_start: 0.9050 (mttp) cc_final: 0.8547 (mttp) REVERT: D 50 GLU cc_start: 0.8352 (pt0) cc_final: 0.7971 (pt0) REVERT: D 53 VAL cc_start: 0.7547 (m) cc_final: 0.6996 (p) REVERT: D 56 ASN cc_start: 0.8145 (p0) cc_final: 0.7602 (t0) REVERT: D 62 SER cc_start: 0.8112 (m) cc_final: 0.7520 (p) REVERT: D 66 LEU cc_start: 0.7608 (tp) cc_final: 0.7406 (tp) REVERT: D 90 GLU cc_start: 0.7788 (tp30) cc_final: 0.6651 (tp30) REVERT: D 91 LYS cc_start: 0.8344 (mmpt) cc_final: 0.7797 (mmpt) REVERT: D 141 VAL cc_start: 0.8043 (p) cc_final: 0.7668 (t) REVERT: D 144 LYS cc_start: 0.8098 (mtmt) cc_final: 0.7570 (mtmt) REVERT: D 145 LEU cc_start: 0.8167 (tp) cc_final: 0.7621 (mm) REVERT: D 146 GLU cc_start: 0.7950 (tp30) cc_final: 0.7370 (tm-30) REVERT: D 149 LEU cc_start: 0.8037 (mt) cc_final: 0.7619 (mt) REVERT: D 150 LYS cc_start: 0.8634 (ttmm) cc_final: 0.8355 (ttmm) REVERT: D 160 ASP cc_start: 0.8133 (t0) cc_final: 0.7764 (t0) REVERT: D 175 GLN cc_start: 0.7725 (pp30) cc_final: 0.7483 (pp30) REVERT: D 177 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7328 (pm20) REVERT: D 219 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8318 (mm-30) REVERT: D 226 LEU cc_start: 0.8845 (tp) cc_final: 0.8569 (tp) REVERT: D 230 LEU cc_start: 0.8532 (tp) cc_final: 0.8295 (tp) REVERT: D 240 GLN cc_start: 0.7169 (tm-30) cc_final: 0.6658 (tm-30) REVERT: D 241 GLN cc_start: 0.8127 (tp40) cc_final: 0.7716 (tp40) REVERT: D 245 MET cc_start: 0.8589 (tpp) cc_final: 0.8240 (tpp) REVERT: D 266 LYS cc_start: 0.8907 (mttt) cc_final: 0.8610 (mttt) REVERT: D 268 TYR cc_start: 0.8761 (t80) cc_final: 0.8513 (t80) REVERT: D 271 ARG cc_start: 0.7998 (mmt-90) cc_final: 0.7779 (mmt-90) REVERT: D 279 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7537 (mp10) REVERT: D 286 MET cc_start: 0.8370 (tpp) cc_final: 0.7381 (mpp) REVERT: D 289 GLN cc_start: 0.8842 (mt0) cc_final: 0.8475 (mt0) REVERT: D 301 ASP cc_start: 0.7399 (m-30) cc_final: 0.6998 (m-30) REVERT: D 306 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7649 (mt-10) REVERT: D 322 GLU cc_start: 0.8471 (mp0) cc_final: 0.8258 (mp0) REVERT: D 323 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7544 (mt-10) REVERT: D 329 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7223 (mm-30) REVERT: D 336 GLU cc_start: 0.8662 (tt0) cc_final: 0.8333 (tt0) REVERT: D 342 MET cc_start: 0.8629 (ttp) cc_final: 0.8328 (ttm) REVERT: D 354 GLN cc_start: 0.8458 (tt0) cc_final: 0.8167 (tt0) REVERT: D 358 ILE cc_start: 0.8525 (mt) cc_final: 0.8180 (mm) REVERT: D 380 GLN cc_start: 0.8383 (mm110) cc_final: 0.8115 (mm-40) REVERT: E 252 SER cc_start: 0.8491 (m) cc_final: 0.8200 (m) REVERT: E 254 SER cc_start: 0.8065 (t) cc_final: 0.7134 (t) REVERT: E 258 ASN cc_start: 0.8625 (m-40) cc_final: 0.8124 (m-40) REVERT: E 262 THR cc_start: 0.9147 (m) cc_final: 0.8891 (p) REVERT: E 305 ARG cc_start: 0.8348 (mtp-110) cc_final: 0.7594 (mtp-110) REVERT: E 308 CYS cc_start: 0.8874 (m) cc_final: 0.8556 (m) REVERT: E 309 LYS cc_start: 0.8932 (tttt) cc_final: 0.8444 (tttt) REVERT: E 313 GLU cc_start: 0.8506 (tp30) cc_final: 0.7866 (tp30) REVERT: E 321 GLN cc_start: 0.8838 (mm110) cc_final: 0.8584 (mm110) REVERT: F 240 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7439 (mt-10) REVERT: F 241 TYR cc_start: 0.8697 (t80) cc_final: 0.8441 (t80) REVERT: F 256 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8517 (mp) REVERT: F 258 ARG cc_start: 0.8355 (mtt180) cc_final: 0.8045 (ttm170) REVERT: F 270 LEU cc_start: 0.8685 (tp) cc_final: 0.8242 (tp) REVERT: F 278 ASP cc_start: 0.8323 (m-30) cc_final: 0.7877 (m-30) REVERT: F 283 CYS cc_start: 0.9134 (m) cc_final: 0.8663 (m) REVERT: F 301 THR cc_start: 0.8740 (m) cc_final: 0.8281 (p) REVERT: G 14 GLN cc_start: 0.8159 (mt0) cc_final: 0.7694 (mt0) REVERT: G 36 GLU cc_start: 0.8050 (pt0) cc_final: 0.7717 (pt0) REVERT: G 65 GLN cc_start: 0.8154 (tp-100) cc_final: 0.7259 (tp-100) REVERT: G 66 LEU cc_start: 0.8750 (tt) cc_final: 0.8535 (tt) REVERT: G 74 THR cc_start: 0.7499 (p) cc_final: 0.7113 (p) REVERT: G 92 GLN cc_start: 0.8767 (mt0) cc_final: 0.8388 (mt0) REVERT: G 93 GLN cc_start: 0.8599 (pt0) cc_final: 0.8382 (pt0) REVERT: G 95 LYS cc_start: 0.9169 (mtpp) cc_final: 0.8906 (mtpp) REVERT: G 97 LYS cc_start: 0.8735 (mttt) cc_final: 0.8318 (mmtp) REVERT: G 99 LEU cc_start: 0.8807 (mt) cc_final: 0.8585 (mt) REVERT: G 120 LEU cc_start: 0.8669 (mt) cc_final: 0.8310 (mm) REVERT: G 125 LEU cc_start: 0.8534 (mt) cc_final: 0.7855 (mt) REVERT: G 129 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7885 (mt-10) REVERT: G 133 ILE cc_start: 0.8299 (mm) cc_final: 0.8034 (mm) REVERT: G 150 GLN cc_start: 0.8516 (mm-40) cc_final: 0.8029 (mm-40) REVERT: G 155 ASP cc_start: 0.8401 (m-30) cc_final: 0.8164 (m-30) REVERT: G 161 ASP cc_start: 0.7132 (m-30) cc_final: 0.5568 (m-30) REVERT: G 169 ASN cc_start: 0.8475 (m110) cc_final: 0.8226 (m-40) REVERT: G 181 CYS cc_start: 0.8510 (m) cc_final: 0.8302 (m) REVERT: G 188 ILE cc_start: 0.8301 (mt) cc_final: 0.7943 (tp) REVERT: G 193 LEU cc_start: 0.9034 (tp) cc_final: 0.8802 (tp) REVERT: G 197 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8157 (tm-30) REVERT: G 202 HIS cc_start: 0.8300 (t70) cc_final: 0.7946 (t70) REVERT: H 17 LEU cc_start: 0.8462 (tp) cc_final: 0.8074 (tp) REVERT: H 18 ASP cc_start: 0.7921 (m-30) cc_final: 0.7612 (m-30) REVERT: H 21 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8001 (mt-10) REVERT: H 23 GLN cc_start: 0.8639 (tt0) cc_final: 0.8397 (tt0) REVERT: H 45 LEU cc_start: 0.8676 (mm) cc_final: 0.8433 (mm) REVERT: H 49 ASP cc_start: 0.7969 (t70) cc_final: 0.7388 (t0) REVERT: H 52 ASN cc_start: 0.8723 (m110) cc_final: 0.8439 (m110) REVERT: H 58 LYS cc_start: 0.8577 (ttmt) cc_final: 0.8354 (ttmt) REVERT: I 18 ASP cc_start: 0.7255 (p0) cc_final: 0.6615 (p0) REVERT: I 95 PHE cc_start: 0.6975 (t80) cc_final: 0.6720 (t80) REVERT: I 121 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8505 (tm-30) REVERT: I 243 PHE cc_start: 0.8088 (t80) cc_final: 0.7698 (t80) REVERT: I 262 LYS cc_start: 0.8596 (pttp) cc_final: 0.8263 (pttp) REVERT: I 287 LEU cc_start: 0.8811 (tp) cc_final: 0.8450 (tt) REVERT: I 312 ASP cc_start: 0.8574 (p0) cc_final: 0.8337 (p0) REVERT: I 322 MET cc_start: 0.8230 (ttm) cc_final: 0.7955 (ttm) REVERT: I 374 HIS cc_start: 0.8875 (t-90) cc_final: 0.8543 (t70) REVERT: I 381 VAL cc_start: 0.8896 (m) cc_final: 0.8680 (p) REVERT: I 404 ASN cc_start: 0.8240 (m-40) cc_final: 0.7812 (m-40) REVERT: I 429 LEU cc_start: 0.8384 (tp) cc_final: 0.8154 (tp) REVERT: I 464 LYS cc_start: 0.8446 (tptm) cc_final: 0.8035 (tptm) REVERT: I 468 LYS cc_start: 0.8706 (tppt) cc_final: 0.8119 (tppt) REVERT: I 503 LYS cc_start: 0.8436 (ttmm) cc_final: 0.8115 (ttmm) REVERT: I 522 LYS cc_start: 0.8360 (tppp) cc_final: 0.7996 (tppp) REVERT: I 564 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8126 (mt0) REVERT: I 607 GLN cc_start: 0.7990 (mp10) cc_final: 0.7498 (mp10) REVERT: I 630 GLN cc_start: 0.7346 (tm-30) cc_final: 0.6875 (tm-30) REVERT: I 638 GLN cc_start: 0.8800 (mp10) cc_final: 0.8415 (mp10) REVERT: I 721 MET cc_start: 0.8608 (mtm) cc_final: 0.8348 (mtm) REVERT: J 23 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7698 (tm-30) REVERT: J 50 MET cc_start: 0.1222 (mtt) cc_final: 0.0584 (mtt) REVERT: L 57 LYS cc_start: 0.8503 (ptpt) cc_final: 0.8268 (ptpt) REVERT: L 126 MET cc_start: 0.8319 (mmp) cc_final: 0.7954 (mmp) REVERT: L 142 LYS cc_start: 0.6834 (mppt) cc_final: 0.6484 (mppt) REVERT: M 102 ASP cc_start: 0.7256 (p0) cc_final: 0.6786 (p0) REVERT: M 118 LEU cc_start: 0.9101 (mp) cc_final: 0.8392 (tt) REVERT: M 214 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7366 (pp20) REVERT: M 259 ASP cc_start: 0.8050 (p0) cc_final: 0.7755 (p0) REVERT: M 323 LEU cc_start: 0.8742 (mp) cc_final: 0.8072 (pp) REVERT: M 368 PHE cc_start: 0.8850 (m-10) cc_final: 0.8521 (m-10) REVERT: N 58 MET cc_start: 0.7786 (mtp) cc_final: 0.7247 (mtp) REVERT: P 43 PHE cc_start: 0.8678 (p90) cc_final: 0.8211 (p90) REVERT: P 44 PHE cc_start: 0.7784 (t80) cc_final: 0.7506 (t80) REVERT: P 52 ASP cc_start: 0.7599 (t0) cc_final: 0.7025 (t0) REVERT: A 87 ASN cc_start: 0.7658 (t0) cc_final: 0.7377 (m-40) REVERT: A 90 MET cc_start: 0.8373 (tpt) cc_final: 0.7634 (tpt) REVERT: A 98 LEU cc_start: 0.9184 (mm) cc_final: 0.8967 (mm) REVERT: A 130 TRP cc_start: 0.7113 (t60) cc_final: 0.6505 (t60) REVERT: A 132 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8108 (pm20) REVERT: A 148 ASP cc_start: 0.8519 (p0) cc_final: 0.8193 (p0) REVERT: A 152 TYR cc_start: 0.8208 (m-10) cc_final: 0.7786 (m-10) REVERT: A 165 HIS cc_start: 0.8965 (m-70) cc_final: 0.8241 (m90) REVERT: A 172 TYR cc_start: 0.8212 (m-10) cc_final: 0.7949 (m-80) REVERT: A 174 ASP cc_start: 0.8707 (m-30) cc_final: 0.8001 (t0) REVERT: A 196 LYS cc_start: 0.9000 (mptt) cc_final: 0.8654 (mptt) REVERT: A 226 GLU cc_start: 0.7813 (pt0) cc_final: 0.7191 (tm-30) REVERT: A 288 ASN cc_start: 0.7600 (m110) cc_final: 0.7218 (m110) REVERT: A 296 CYS cc_start: 0.8298 (m) cc_final: 0.7893 (m) REVERT: A 301 PHE cc_start: 0.8012 (m-10) cc_final: 0.7461 (m-80) REVERT: A 317 LYS cc_start: 0.8552 (ptpt) cc_final: 0.8252 (ptpp) REVERT: A 321 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7742 (mt-10) REVERT: A 322 LEU cc_start: 0.8852 (mt) cc_final: 0.8451 (tp) REVERT: A 323 GLU cc_start: 0.7513 (mp0) cc_final: 0.6888 (mp0) REVERT: A 332 LYS cc_start: 0.8458 (mttt) cc_final: 0.8094 (mttt) REVERT: A 348 MET cc_start: 0.7464 (tmm) cc_final: 0.7217 (tmm) REVERT: A 367 THR cc_start: 0.8392 (m) cc_final: 0.8109 (p) REVERT: A 378 PHE cc_start: 0.8611 (t80) cc_final: 0.8406 (t80) REVERT: A 386 MET cc_start: 0.8702 (mtp) cc_final: 0.8346 (mtp) REVERT: A 402 ASP cc_start: 0.7880 (t0) cc_final: 0.7634 (t0) REVERT: A 437 GLU cc_start: 0.8291 (tp30) cc_final: 0.8043 (tp30) REVERT: A 451 LYS cc_start: 0.8478 (mtmt) cc_final: 0.7753 (mtmt) outliers start: 67 outliers final: 39 residues processed: 1216 average time/residue: 0.1676 time to fit residues: 315.4932 Evaluate side-chains 1205 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 1163 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 366 TYR Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 170 CYS Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain F residue 253 ASN Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain H residue 51 ASN Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain I residue 450 MET Chi-restraints excluded: chain I residue 587 LYS Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 190 ASN Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 460 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 59 optimal weight: 0.2980 chunk 192 optimal weight: 4.9990 chunk 309 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 281 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 259 optimal weight: 5.9990 chunk 221 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN B 211 ASN D 75 ASN D 240 GLN D 360 HIS G 98 HIS ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 134 ASN I 505 GLN I 520 GLN I 613 GLN L 65 HIS L 108 ASN ** M 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 236 ASN M 262 ASN M 387 GLN N 65 HIS A 447 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.138895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.112710 restraints weight = 61101.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.116535 restraints weight = 31010.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.119050 restraints weight = 18976.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.120696 restraints weight = 13159.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.121863 restraints weight = 10082.604| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26963 Z= 0.135 Angle : 0.637 12.805 36489 Z= 0.330 Chirality : 0.041 0.215 4207 Planarity : 0.004 0.048 4645 Dihedral : 5.039 50.688 3635 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.53 % Favored : 95.44 % Rotamer: Outliers : 2.62 % Allowed : 17.51 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.15), residues: 3290 helix: 1.65 (0.11), residues: 2142 sheet: -0.91 (0.46), residues: 137 loop : -1.82 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 193 TYR 0.025 0.001 TYR D 155 PHE 0.030 0.002 PHE M 332 TRP 0.021 0.001 TRP D 395 HIS 0.008 0.001 HIS D 307 Details of bonding type rmsd covalent geometry : bond 0.00281 (26952) covalent geometry : angle 0.63704 (36484) SS BOND : bond 0.00900 ( 1) SS BOND : angle 1.18797 ( 2) hydrogen bonds : bond 0.04801 ( 1569) hydrogen bonds : angle 4.30127 ( 4605) metal coordination : bond 0.00499 ( 10) metal coordination : angle 1.26179 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1269 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 1195 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 GLN cc_start: 0.8474 (mp10) cc_final: 0.7820 (mp10) REVERT: B 56 LYS cc_start: 0.8916 (mptt) cc_final: 0.8354 (mptt) REVERT: B 70 LYS cc_start: 0.9090 (tmtt) cc_final: 0.8871 (tmtt) REVERT: B 72 LEU cc_start: 0.8725 (mt) cc_final: 0.7843 (mt) REVERT: B 74 GLN cc_start: 0.8571 (tp40) cc_final: 0.7677 (tp40) REVERT: B 75 MET cc_start: 0.7662 (ppp) cc_final: 0.7090 (ppp) REVERT: B 76 ILE cc_start: 0.8562 (mt) cc_final: 0.7976 (mt) REVERT: B 100 ARG cc_start: 0.7327 (ttp-110) cc_final: 0.6928 (ttp-110) REVERT: B 109 GLU cc_start: 0.7956 (tp30) cc_final: 0.7250 (tp30) REVERT: B 115 ILE cc_start: 0.8669 (mt) cc_final: 0.8420 (tp) REVERT: B 124 GLN cc_start: 0.8297 (tt0) cc_final: 0.7541 (tt0) REVERT: B 127 LEU cc_start: 0.8714 (mt) cc_final: 0.8327 (mt) REVERT: B 133 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8463 (tt0) REVERT: B 149 PHE cc_start: 0.7938 (t80) cc_final: 0.7561 (t80) REVERT: B 152 ASN cc_start: 0.8080 (t0) cc_final: 0.7512 (t0) REVERT: B 155 LEU cc_start: 0.8664 (tt) cc_final: 0.8357 (tt) REVERT: B 161 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7301 (tm-30) REVERT: B 226 SER cc_start: 0.8439 (m) cc_final: 0.8186 (p) REVERT: B 234 MET cc_start: 0.7787 (mmm) cc_final: 0.7416 (mmm) REVERT: B 247 ARG cc_start: 0.8048 (ttm170) cc_final: 0.7594 (ttm170) REVERT: B 253 LYS cc_start: 0.7782 (mmtp) cc_final: 0.7160 (mtmm) REVERT: B 257 ASP cc_start: 0.8433 (m-30) cc_final: 0.7806 (m-30) REVERT: B 260 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7840 (mm-30) REVERT: B 291 ILE cc_start: 0.9295 (mp) cc_final: 0.8722 (tp) REVERT: B 318 TYR cc_start: 0.8836 (t80) cc_final: 0.8580 (t80) REVERT: B 322 ASP cc_start: 0.8366 (t0) cc_final: 0.8014 (t0) REVERT: B 325 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7485 (mm-30) REVERT: B 328 LYS cc_start: 0.9111 (ttpp) cc_final: 0.8784 (ttmm) REVERT: B 338 MET cc_start: 0.7197 (tpt) cc_final: 0.6283 (tpt) REVERT: B 345 GLU cc_start: 0.8168 (tt0) cc_final: 0.7928 (tt0) REVERT: B 358 VAL cc_start: 0.8980 (t) cc_final: 0.8754 (p) REVERT: B 361 LYS cc_start: 0.8715 (tptp) cc_final: 0.8340 (tptp) REVERT: B 363 ILE cc_start: 0.8873 (pt) cc_final: 0.8509 (tp) REVERT: B 368 ARG cc_start: 0.8334 (mtp-110) cc_final: 0.8001 (mtp-110) REVERT: B 391 GLN cc_start: 0.8166 (tm-30) cc_final: 0.7590 (tm-30) REVERT: B 407 GLN cc_start: 0.7768 (mm-40) cc_final: 0.7361 (mm-40) REVERT: B 411 LEU cc_start: 0.8162 (mp) cc_final: 0.7867 (mp) REVERT: B 415 LYS cc_start: 0.8424 (tttp) cc_final: 0.8132 (tttp) REVERT: B 429 ASN cc_start: 0.8839 (m110) cc_final: 0.8583 (m110) REVERT: B 431 LEU cc_start: 0.8216 (mt) cc_final: 0.7928 (mt) REVERT: B 433 SER cc_start: 0.9174 (m) cc_final: 0.8833 (p) REVERT: C 78 PHE cc_start: 0.8717 (t80) cc_final: 0.8371 (t80) REVERT: C 82 GLN cc_start: 0.8443 (mt0) cc_final: 0.7985 (mt0) REVERT: C 104 CYS cc_start: 0.8684 (m) cc_final: 0.8283 (m) REVERT: C 106 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8023 (mm-40) REVERT: C 126 GLN cc_start: 0.8371 (mt0) cc_final: 0.7619 (mm-40) REVERT: C 129 ASP cc_start: 0.7661 (m-30) cc_final: 0.7179 (m-30) REVERT: C 136 ASN cc_start: 0.8915 (p0) cc_final: 0.8358 (p0) REVERT: C 147 GLN cc_start: 0.8280 (tm-30) cc_final: 0.7966 (tm-30) REVERT: C 177 ASP cc_start: 0.8385 (p0) cc_final: 0.8146 (p0) REVERT: C 190 MET cc_start: 0.7832 (ttm) cc_final: 0.7606 (tpp) REVERT: C 203 TYR cc_start: 0.8439 (t80) cc_final: 0.8085 (t80) REVERT: C 207 GLN cc_start: 0.8343 (mm-40) cc_final: 0.7863 (mp10) REVERT: C 219 ILE cc_start: 0.7902 (mt) cc_final: 0.7540 (mm) REVERT: C 244 TYR cc_start: 0.7893 (p90) cc_final: 0.7434 (p90) REVERT: C 247 GLN cc_start: 0.7982 (pp30) cc_final: 0.7383 (tm-30) REVERT: C 271 ASN cc_start: 0.7798 (t0) cc_final: 0.6969 (t0) REVERT: C 291 ASN cc_start: 0.8377 (m110) cc_final: 0.8024 (m110) REVERT: C 292 MET cc_start: 0.7880 (tmm) cc_final: 0.7604 (tmm) REVERT: C 304 LYS cc_start: 0.8816 (mttp) cc_final: 0.8411 (mmtp) REVERT: C 320 GLN cc_start: 0.8212 (tp-100) cc_final: 0.7807 (tp40) REVERT: C 366 LYS cc_start: 0.8747 (mmmm) cc_final: 0.8379 (mtpp) REVERT: C 380 MET cc_start: 0.8310 (mtt) cc_final: 0.7587 (mmm) REVERT: C 383 CYS cc_start: 0.8188 (t) cc_final: 0.7874 (p) REVERT: C 384 ILE cc_start: 0.8162 (mt) cc_final: 0.7816 (mt) REVERT: C 385 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7347 (tm-30) REVERT: C 393 MET cc_start: 0.7505 (tpp) cc_final: 0.7052 (tpp) REVERT: C 405 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8180 (tm-30) REVERT: C 406 LYS cc_start: 0.9044 (mttp) cc_final: 0.8525 (mttp) REVERT: D 50 GLU cc_start: 0.8364 (pt0) cc_final: 0.7950 (pt0) REVERT: D 53 VAL cc_start: 0.7397 (m) cc_final: 0.7033 (p) REVERT: D 56 ASN cc_start: 0.8163 (p0) cc_final: 0.7676 (t0) REVERT: D 62 SER cc_start: 0.8225 (m) cc_final: 0.7605 (p) REVERT: D 90 GLU cc_start: 0.7767 (tp30) cc_final: 0.6677 (tp30) REVERT: D 91 LYS cc_start: 0.8445 (mmpt) cc_final: 0.7899 (mmpt) REVERT: D 95 ARG cc_start: 0.7053 (mtp180) cc_final: 0.6748 (mtp180) REVERT: D 141 VAL cc_start: 0.7950 (p) cc_final: 0.7655 (t) REVERT: D 142 ASP cc_start: 0.8117 (p0) cc_final: 0.7735 (p0) REVERT: D 144 LYS cc_start: 0.8135 (mtmt) cc_final: 0.7592 (mtmt) REVERT: D 145 LEU cc_start: 0.8163 (tp) cc_final: 0.7651 (mm) REVERT: D 146 GLU cc_start: 0.7936 (tp30) cc_final: 0.7123 (tp30) REVERT: D 149 LEU cc_start: 0.8032 (mt) cc_final: 0.7586 (mt) REVERT: D 150 LYS cc_start: 0.8618 (ttmm) cc_final: 0.8252 (ttmm) REVERT: D 160 ASP cc_start: 0.8137 (t0) cc_final: 0.7874 (t0) REVERT: D 202 ILE cc_start: 0.8547 (tp) cc_final: 0.8297 (pt) REVERT: D 219 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8328 (mm-30) REVERT: D 224 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8018 (mm-30) REVERT: D 226 LEU cc_start: 0.8867 (tp) cc_final: 0.8581 (tp) REVERT: D 230 LEU cc_start: 0.8553 (tp) cc_final: 0.8315 (tp) REVERT: D 241 GLN cc_start: 0.8022 (tp40) cc_final: 0.7702 (tp40) REVERT: D 245 MET cc_start: 0.8574 (tpp) cc_final: 0.8256 (tpp) REVERT: D 266 LYS cc_start: 0.8910 (mttt) cc_final: 0.8618 (mttt) REVERT: D 268 TYR cc_start: 0.8726 (t80) cc_final: 0.8438 (t80) REVERT: D 271 ARG cc_start: 0.8010 (mmt-90) cc_final: 0.7765 (mmt-90) REVERT: D 279 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7461 (mp10) REVERT: D 285 LEU cc_start: 0.8766 (mp) cc_final: 0.8436 (mp) REVERT: D 286 MET cc_start: 0.8291 (tpp) cc_final: 0.7298 (mpp) REVERT: D 289 GLN cc_start: 0.8854 (mt0) cc_final: 0.8447 (mt0) REVERT: D 301 ASP cc_start: 0.7411 (m-30) cc_final: 0.6988 (m-30) REVERT: D 306 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7682 (mt-10) REVERT: D 323 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7493 (mt-10) REVERT: D 329 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7204 (mm-30) REVERT: D 336 GLU cc_start: 0.8637 (tt0) cc_final: 0.8297 (tt0) REVERT: D 342 MET cc_start: 0.8590 (ttp) cc_final: 0.8212 (mtp) REVERT: D 354 GLN cc_start: 0.8461 (tt0) cc_final: 0.8209 (tt0) REVERT: D 358 ILE cc_start: 0.8463 (mt) cc_final: 0.8105 (mm) REVERT: D 372 LYS cc_start: 0.8686 (tptt) cc_final: 0.8238 (tptt) REVERT: D 380 GLN cc_start: 0.8354 (mm110) cc_final: 0.8106 (mm-40) REVERT: D 383 ASN cc_start: 0.7945 (m-40) cc_final: 0.7734 (m-40) REVERT: D 387 LYS cc_start: 0.9185 (tttt) cc_final: 0.8957 (tttt) REVERT: D 400 MET cc_start: 0.8758 (mtt) cc_final: 0.8549 (mtt) REVERT: E 252 SER cc_start: 0.8363 (m) cc_final: 0.8106 (m) REVERT: E 254 SER cc_start: 0.7917 (t) cc_final: 0.6974 (t) REVERT: E 258 ASN cc_start: 0.8617 (m-40) cc_final: 0.8072 (m-40) REVERT: E 262 THR cc_start: 0.9189 (m) cc_final: 0.8922 (p) REVERT: E 305 ARG cc_start: 0.8304 (mtp-110) cc_final: 0.7560 (mtp-110) REVERT: E 308 CYS cc_start: 0.8780 (m) cc_final: 0.8475 (m) REVERT: E 309 LYS cc_start: 0.8881 (tttt) cc_final: 0.8392 (tttt) REVERT: E 313 GLU cc_start: 0.8461 (tp30) cc_final: 0.7883 (tp30) REVERT: E 321 GLN cc_start: 0.8848 (mm110) cc_final: 0.8566 (mm110) REVERT: F 240 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7444 (mt-10) REVERT: F 241 TYR cc_start: 0.8706 (t80) cc_final: 0.8415 (t80) REVERT: F 258 ARG cc_start: 0.8337 (mtt180) cc_final: 0.7848 (mtt180) REVERT: F 278 ASP cc_start: 0.8309 (m-30) cc_final: 0.7847 (m-30) REVERT: F 279 PHE cc_start: 0.8713 (t80) cc_final: 0.8046 (t80) REVERT: F 283 CYS cc_start: 0.9155 (m) cc_final: 0.8576 (m) REVERT: F 285 ASP cc_start: 0.8150 (m-30) cc_final: 0.7889 (m-30) REVERT: F 301 THR cc_start: 0.8717 (m) cc_final: 0.8211 (p) REVERT: F 302 MET cc_start: 0.8076 (ttt) cc_final: 0.7522 (mmm) REVERT: G 14 GLN cc_start: 0.8135 (mt0) cc_final: 0.7670 (mt0) REVERT: G 36 GLU cc_start: 0.7898 (pt0) cc_final: 0.7664 (pt0) REVERT: G 45 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7419 (tp30) REVERT: G 65 GLN cc_start: 0.8080 (tp-100) cc_final: 0.7148 (tp-100) REVERT: G 66 LEU cc_start: 0.8690 (tt) cc_final: 0.8478 (tt) REVERT: G 92 GLN cc_start: 0.8720 (mt0) cc_final: 0.8395 (mt0) REVERT: G 93 GLN cc_start: 0.8563 (pt0) cc_final: 0.8322 (pt0) REVERT: G 97 LYS cc_start: 0.8760 (mttt) cc_final: 0.8248 (mmtp) REVERT: G 99 LEU cc_start: 0.8804 (mt) cc_final: 0.8551 (mt) REVERT: G 120 LEU cc_start: 0.8571 (mt) cc_final: 0.8301 (mm) REVERT: G 125 LEU cc_start: 0.8510 (mt) cc_final: 0.7741 (mt) REVERT: G 129 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7499 (mt-10) REVERT: G 133 ILE cc_start: 0.8254 (mm) cc_final: 0.8001 (mm) REVERT: G 150 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8081 (mm-40) REVERT: G 155 ASP cc_start: 0.8421 (m-30) cc_final: 0.8198 (m-30) REVERT: G 161 ASP cc_start: 0.7127 (m-30) cc_final: 0.5603 (m-30) REVERT: G 181 CYS cc_start: 0.8557 (m) cc_final: 0.8302 (m) REVERT: G 188 ILE cc_start: 0.8330 (mt) cc_final: 0.7957 (tp) REVERT: G 193 LEU cc_start: 0.9020 (tp) cc_final: 0.8784 (tp) REVERT: G 197 GLN cc_start: 0.8533 (tm-30) cc_final: 0.8136 (tm-30) REVERT: G 202 HIS cc_start: 0.8290 (t70) cc_final: 0.7936 (t70) REVERT: G 204 ARG cc_start: 0.8812 (ttm170) cc_final: 0.8500 (ttm170) REVERT: G 210 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7661 (mm-30) REVERT: H 17 LEU cc_start: 0.8447 (tp) cc_final: 0.8013 (tp) REVERT: H 18 ASP cc_start: 0.7788 (m-30) cc_final: 0.7549 (m-30) REVERT: H 21 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7950 (mt-10) REVERT: H 23 GLN cc_start: 0.8606 (tt0) cc_final: 0.8215 (tt0) REVERT: H 26 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7309 (mp0) REVERT: H 41 LEU cc_start: 0.8993 (tt) cc_final: 0.8722 (tp) REVERT: H 58 LYS cc_start: 0.8532 (ttmt) cc_final: 0.8305 (ttmt) REVERT: H 115 ARG cc_start: 0.7448 (tpt90) cc_final: 0.7151 (tpt90) REVERT: H 123 GLN cc_start: 0.8645 (tp-100) cc_final: 0.8316 (tp-100) REVERT: I 23 ASP cc_start: 0.7513 (p0) cc_final: 0.7302 (p0) REVERT: I 121 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8502 (tm-30) REVERT: I 262 LYS cc_start: 0.8552 (pttp) cc_final: 0.8201 (pttp) REVERT: I 287 LEU cc_start: 0.8814 (tp) cc_final: 0.8526 (tt) REVERT: I 312 ASP cc_start: 0.8524 (p0) cc_final: 0.8214 (p0) REVERT: I 322 MET cc_start: 0.8214 (ttm) cc_final: 0.7923 (ttm) REVERT: I 374 HIS cc_start: 0.8838 (t-90) cc_final: 0.8572 (t-170) REVERT: I 381 VAL cc_start: 0.8917 (m) cc_final: 0.8696 (p) REVERT: I 420 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7774 (tm-30) REVERT: I 424 ARG cc_start: 0.8465 (mmm-85) cc_final: 0.8117 (mmm-85) REVERT: I 431 LYS cc_start: 0.8484 (ptpp) cc_final: 0.8235 (ptpp) REVERT: I 464 LYS cc_start: 0.8380 (tptm) cc_final: 0.7968 (tptm) REVERT: I 466 TYR cc_start: 0.7945 (t80) cc_final: 0.7730 (t80) REVERT: I 468 LYS cc_start: 0.8660 (tppt) cc_final: 0.8083 (tppt) REVERT: I 503 LYS cc_start: 0.8453 (ttmm) cc_final: 0.8098 (ttmm) REVERT: I 522 LYS cc_start: 0.8433 (tppp) cc_final: 0.8079 (tppp) REVERT: I 545 TRP cc_start: 0.8569 (m100) cc_final: 0.8286 (m-10) REVERT: I 563 TYR cc_start: 0.8856 (t80) cc_final: 0.8204 (t80) REVERT: I 607 GLN cc_start: 0.7834 (mp10) cc_final: 0.7426 (mp10) REVERT: I 630 GLN cc_start: 0.7415 (tm-30) cc_final: 0.7003 (tm-30) REVERT: I 638 GLN cc_start: 0.8817 (mp10) cc_final: 0.8478 (mp10) REVERT: I 642 ILE cc_start: 0.8901 (mt) cc_final: 0.8531 (tt) REVERT: I 643 LEU cc_start: 0.8939 (mp) cc_final: 0.8455 (tp) REVERT: I 721 MET cc_start: 0.8627 (mtm) cc_final: 0.8360 (mtm) REVERT: J 23 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7268 (tm-30) REVERT: J 25 LYS cc_start: 0.7554 (ptpp) cc_final: 0.7054 (ptpp) REVERT: J 50 MET cc_start: 0.1203 (mtt) cc_final: 0.0546 (mtt) REVERT: L 32 GLU cc_start: 0.7969 (tp30) cc_final: 0.7521 (tp30) REVERT: L 57 LYS cc_start: 0.8394 (ptpt) cc_final: 0.8171 (ptpt) REVERT: L 126 MET cc_start: 0.8203 (mmp) cc_final: 0.7755 (mmp) REVERT: L 142 LYS cc_start: 0.6916 (mppt) cc_final: 0.6564 (mppt) REVERT: M 102 ASP cc_start: 0.7422 (p0) cc_final: 0.7135 (p0) REVERT: M 118 LEU cc_start: 0.9043 (mp) cc_final: 0.8352 (tt) REVERT: M 167 ARG cc_start: 0.7672 (mpp80) cc_final: 0.7407 (mpp80) REVERT: M 190 ASN cc_start: 0.6251 (p0) cc_final: 0.4892 (p0) REVERT: M 259 ASP cc_start: 0.7934 (p0) cc_final: 0.7602 (p0) REVERT: M 323 LEU cc_start: 0.8667 (mp) cc_final: 0.8038 (pp) REVERT: N 23 MET cc_start: 0.7108 (ttm) cc_final: 0.6637 (ttm) REVERT: N 36 HIS cc_start: 0.7697 (p90) cc_final: 0.7381 (p-80) REVERT: N 58 MET cc_start: 0.7636 (mtp) cc_final: 0.7217 (mtp) REVERT: P 43 PHE cc_start: 0.8623 (p90) cc_final: 0.8141 (p90) REVERT: P 44 PHE cc_start: 0.7727 (t80) cc_final: 0.7441 (t80) REVERT: P 52 ASP cc_start: 0.7574 (t0) cc_final: 0.7041 (t0) REVERT: A 87 ASN cc_start: 0.7557 (t0) cc_final: 0.7239 (m-40) REVERT: A 90 MET cc_start: 0.8365 (tpt) cc_final: 0.7827 (tpt) REVERT: A 132 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8061 (pm20) REVERT: A 148 ASP cc_start: 0.8514 (p0) cc_final: 0.8182 (p0) REVERT: A 152 TYR cc_start: 0.8235 (m-10) cc_final: 0.7823 (m-10) REVERT: A 165 HIS cc_start: 0.9007 (m-70) cc_final: 0.8268 (m90) REVERT: A 172 TYR cc_start: 0.8190 (m-10) cc_final: 0.7919 (m-80) REVERT: A 174 ASP cc_start: 0.8766 (m-30) cc_final: 0.8040 (t0) REVERT: A 196 LYS cc_start: 0.8820 (mptt) cc_final: 0.8450 (mptt) REVERT: A 226 GLU cc_start: 0.7833 (pt0) cc_final: 0.7195 (tm-30) REVERT: A 288 ASN cc_start: 0.7532 (m110) cc_final: 0.7039 (m110) REVERT: A 296 CYS cc_start: 0.8295 (m) cc_final: 0.7930 (m) REVERT: A 301 PHE cc_start: 0.7945 (m-10) cc_final: 0.7361 (m-80) REVERT: A 304 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7616 (mm-40) REVERT: A 317 LYS cc_start: 0.8516 (ptpt) cc_final: 0.8193 (ptpp) REVERT: A 321 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7795 (mt-10) REVERT: A 322 LEU cc_start: 0.8868 (mt) cc_final: 0.8487 (tp) REVERT: A 323 GLU cc_start: 0.7525 (mp0) cc_final: 0.7113 (mp0) REVERT: A 332 LYS cc_start: 0.8388 (mttt) cc_final: 0.8086 (mttt) REVERT: A 348 MET cc_start: 0.7445 (tmm) cc_final: 0.7241 (tmm) REVERT: A 355 ASP cc_start: 0.8551 (t0) cc_final: 0.8313 (t0) REVERT: A 367 THR cc_start: 0.8361 (m) cc_final: 0.8056 (p) REVERT: A 386 MET cc_start: 0.8668 (mtp) cc_final: 0.8334 (mtp) REVERT: A 408 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8432 (tp) REVERT: A 437 GLU cc_start: 0.8235 (tp30) cc_final: 0.7996 (tp30) REVERT: A 451 LYS cc_start: 0.8465 (mtmt) cc_final: 0.7918 (mtmt) outliers start: 74 outliers final: 54 residues processed: 1212 average time/residue: 0.1668 time to fit residues: 313.7066 Evaluate side-chains 1225 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 1169 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 288 HIS Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain F residue 253 ASN Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain F residue 304 GLN Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain H residue 51 ASN Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 450 MET Chi-restraints excluded: chain I residue 550 SER Chi-restraints excluded: chain I residue 587 LYS Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 207 LYS Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 236 ASN Chi-restraints excluded: chain M residue 240 CYS Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 460 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 252 optimal weight: 6.9990 chunk 316 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 305 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 192 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 249 optimal weight: 0.0670 chunk 101 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN C 105 HIS D 75 ASN D 176 ASN D 360 HIS G 98 HIS ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 HIS M 190 ASN M 236 ASN ** M 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.138396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.112527 restraints weight = 60097.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.116313 restraints weight = 30552.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.118791 restraints weight = 18682.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.120422 restraints weight = 12980.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.121606 restraints weight = 9865.983| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26963 Z= 0.133 Angle : 0.641 13.911 36489 Z= 0.332 Chirality : 0.042 0.254 4207 Planarity : 0.004 0.077 4645 Dihedral : 5.047 59.087 3635 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.89 % Favored : 95.08 % Rotamer: Outliers : 3.25 % Allowed : 18.82 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.15), residues: 3290 helix: 1.66 (0.12), residues: 2147 sheet: -0.98 (0.48), residues: 127 loop : -1.83 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 561 TYR 0.035 0.001 TYR A 211 PHE 0.030 0.002 PHE H 133 TRP 0.021 0.001 TRP N 43 HIS 0.007 0.001 HIS D 307 Details of bonding type rmsd covalent geometry : bond 0.00281 (26952) covalent geometry : angle 0.64112 (36484) SS BOND : bond 0.00076 ( 1) SS BOND : angle 2.28068 ( 2) hydrogen bonds : bond 0.04627 ( 1569) hydrogen bonds : angle 4.21530 ( 4605) metal coordination : bond 0.00421 ( 10) metal coordination : angle 1.22011 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1272 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 1180 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 GLN cc_start: 0.8444 (mp10) cc_final: 0.7770 (mp10) REVERT: B 56 LYS cc_start: 0.8874 (mptt) cc_final: 0.8328 (mptt) REVERT: B 72 LEU cc_start: 0.8745 (mt) cc_final: 0.8324 (mt) REVERT: B 74 GLN cc_start: 0.8591 (tp40) cc_final: 0.7714 (tp40) REVERT: B 100 ARG cc_start: 0.7382 (ttp-110) cc_final: 0.6956 (ttp-110) REVERT: B 109 GLU cc_start: 0.8001 (tp30) cc_final: 0.7266 (tp30) REVERT: B 115 ILE cc_start: 0.8658 (mt) cc_final: 0.8407 (tp) REVERT: B 124 GLN cc_start: 0.8144 (tt0) cc_final: 0.7943 (tt0) REVERT: B 133 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8447 (tt0) REVERT: B 140 LYS cc_start: 0.8647 (ptpp) cc_final: 0.8129 (ptpt) REVERT: B 149 PHE cc_start: 0.7987 (t80) cc_final: 0.7593 (t80) REVERT: B 152 ASN cc_start: 0.8090 (t0) cc_final: 0.7488 (t0) REVERT: B 155 LEU cc_start: 0.8644 (tt) cc_final: 0.8373 (tt) REVERT: B 161 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7323 (tm-30) REVERT: B 164 GLU cc_start: 0.8103 (tp30) cc_final: 0.7469 (tm-30) REVERT: B 198 TYR cc_start: 0.8348 (m-10) cc_final: 0.7953 (m-10) REVERT: B 225 LYS cc_start: 0.8774 (mptt) cc_final: 0.8407 (mptt) REVERT: B 226 SER cc_start: 0.8471 (m) cc_final: 0.8222 (p) REVERT: B 234 MET cc_start: 0.7781 (mmm) cc_final: 0.7409 (mmm) REVERT: B 253 LYS cc_start: 0.7776 (mmtp) cc_final: 0.6799 (mmtp) REVERT: B 257 ASP cc_start: 0.8399 (m-30) cc_final: 0.7791 (m-30) REVERT: B 260 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7823 (mm-30) REVERT: B 285 MET cc_start: 0.8313 (ttm) cc_final: 0.8061 (ttm) REVERT: B 291 ILE cc_start: 0.9308 (mp) cc_final: 0.8737 (tp) REVERT: B 318 TYR cc_start: 0.8822 (t80) cc_final: 0.8573 (t80) REVERT: B 322 ASP cc_start: 0.8356 (t0) cc_final: 0.7996 (t0) REVERT: B 325 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7489 (mm-30) REVERT: B 328 LYS cc_start: 0.9119 (ttpp) cc_final: 0.8783 (ttmm) REVERT: B 338 MET cc_start: 0.7220 (tpt) cc_final: 0.6257 (tpt) REVERT: B 358 VAL cc_start: 0.8975 (t) cc_final: 0.8740 (p) REVERT: B 361 LYS cc_start: 0.8724 (tptp) cc_final: 0.8336 (tptp) REVERT: B 363 ILE cc_start: 0.8908 (pt) cc_final: 0.8516 (tp) REVERT: B 368 ARG cc_start: 0.8333 (mtp-110) cc_final: 0.7962 (mtp-110) REVERT: B 391 GLN cc_start: 0.8150 (tm-30) cc_final: 0.7542 (tm-30) REVERT: B 407 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7373 (mm-40) REVERT: B 410 GLU cc_start: 0.7687 (pp20) cc_final: 0.7262 (pp20) REVERT: B 411 LEU cc_start: 0.8139 (mp) cc_final: 0.7606 (mp) REVERT: B 415 LYS cc_start: 0.8403 (tttp) cc_final: 0.8099 (tttp) REVERT: B 429 ASN cc_start: 0.8823 (m110) cc_final: 0.8567 (m110) REVERT: B 431 LEU cc_start: 0.8197 (mt) cc_final: 0.7918 (mt) REVERT: B 433 SER cc_start: 0.9148 (m) cc_final: 0.8795 (p) REVERT: C 78 PHE cc_start: 0.8721 (t80) cc_final: 0.8475 (t80) REVERT: C 82 GLN cc_start: 0.8456 (mt0) cc_final: 0.7909 (mt0) REVERT: C 100 PHE cc_start: 0.7518 (t80) cc_final: 0.6938 (t80) REVERT: C 104 CYS cc_start: 0.8650 (m) cc_final: 0.8156 (m) REVERT: C 106 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8074 (mm-40) REVERT: C 126 GLN cc_start: 0.8290 (mt0) cc_final: 0.7609 (mm-40) REVERT: C 129 ASP cc_start: 0.7658 (m-30) cc_final: 0.7157 (m-30) REVERT: C 136 ASN cc_start: 0.8963 (p0) cc_final: 0.8309 (p0) REVERT: C 147 GLN cc_start: 0.8306 (tm-30) cc_final: 0.7993 (tm-30) REVERT: C 203 TYR cc_start: 0.8466 (t80) cc_final: 0.8112 (t80) REVERT: C 207 GLN cc_start: 0.8383 (mm-40) cc_final: 0.7855 (mp10) REVERT: C 244 TYR cc_start: 0.7926 (p90) cc_final: 0.7581 (p90) REVERT: C 247 GLN cc_start: 0.7960 (pp30) cc_final: 0.7392 (tm-30) REVERT: C 271 ASN cc_start: 0.7679 (t0) cc_final: 0.6920 (t0) REVERT: C 291 ASN cc_start: 0.8376 (m110) cc_final: 0.8044 (m110) REVERT: C 292 MET cc_start: 0.7883 (tmm) cc_final: 0.7623 (tmm) REVERT: C 304 LYS cc_start: 0.8781 (mttp) cc_final: 0.8394 (mmtp) REVERT: C 309 ARG cc_start: 0.8930 (ttm170) cc_final: 0.8567 (ttp-170) REVERT: C 320 GLN cc_start: 0.8183 (tp-100) cc_final: 0.7769 (tp40) REVERT: C 365 GLU cc_start: 0.8105 (tp30) cc_final: 0.7760 (tp30) REVERT: C 366 LYS cc_start: 0.8728 (mmmm) cc_final: 0.8371 (mtpp) REVERT: C 379 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7306 (mm-30) REVERT: C 380 MET cc_start: 0.8271 (mtt) cc_final: 0.7518 (mmm) REVERT: C 383 CYS cc_start: 0.8147 (t) cc_final: 0.7811 (p) REVERT: C 384 ILE cc_start: 0.8216 (mt) cc_final: 0.7890 (mt) REVERT: C 385 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7370 (tm-30) REVERT: C 393 MET cc_start: 0.7435 (tpp) cc_final: 0.7104 (tpp) REVERT: C 405 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8162 (tm-30) REVERT: C 406 LYS cc_start: 0.9037 (mttp) cc_final: 0.8525 (mttp) REVERT: D 50 GLU cc_start: 0.8297 (pt0) cc_final: 0.7884 (pt0) REVERT: D 53 VAL cc_start: 0.7414 (m) cc_final: 0.7088 (p) REVERT: D 56 ASN cc_start: 0.8127 (p0) cc_final: 0.7737 (t0) REVERT: D 62 SER cc_start: 0.8192 (m) cc_final: 0.7596 (p) REVERT: D 90 GLU cc_start: 0.7783 (tp30) cc_final: 0.6731 (tp30) REVERT: D 91 LYS cc_start: 0.8486 (mmpt) cc_final: 0.7906 (mmpt) REVERT: D 95 ARG cc_start: 0.7090 (mtp180) cc_final: 0.6887 (mmm-85) REVERT: D 141 VAL cc_start: 0.7968 (p) cc_final: 0.7717 (t) REVERT: D 142 ASP cc_start: 0.8052 (p0) cc_final: 0.7753 (p0) REVERT: D 144 LYS cc_start: 0.8155 (mtmt) cc_final: 0.7597 (mtmt) REVERT: D 145 LEU cc_start: 0.8179 (tp) cc_final: 0.7679 (mm) REVERT: D 146 GLU cc_start: 0.7930 (tp30) cc_final: 0.7128 (tp30) REVERT: D 149 LEU cc_start: 0.8038 (mt) cc_final: 0.7607 (mt) REVERT: D 150 LYS cc_start: 0.8619 (ttmm) cc_final: 0.8242 (ttmm) REVERT: D 160 ASP cc_start: 0.8133 (t0) cc_final: 0.7907 (t0) REVERT: D 203 GLU cc_start: 0.8000 (mp0) cc_final: 0.7405 (mp0) REVERT: D 219 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8357 (mm-30) REVERT: D 224 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8049 (mm-30) REVERT: D 226 LEU cc_start: 0.8882 (tp) cc_final: 0.8591 (tp) REVERT: D 227 LYS cc_start: 0.9016 (ttpp) cc_final: 0.8613 (ttpp) REVERT: D 230 LEU cc_start: 0.8586 (tp) cc_final: 0.8353 (tp) REVERT: D 241 GLN cc_start: 0.8121 (tp40) cc_final: 0.7669 (tp40) REVERT: D 245 MET cc_start: 0.8612 (tpp) cc_final: 0.8311 (tpp) REVERT: D 266 LYS cc_start: 0.8906 (mttt) cc_final: 0.8619 (mttt) REVERT: D 268 TYR cc_start: 0.8694 (t80) cc_final: 0.8428 (t80) REVERT: D 271 ARG cc_start: 0.8017 (mmt-90) cc_final: 0.7752 (mmt-90) REVERT: D 280 GLU cc_start: 0.7423 (pm20) cc_final: 0.6755 (pm20) REVERT: D 285 LEU cc_start: 0.8755 (mp) cc_final: 0.8545 (mt) REVERT: D 286 MET cc_start: 0.8279 (tpp) cc_final: 0.7225 (mpp) REVERT: D 289 GLN cc_start: 0.8838 (mt0) cc_final: 0.8444 (mt0) REVERT: D 301 ASP cc_start: 0.7396 (m-30) cc_final: 0.7005 (m-30) REVERT: D 306 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7683 (mt-10) REVERT: D 323 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7379 (mt-10) REVERT: D 329 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7135 (mm-30) REVERT: D 336 GLU cc_start: 0.8645 (tt0) cc_final: 0.8309 (tt0) REVERT: D 342 MET cc_start: 0.8593 (ttp) cc_final: 0.8230 (mtp) REVERT: D 354 GLN cc_start: 0.8472 (tt0) cc_final: 0.8200 (tt0) REVERT: D 358 ILE cc_start: 0.8424 (mt) cc_final: 0.8092 (mm) REVERT: D 372 LYS cc_start: 0.8667 (tptt) cc_final: 0.8190 (tptt) REVERT: D 380 GLN cc_start: 0.8368 (mm110) cc_final: 0.8088 (mm-40) REVERT: D 383 ASN cc_start: 0.7942 (m-40) cc_final: 0.7609 (m-40) REVERT: D 387 LYS cc_start: 0.9170 (tttt) cc_final: 0.8880 (tttt) REVERT: E 252 SER cc_start: 0.8259 (m) cc_final: 0.7970 (m) REVERT: E 254 SER cc_start: 0.7957 (t) cc_final: 0.6964 (t) REVERT: E 258 ASN cc_start: 0.8644 (m-40) cc_final: 0.8101 (m-40) REVERT: E 262 THR cc_start: 0.9207 (m) cc_final: 0.8891 (p) REVERT: E 272 LYS cc_start: 0.8918 (mtpt) cc_final: 0.8704 (mttt) REVERT: E 305 ARG cc_start: 0.8276 (mtp-110) cc_final: 0.7571 (mtp-110) REVERT: E 308 CYS cc_start: 0.8732 (m) cc_final: 0.8458 (m) REVERT: E 309 LYS cc_start: 0.8866 (tttt) cc_final: 0.8395 (tttt) REVERT: E 313 GLU cc_start: 0.8471 (tp30) cc_final: 0.7895 (tp30) REVERT: E 321 GLN cc_start: 0.8862 (mm110) cc_final: 0.8576 (mm110) REVERT: F 230 MET cc_start: 0.8386 (mmt) cc_final: 0.7986 (mmt) REVERT: F 240 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7426 (mt-10) REVERT: F 241 TYR cc_start: 0.8703 (t80) cc_final: 0.8414 (t80) REVERT: F 258 ARG cc_start: 0.8286 (mtt180) cc_final: 0.8068 (mtt180) REVERT: F 278 ASP cc_start: 0.8287 (m-30) cc_final: 0.7827 (m-30) REVERT: F 279 PHE cc_start: 0.8727 (t80) cc_final: 0.8065 (t80) REVERT: F 283 CYS cc_start: 0.9161 (m) cc_final: 0.8570 (m) REVERT: F 285 ASP cc_start: 0.8196 (m-30) cc_final: 0.7900 (m-30) REVERT: F 301 THR cc_start: 0.8707 (m) cc_final: 0.8207 (p) REVERT: F 302 MET cc_start: 0.8059 (ttt) cc_final: 0.7523 (mmm) REVERT: G 14 GLN cc_start: 0.8114 (mt0) cc_final: 0.7640 (mt0) REVERT: G 36 GLU cc_start: 0.7908 (pt0) cc_final: 0.7665 (pt0) REVERT: G 65 GLN cc_start: 0.8115 (tp-100) cc_final: 0.7150 (tp-100) REVERT: G 66 LEU cc_start: 0.8715 (tt) cc_final: 0.8503 (tt) REVERT: G 75 TYR cc_start: 0.8225 (t80) cc_final: 0.7904 (t80) REVERT: G 92 GLN cc_start: 0.8706 (mt0) cc_final: 0.8369 (mt0) REVERT: G 93 GLN cc_start: 0.8572 (pt0) cc_final: 0.8319 (pt0) REVERT: G 97 LYS cc_start: 0.8723 (mttt) cc_final: 0.8082 (mmtp) REVERT: G 99 LEU cc_start: 0.8788 (mt) cc_final: 0.8515 (mt) REVERT: G 120 LEU cc_start: 0.8474 (mt) cc_final: 0.8207 (mm) REVERT: G 125 LEU cc_start: 0.8487 (mt) cc_final: 0.7738 (mt) REVERT: G 129 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7444 (mt-10) REVERT: G 133 ILE cc_start: 0.8275 (mm) cc_final: 0.8019 (mm) REVERT: G 150 GLN cc_start: 0.8544 (mm-40) cc_final: 0.8091 (mm-40) REVERT: G 155 ASP cc_start: 0.8420 (m-30) cc_final: 0.8213 (m-30) REVERT: G 181 CYS cc_start: 0.8517 (m) cc_final: 0.8291 (m) REVERT: G 188 ILE cc_start: 0.8322 (mt) cc_final: 0.7996 (tp) REVERT: G 193 LEU cc_start: 0.9003 (tp) cc_final: 0.8769 (tp) REVERT: G 197 GLN cc_start: 0.8520 (tm-30) cc_final: 0.8114 (tm-30) REVERT: G 202 HIS cc_start: 0.8265 (t70) cc_final: 0.7875 (t70) REVERT: G 204 ARG cc_start: 0.8832 (ttm170) cc_final: 0.8505 (ttm170) REVERT: G 210 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7664 (mm-30) REVERT: H 17 LEU cc_start: 0.8441 (tp) cc_final: 0.7998 (tp) REVERT: H 18 ASP cc_start: 0.7771 (m-30) cc_final: 0.7526 (m-30) REVERT: H 21 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7919 (mt-10) REVERT: H 23 GLN cc_start: 0.8588 (tt0) cc_final: 0.8187 (tt0) REVERT: H 26 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7336 (mp0) REVERT: H 41 LEU cc_start: 0.8997 (tt) cc_final: 0.8791 (tp) REVERT: H 58 LYS cc_start: 0.8569 (ttmt) cc_final: 0.8323 (ttmt) REVERT: H 59 ARG cc_start: 0.7808 (ttm170) cc_final: 0.7581 (ttp-170) REVERT: H 123 GLN cc_start: 0.8635 (tp-100) cc_final: 0.8284 (tp-100) REVERT: I 95 PHE cc_start: 0.7083 (t80) cc_final: 0.6842 (t80) REVERT: I 121 GLN cc_start: 0.8846 (tm-30) cc_final: 0.8561 (tm-30) REVERT: I 206 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7972 (tm-30) REVERT: I 243 PHE cc_start: 0.8044 (t80) cc_final: 0.7724 (t80) REVERT: I 262 LYS cc_start: 0.8518 (pttp) cc_final: 0.8194 (pttp) REVERT: I 287 LEU cc_start: 0.8821 (tp) cc_final: 0.8172 (tt) REVERT: I 291 CYS cc_start: 0.8876 (m) cc_final: 0.8249 (m) REVERT: I 322 MET cc_start: 0.8144 (ttm) cc_final: 0.7801 (ttm) REVERT: I 347 GLN cc_start: 0.7497 (mt0) cc_final: 0.7285 (mt0) REVERT: I 374 HIS cc_start: 0.8787 (t-90) cc_final: 0.8519 (t-170) REVERT: I 381 VAL cc_start: 0.8935 (m) cc_final: 0.8723 (p) REVERT: I 420 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7586 (tm-30) REVERT: I 424 ARG cc_start: 0.8467 (mmm-85) cc_final: 0.8097 (mmm-85) REVERT: I 428 SER cc_start: 0.8870 (t) cc_final: 0.8489 (p) REVERT: I 429 LEU cc_start: 0.8363 (tp) cc_final: 0.8039 (tp) REVERT: I 464 LYS cc_start: 0.8356 (tptm) cc_final: 0.7961 (tptm) REVERT: I 466 TYR cc_start: 0.7952 (t80) cc_final: 0.7733 (t80) REVERT: I 468 LYS cc_start: 0.8651 (tppt) cc_final: 0.8106 (tppt) REVERT: I 494 GLN cc_start: 0.8781 (tp-100) cc_final: 0.8535 (tp-100) REVERT: I 503 LYS cc_start: 0.8475 (ttmm) cc_final: 0.8125 (ttmm) REVERT: I 522 LYS cc_start: 0.8397 (tppp) cc_final: 0.8010 (tppp) REVERT: I 560 GLU cc_start: 0.7644 (tt0) cc_final: 0.7395 (tt0) REVERT: I 564 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8400 (mt0) REVERT: I 602 GLN cc_start: 0.6933 (tp40) cc_final: 0.6626 (tp40) REVERT: I 607 GLN cc_start: 0.7853 (mp10) cc_final: 0.7414 (mp10) REVERT: I 630 GLN cc_start: 0.7434 (tm-30) cc_final: 0.6995 (tm-30) REVERT: I 638 GLN cc_start: 0.8812 (mp10) cc_final: 0.8427 (mp10) REVERT: I 642 ILE cc_start: 0.8896 (mt) cc_final: 0.8523 (tt) REVERT: I 643 LEU cc_start: 0.8923 (mp) cc_final: 0.8429 (tp) REVERT: I 721 MET cc_start: 0.8626 (mtm) cc_final: 0.8349 (mtm) REVERT: J 23 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7217 (tm-30) REVERT: J 25 LYS cc_start: 0.7544 (ptpp) cc_final: 0.7088 (ptpp) REVERT: J 50 MET cc_start: 0.1277 (mtt) cc_final: 0.0658 (mtt) REVERT: L 32 GLU cc_start: 0.8017 (tp30) cc_final: 0.7500 (tp30) REVERT: L 57 LYS cc_start: 0.8375 (ptpt) cc_final: 0.8127 (ptpt) REVERT: L 126 MET cc_start: 0.8120 (mmp) cc_final: 0.7651 (mmp) REVERT: L 142 LYS cc_start: 0.6953 (mppt) cc_final: 0.6599 (mppt) REVERT: M 102 ASP cc_start: 0.7507 (p0) cc_final: 0.7100 (p0) REVERT: M 118 LEU cc_start: 0.9046 (mp) cc_final: 0.8318 (tt) REVERT: M 167 ARG cc_start: 0.7715 (mpp80) cc_final: 0.7492 (mpp80) REVERT: M 217 ARG cc_start: 0.5702 (OUTLIER) cc_final: 0.3646 (ptp90) REVERT: M 218 LEU cc_start: 0.7722 (mm) cc_final: 0.7377 (mm) REVERT: M 251 LEU cc_start: 0.8813 (tt) cc_final: 0.8459 (pp) REVERT: M 259 ASP cc_start: 0.8028 (p0) cc_final: 0.7675 (p0) REVERT: M 323 LEU cc_start: 0.8689 (mp) cc_final: 0.8067 (pp) REVERT: N 36 HIS cc_start: 0.7720 (p90) cc_final: 0.7386 (p-80) REVERT: N 58 MET cc_start: 0.7572 (mtp) cc_final: 0.7164 (mtp) REVERT: P 43 PHE cc_start: 0.8608 (p90) cc_final: 0.8388 (p90) REVERT: P 44 PHE cc_start: 0.7762 (t80) cc_final: 0.7517 (t80) REVERT: P 52 ASP cc_start: 0.7549 (t0) cc_final: 0.7032 (t0) REVERT: A 87 ASN cc_start: 0.7519 (t0) cc_final: 0.7206 (m-40) REVERT: A 90 MET cc_start: 0.8179 (tpt) cc_final: 0.7455 (tpt) REVERT: A 130 TRP cc_start: 0.7339 (t60) cc_final: 0.7024 (t60) REVERT: A 132 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.8028 (pm20) REVERT: A 148 ASP cc_start: 0.8520 (p0) cc_final: 0.8122 (p0) REVERT: A 152 TYR cc_start: 0.8209 (m-10) cc_final: 0.7748 (m-10) REVERT: A 165 HIS cc_start: 0.9006 (m-70) cc_final: 0.8298 (m90) REVERT: A 172 TYR cc_start: 0.8210 (m-10) cc_final: 0.7928 (m-80) REVERT: A 174 ASP cc_start: 0.8771 (m-30) cc_final: 0.8054 (t0) REVERT: A 196 LYS cc_start: 0.8750 (mptt) cc_final: 0.8380 (mptt) REVERT: A 226 GLU cc_start: 0.7815 (pt0) cc_final: 0.7219 (tm-30) REVERT: A 262 LYS cc_start: 0.8609 (ttpp) cc_final: 0.8136 (ttpt) REVERT: A 288 ASN cc_start: 0.7503 (m110) cc_final: 0.6876 (m110) REVERT: A 296 CYS cc_start: 0.8319 (m) cc_final: 0.7956 (m) REVERT: A 304 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7491 (mm-40) REVERT: A 307 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8339 (tm-30) REVERT: A 317 LYS cc_start: 0.8462 (ptpt) cc_final: 0.8160 (ptpt) REVERT: A 321 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7739 (mt-10) REVERT: A 322 LEU cc_start: 0.8858 (mt) cc_final: 0.8461 (tp) REVERT: A 323 GLU cc_start: 0.7534 (mp0) cc_final: 0.7059 (mp0) REVERT: A 332 LYS cc_start: 0.8324 (mttt) cc_final: 0.8025 (mttt) REVERT: A 348 MET cc_start: 0.7464 (tmm) cc_final: 0.7227 (tmm) REVERT: A 355 ASP cc_start: 0.8459 (t0) cc_final: 0.8179 (t0) REVERT: A 367 THR cc_start: 0.8341 (m) cc_final: 0.8027 (p) REVERT: A 386 MET cc_start: 0.8649 (mtp) cc_final: 0.8295 (mtp) REVERT: A 408 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8450 (tp) REVERT: A 437 GLU cc_start: 0.8229 (tp30) cc_final: 0.8014 (tp30) outliers start: 92 outliers final: 66 residues processed: 1205 average time/residue: 0.1683 time to fit residues: 315.1742 Evaluate side-chains 1215 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 1146 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 288 HIS Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain F residue 253 ASN Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain F residue 304 GLN Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 190 GLN Chi-restraints excluded: chain H residue 51 ASN Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain I residue 247 GLU Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 450 MET Chi-restraints excluded: chain I residue 550 SER Chi-restraints excluded: chain I residue 587 LYS Chi-restraints excluded: chain I residue 589 GLU Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain M residue 190 ASN Chi-restraints excluded: chain M residue 217 ARG Chi-restraints excluded: chain M residue 240 CYS Chi-restraints excluded: chain M residue 262 ASN Chi-restraints excluded: chain M residue 275 GLN Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 460 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 212 optimal weight: 4.9990 chunk 188 optimal weight: 0.9980 chunk 180 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 chunk 234 optimal weight: 5.9990 chunk 279 optimal weight: 0.7980 chunk 270 optimal weight: 0.6980 chunk 325 optimal weight: 0.7980 chunk 179 optimal weight: 0.9980 chunk 247 optimal weight: 0.8980 chunk 162 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS C 116 GLN D 75 ASN D 176 ASN ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 HIS G 98 HIS G 147 GLN H 52 ASN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 613 GLN ** J 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 65 HIS ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.137721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.111725 restraints weight = 59982.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.115503 restraints weight = 30640.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.117976 restraints weight = 18809.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.119590 restraints weight = 13090.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.120743 restraints weight = 10055.747| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26963 Z= 0.137 Angle : 0.640 13.891 36489 Z= 0.329 Chirality : 0.042 0.330 4207 Planarity : 0.004 0.047 4645 Dihedral : 4.999 53.392 3635 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.65 % Favored : 95.32 % Rotamer: Outliers : 3.43 % Allowed : 20.34 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.15), residues: 3290 helix: 1.67 (0.12), residues: 2145 sheet: -0.84 (0.46), residues: 137 loop : -1.84 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 561 TYR 0.023 0.001 TYR A 91 PHE 0.025 0.001 PHE M 332 TRP 0.021 0.001 TRP N 43 HIS 0.004 0.001 HIS D 307 Details of bonding type rmsd covalent geometry : bond 0.00288 (26952) covalent geometry : angle 0.63974 (36484) SS BOND : bond 0.00120 ( 1) SS BOND : angle 2.02632 ( 2) hydrogen bonds : bond 0.04567 ( 1569) hydrogen bonds : angle 4.17511 ( 4605) metal coordination : bond 0.00421 ( 10) metal coordination : angle 1.27003 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1265 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 1168 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 GLN cc_start: 0.8441 (mp10) cc_final: 0.7845 (mp10) REVERT: B 56 LYS cc_start: 0.8868 (mptt) cc_final: 0.8653 (tptt) REVERT: B 66 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7183 (mm-30) REVERT: B 70 LYS cc_start: 0.8953 (tmtt) cc_final: 0.8706 (tmtt) REVERT: B 72 LEU cc_start: 0.8722 (mt) cc_final: 0.8006 (mt) REVERT: B 74 GLN cc_start: 0.8624 (tp40) cc_final: 0.7709 (tp40) REVERT: B 75 MET cc_start: 0.7751 (ppp) cc_final: 0.7145 (ppp) REVERT: B 76 ILE cc_start: 0.8371 (mt) cc_final: 0.8140 (tp) REVERT: B 109 GLU cc_start: 0.8019 (tp30) cc_final: 0.7304 (tp30) REVERT: B 115 ILE cc_start: 0.8635 (mt) cc_final: 0.8375 (tp) REVERT: B 124 GLN cc_start: 0.8088 (tt0) cc_final: 0.7595 (tt0) REVERT: B 127 LEU cc_start: 0.8818 (mt) cc_final: 0.8616 (mp) REVERT: B 133 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8462 (tt0) REVERT: B 136 LEU cc_start: 0.8600 (mt) cc_final: 0.8370 (mt) REVERT: B 140 LYS cc_start: 0.8643 (ptpp) cc_final: 0.8428 (ptpt) REVERT: B 149 PHE cc_start: 0.7982 (t80) cc_final: 0.7606 (t80) REVERT: B 152 ASN cc_start: 0.8031 (t0) cc_final: 0.7460 (t0) REVERT: B 161 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7294 (tm-30) REVERT: B 164 GLU cc_start: 0.8128 (tp30) cc_final: 0.7603 (tm-30) REVERT: B 198 TYR cc_start: 0.8361 (m-10) cc_final: 0.7855 (m-80) REVERT: B 225 LYS cc_start: 0.8766 (mptt) cc_final: 0.8535 (mptt) REVERT: B 226 SER cc_start: 0.8463 (m) cc_final: 0.8217 (p) REVERT: B 234 MET cc_start: 0.7799 (mmm) cc_final: 0.7442 (mmm) REVERT: B 250 GLU cc_start: 0.8380 (tt0) cc_final: 0.7979 (tt0) REVERT: B 257 ASP cc_start: 0.8403 (m-30) cc_final: 0.7753 (m-30) REVERT: B 260 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7811 (mm-30) REVERT: B 291 ILE cc_start: 0.9291 (mp) cc_final: 0.8708 (tp) REVERT: B 322 ASP cc_start: 0.8383 (t0) cc_final: 0.8019 (t0) REVERT: B 325 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7458 (mm-30) REVERT: B 328 LYS cc_start: 0.9120 (ttpp) cc_final: 0.8790 (ttmm) REVERT: B 338 MET cc_start: 0.7266 (tpt) cc_final: 0.6237 (tpt) REVERT: B 347 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8401 (mm) REVERT: B 361 LYS cc_start: 0.8711 (tptp) cc_final: 0.8330 (tptp) REVERT: B 363 ILE cc_start: 0.8920 (pt) cc_final: 0.8573 (tp) REVERT: B 368 ARG cc_start: 0.8366 (mtp-110) cc_final: 0.8090 (mtp-110) REVERT: B 391 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7562 (tm-30) REVERT: B 407 GLN cc_start: 0.7782 (mm-40) cc_final: 0.7137 (mm-40) REVERT: B 410 GLU cc_start: 0.7654 (pp20) cc_final: 0.7260 (pp20) REVERT: B 411 LEU cc_start: 0.8193 (mp) cc_final: 0.7573 (mp) REVERT: B 415 LYS cc_start: 0.8399 (tttp) cc_final: 0.8092 (tttp) REVERT: B 421 TYR cc_start: 0.8585 (m-10) cc_final: 0.8274 (m-80) REVERT: B 431 LEU cc_start: 0.8229 (mt) cc_final: 0.8012 (mt) REVERT: B 433 SER cc_start: 0.9113 (m) cc_final: 0.8768 (p) REVERT: C 82 GLN cc_start: 0.8466 (mt0) cc_final: 0.8020 (mt0) REVERT: C 98 ASP cc_start: 0.8604 (t0) cc_final: 0.8240 (m-30) REVERT: C 100 PHE cc_start: 0.7535 (t80) cc_final: 0.6975 (t80) REVERT: C 104 CYS cc_start: 0.8698 (m) cc_final: 0.8236 (m) REVERT: C 106 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8026 (mm-40) REVERT: C 121 ILE cc_start: 0.8957 (mm) cc_final: 0.8750 (tp) REVERT: C 126 GLN cc_start: 0.8305 (mt0) cc_final: 0.7554 (mm-40) REVERT: C 129 ASP cc_start: 0.7659 (m-30) cc_final: 0.7170 (m-30) REVERT: C 136 ASN cc_start: 0.8971 (p0) cc_final: 0.8171 (p0) REVERT: C 147 GLN cc_start: 0.8316 (tm-30) cc_final: 0.8001 (tm-30) REVERT: C 166 MET cc_start: 0.7633 (mpp) cc_final: 0.7396 (mpp) REVERT: C 207 GLN cc_start: 0.8380 (mm-40) cc_final: 0.8051 (mm-40) REVERT: C 219 ILE cc_start: 0.7956 (mt) cc_final: 0.7594 (mm) REVERT: C 244 TYR cc_start: 0.7929 (p90) cc_final: 0.7646 (p90) REVERT: C 247 GLN cc_start: 0.7926 (pp30) cc_final: 0.7390 (tm-30) REVERT: C 271 ASN cc_start: 0.7688 (t0) cc_final: 0.6911 (t0) REVERT: C 291 ASN cc_start: 0.8341 (m110) cc_final: 0.8040 (m110) REVERT: C 292 MET cc_start: 0.7873 (tmm) cc_final: 0.7587 (tmm) REVERT: C 304 LYS cc_start: 0.8788 (mttp) cc_final: 0.8410 (mmtp) REVERT: C 309 ARG cc_start: 0.8938 (ttm170) cc_final: 0.8563 (ttp-170) REVERT: C 320 GLN cc_start: 0.8182 (tp-100) cc_final: 0.7768 (tp40) REVERT: C 365 GLU cc_start: 0.8162 (tp30) cc_final: 0.7708 (tp30) REVERT: C 366 LYS cc_start: 0.8724 (mmmm) cc_final: 0.8363 (mtpp) REVERT: C 379 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7314 (mm-30) REVERT: C 380 MET cc_start: 0.8377 (mtt) cc_final: 0.7517 (mmm) REVERT: C 383 CYS cc_start: 0.8157 (t) cc_final: 0.7801 (p) REVERT: C 385 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7360 (tm-30) REVERT: C 393 MET cc_start: 0.7465 (tpp) cc_final: 0.7135 (tpp) REVERT: C 405 GLN cc_start: 0.8486 (tm-30) cc_final: 0.8146 (tm-30) REVERT: C 406 LYS cc_start: 0.9027 (mttp) cc_final: 0.8506 (mttp) REVERT: D 28 GLN cc_start: 0.8214 (mp10) cc_final: 0.7888 (mm-40) REVERT: D 50 GLU cc_start: 0.8279 (pt0) cc_final: 0.7836 (pt0) REVERT: D 53 VAL cc_start: 0.7563 (m) cc_final: 0.7252 (p) REVERT: D 56 ASN cc_start: 0.8114 (p0) cc_final: 0.7817 (t0) REVERT: D 62 SER cc_start: 0.8327 (m) cc_final: 0.7751 (p) REVERT: D 90 GLU cc_start: 0.7874 (tp30) cc_final: 0.6782 (tp30) REVERT: D 91 LYS cc_start: 0.8526 (mmpt) cc_final: 0.7967 (mmpt) REVERT: D 141 VAL cc_start: 0.7984 (p) cc_final: 0.7760 (t) REVERT: D 142 ASP cc_start: 0.8070 (p0) cc_final: 0.7739 (p0) REVERT: D 144 LYS cc_start: 0.8170 (mtmt) cc_final: 0.7596 (mtmt) REVERT: D 145 LEU cc_start: 0.8196 (tp) cc_final: 0.7699 (mm) REVERT: D 146 GLU cc_start: 0.7937 (tp30) cc_final: 0.7134 (tp30) REVERT: D 149 LEU cc_start: 0.8048 (mt) cc_final: 0.7599 (mt) REVERT: D 150 LYS cc_start: 0.8632 (ttmm) cc_final: 0.8269 (ttmm) REVERT: D 160 ASP cc_start: 0.8133 (t0) cc_final: 0.7921 (t0) REVERT: D 203 GLU cc_start: 0.7951 (mp0) cc_final: 0.7350 (mp0) REVERT: D 224 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8061 (mm-30) REVERT: D 226 LEU cc_start: 0.8902 (tp) cc_final: 0.8602 (tp) REVERT: D 227 LYS cc_start: 0.9007 (ttpp) cc_final: 0.8619 (ttpp) REVERT: D 241 GLN cc_start: 0.8085 (tp40) cc_final: 0.7660 (tp40) REVERT: D 245 MET cc_start: 0.8629 (tpp) cc_final: 0.8272 (tpp) REVERT: D 266 LYS cc_start: 0.8907 (mttt) cc_final: 0.8622 (mttt) REVERT: D 286 MET cc_start: 0.8272 (tpp) cc_final: 0.7169 (mpp) REVERT: D 289 GLN cc_start: 0.8823 (mt0) cc_final: 0.8401 (mt0) REVERT: D 301 ASP cc_start: 0.7409 (m-30) cc_final: 0.7041 (m-30) REVERT: D 302 ARG cc_start: 0.7875 (tpp80) cc_final: 0.6955 (tpp80) REVERT: D 306 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7666 (mt-10) REVERT: D 329 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7142 (mm-30) REVERT: D 336 GLU cc_start: 0.8631 (tt0) cc_final: 0.8246 (tt0) REVERT: D 342 MET cc_start: 0.8573 (ttp) cc_final: 0.8243 (mtp) REVERT: D 354 GLN cc_start: 0.8477 (tt0) cc_final: 0.8130 (tt0) REVERT: D 358 ILE cc_start: 0.8451 (mt) cc_final: 0.8113 (mm) REVERT: D 359 VAL cc_start: 0.8436 (t) cc_final: 0.8118 (p) REVERT: D 372 LYS cc_start: 0.8641 (tptt) cc_final: 0.8194 (tptt) REVERT: D 380 GLN cc_start: 0.8360 (mm110) cc_final: 0.8050 (mm-40) REVERT: D 383 ASN cc_start: 0.7975 (m-40) cc_final: 0.7616 (m-40) REVERT: D 387 LYS cc_start: 0.9181 (tttt) cc_final: 0.8854 (tttt) REVERT: D 400 MET cc_start: 0.8688 (mtt) cc_final: 0.8478 (ptp) REVERT: E 252 SER cc_start: 0.8195 (m) cc_final: 0.7959 (m) REVERT: E 258 ASN cc_start: 0.8613 (m-40) cc_final: 0.8025 (m-40) REVERT: E 262 THR cc_start: 0.9185 (m) cc_final: 0.8849 (p) REVERT: E 272 LYS cc_start: 0.8934 (mtpt) cc_final: 0.8648 (mttt) REVERT: E 305 ARG cc_start: 0.8305 (mtp-110) cc_final: 0.7788 (mtp-110) REVERT: E 308 CYS cc_start: 0.8723 (m) cc_final: 0.8430 (m) REVERT: E 309 LYS cc_start: 0.8886 (tttt) cc_final: 0.8417 (tttt) REVERT: E 313 GLU cc_start: 0.8475 (tp30) cc_final: 0.7891 (tp30) REVERT: E 321 GLN cc_start: 0.8879 (mm110) cc_final: 0.8598 (mm110) REVERT: F 230 MET cc_start: 0.8438 (mmt) cc_final: 0.8040 (mmt) REVERT: F 240 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7434 (mt-10) REVERT: F 241 TYR cc_start: 0.8720 (t80) cc_final: 0.8385 (t80) REVERT: F 258 ARG cc_start: 0.8294 (mtt180) cc_final: 0.8075 (mtt180) REVERT: F 270 LEU cc_start: 0.8601 (tp) cc_final: 0.8094 (tp) REVERT: F 278 ASP cc_start: 0.8287 (m-30) cc_final: 0.7824 (m-30) REVERT: F 279 PHE cc_start: 0.8728 (t80) cc_final: 0.8065 (t80) REVERT: F 283 CYS cc_start: 0.9159 (m) cc_final: 0.8569 (m) REVERT: F 285 ASP cc_start: 0.8118 (m-30) cc_final: 0.7816 (m-30) REVERT: F 301 THR cc_start: 0.8731 (m) cc_final: 0.8240 (p) REVERT: F 302 MET cc_start: 0.8097 (ttt) cc_final: 0.7533 (mmm) REVERT: G 14 GLN cc_start: 0.8103 (mt0) cc_final: 0.7627 (mt0) REVERT: G 36 GLU cc_start: 0.7911 (pt0) cc_final: 0.7655 (pt0) REVERT: G 45 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7859 (tp30) REVERT: G 65 GLN cc_start: 0.8106 (tp-100) cc_final: 0.7165 (tp-100) REVERT: G 66 LEU cc_start: 0.8733 (tt) cc_final: 0.8515 (tt) REVERT: G 92 GLN cc_start: 0.8730 (mt0) cc_final: 0.8392 (mt0) REVERT: G 93 GLN cc_start: 0.8571 (pt0) cc_final: 0.8324 (pt0) REVERT: G 97 LYS cc_start: 0.8709 (mttt) cc_final: 0.8167 (mmtp) REVERT: G 99 LEU cc_start: 0.8778 (mt) cc_final: 0.8497 (mt) REVERT: G 120 LEU cc_start: 0.8460 (mt) cc_final: 0.8167 (mm) REVERT: G 125 LEU cc_start: 0.8495 (mt) cc_final: 0.7714 (mt) REVERT: G 129 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7607 (mt-10) REVERT: G 133 ILE cc_start: 0.8306 (mm) cc_final: 0.8054 (mm) REVERT: G 150 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8100 (mm-40) REVERT: G 155 ASP cc_start: 0.8424 (m-30) cc_final: 0.8190 (m-30) REVERT: G 181 CYS cc_start: 0.8507 (m) cc_final: 0.8292 (m) REVERT: G 188 ILE cc_start: 0.8325 (mt) cc_final: 0.8032 (tp) REVERT: G 193 LEU cc_start: 0.8996 (tp) cc_final: 0.8759 (tp) REVERT: G 197 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8079 (tm-30) REVERT: G 202 HIS cc_start: 0.8208 (t70) cc_final: 0.7879 (t70) REVERT: G 204 ARG cc_start: 0.8830 (ttm170) cc_final: 0.8508 (ttm170) REVERT: G 210 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7653 (mm-30) REVERT: H 17 LEU cc_start: 0.8460 (tp) cc_final: 0.8018 (tp) REVERT: H 18 ASP cc_start: 0.7791 (m-30) cc_final: 0.7539 (m-30) REVERT: H 21 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7917 (mt-10) REVERT: H 23 GLN cc_start: 0.8583 (tt0) cc_final: 0.8163 (tt0) REVERT: H 26 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7303 (mp0) REVERT: H 52 ASN cc_start: 0.8718 (m-40) cc_final: 0.8327 (m110) REVERT: H 58 LYS cc_start: 0.8611 (ttmt) cc_final: 0.8384 (ttmt) REVERT: H 59 ARG cc_start: 0.7818 (ttm170) cc_final: 0.7583 (ttp-170) REVERT: H 123 GLN cc_start: 0.8626 (tp-100) cc_final: 0.8279 (tp-100) REVERT: H 129 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7575 (mt) REVERT: I 121 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8531 (pp30) REVERT: I 206 GLN cc_start: 0.8231 (tm-30) cc_final: 0.7717 (tm-30) REVERT: I 247 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.7072 (mp0) REVERT: I 262 LYS cc_start: 0.8512 (pttp) cc_final: 0.8179 (pttp) REVERT: I 287 LEU cc_start: 0.8838 (tp) cc_final: 0.8186 (tt) REVERT: I 291 CYS cc_start: 0.8881 (m) cc_final: 0.8155 (m) REVERT: I 322 MET cc_start: 0.8139 (ttm) cc_final: 0.7807 (ttm) REVERT: I 347 GLN cc_start: 0.7474 (mt0) cc_final: 0.7261 (mt0) REVERT: I 374 HIS cc_start: 0.8769 (t-90) cc_final: 0.8517 (t-170) REVERT: I 381 VAL cc_start: 0.8921 (m) cc_final: 0.8707 (p) REVERT: I 420 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7558 (tm-30) REVERT: I 424 ARG cc_start: 0.8470 (mmm-85) cc_final: 0.8068 (mmm-85) REVERT: I 428 SER cc_start: 0.8883 (t) cc_final: 0.8502 (p) REVERT: I 429 LEU cc_start: 0.8366 (tp) cc_final: 0.8032 (tp) REVERT: I 464 LYS cc_start: 0.8359 (tptm) cc_final: 0.7984 (tptm) REVERT: I 466 TYR cc_start: 0.7966 (t80) cc_final: 0.7730 (t80) REVERT: I 468 LYS cc_start: 0.8662 (tppt) cc_final: 0.8085 (tppt) REVERT: I 494 GLN cc_start: 0.8821 (tp-100) cc_final: 0.8555 (tp-100) REVERT: I 503 LYS cc_start: 0.8438 (ttmm) cc_final: 0.8072 (ttmm) REVERT: I 522 LYS cc_start: 0.8417 (tppp) cc_final: 0.8023 (tppp) REVERT: I 560 GLU cc_start: 0.7617 (tt0) cc_final: 0.7342 (tt0) REVERT: I 563 TYR cc_start: 0.8853 (t80) cc_final: 0.8104 (t80) REVERT: I 564 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8388 (mt0) REVERT: I 602 GLN cc_start: 0.6905 (tp40) cc_final: 0.6586 (tp40) REVERT: I 607 GLN cc_start: 0.7854 (mp10) cc_final: 0.7424 (mp10) REVERT: I 630 GLN cc_start: 0.7465 (tm-30) cc_final: 0.7044 (tm-30) REVERT: I 638 GLN cc_start: 0.8866 (mp10) cc_final: 0.8467 (mp10) REVERT: I 642 ILE cc_start: 0.8890 (mt) cc_final: 0.8525 (tt) REVERT: I 643 LEU cc_start: 0.8929 (mp) cc_final: 0.8437 (tp) REVERT: I 721 MET cc_start: 0.8627 (mtm) cc_final: 0.8355 (mtm) REVERT: J 50 MET cc_start: 0.1459 (mtt) cc_final: 0.0880 (mtt) REVERT: L 32 GLU cc_start: 0.8003 (tp30) cc_final: 0.7482 (tp30) REVERT: L 57 LYS cc_start: 0.8353 (ptpt) cc_final: 0.8083 (ptpt) REVERT: L 126 MET cc_start: 0.8060 (mmp) cc_final: 0.7590 (mmp) REVERT: M 102 ASP cc_start: 0.7439 (p0) cc_final: 0.7204 (p0) REVERT: M 118 LEU cc_start: 0.9051 (mp) cc_final: 0.8319 (tt) REVERT: M 217 ARG cc_start: 0.5710 (OUTLIER) cc_final: 0.3765 (ptp90) REVERT: M 259 ASP cc_start: 0.7974 (p0) cc_final: 0.7573 (p0) REVERT: M 323 LEU cc_start: 0.8690 (mp) cc_final: 0.8041 (pp) REVERT: N 23 MET cc_start: 0.7226 (ttm) cc_final: 0.7017 (ttm) REVERT: N 36 HIS cc_start: 0.7725 (p90) cc_final: 0.7359 (p-80) REVERT: N 38 MET cc_start: 0.7153 (mtp) cc_final: 0.6709 (mpp) REVERT: N 58 MET cc_start: 0.7559 (mtp) cc_final: 0.7151 (mtp) REVERT: P 43 PHE cc_start: 0.8568 (p90) cc_final: 0.8146 (p90) REVERT: P 44 PHE cc_start: 0.7797 (t80) cc_final: 0.7539 (t80) REVERT: P 52 ASP cc_start: 0.7544 (t0) cc_final: 0.7023 (t0) REVERT: A 73 GLU cc_start: 0.8506 (mp0) cc_final: 0.8236 (mp0) REVERT: A 83 GLN cc_start: 0.8889 (pm20) cc_final: 0.8652 (pm20) REVERT: A 90 MET cc_start: 0.8261 (tpt) cc_final: 0.7550 (tpt) REVERT: A 98 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8796 (mm) REVERT: A 130 TRP cc_start: 0.7395 (t60) cc_final: 0.6898 (t60) REVERT: A 132 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.8005 (pm20) REVERT: A 148 ASP cc_start: 0.8500 (p0) cc_final: 0.8084 (p0) REVERT: A 152 TYR cc_start: 0.8224 (m-10) cc_final: 0.7877 (m-80) REVERT: A 165 HIS cc_start: 0.8992 (m-70) cc_final: 0.8305 (m90) REVERT: A 172 TYR cc_start: 0.8204 (m-10) cc_final: 0.7941 (m-80) REVERT: A 174 ASP cc_start: 0.8782 (m-30) cc_final: 0.8247 (t0) REVERT: A 196 LYS cc_start: 0.8687 (mptt) cc_final: 0.8390 (mptt) REVERT: A 262 LYS cc_start: 0.8678 (ttpp) cc_final: 0.8182 (ttpt) REVERT: A 277 HIS cc_start: 0.6973 (p90) cc_final: 0.6737 (p90) REVERT: A 288 ASN cc_start: 0.7432 (m110) cc_final: 0.6974 (m110) REVERT: A 296 CYS cc_start: 0.8292 (m) cc_final: 0.7933 (m) REVERT: A 304 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7482 (mm-40) REVERT: A 307 GLN cc_start: 0.8596 (tm-30) cc_final: 0.8272 (tm-30) REVERT: A 310 VAL cc_start: 0.8401 (t) cc_final: 0.7950 (m) REVERT: A 317 LYS cc_start: 0.8431 (ptpt) cc_final: 0.8117 (ptpt) REVERT: A 321 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7721 (mt-10) REVERT: A 322 LEU cc_start: 0.8855 (mt) cc_final: 0.8479 (tp) REVERT: A 323 GLU cc_start: 0.7490 (mp0) cc_final: 0.7082 (mp0) REVERT: A 348 MET cc_start: 0.7492 (tmm) cc_final: 0.7242 (tmm) REVERT: A 355 ASP cc_start: 0.8417 (t0) cc_final: 0.8083 (t0) REVERT: A 358 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7673 (mp) REVERT: A 367 THR cc_start: 0.8335 (m) cc_final: 0.8022 (p) REVERT: A 386 MET cc_start: 0.8635 (mtp) cc_final: 0.8288 (mtp) REVERT: A 408 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8453 (tp) REVERT: A 437 GLU cc_start: 0.8214 (tp30) cc_final: 0.8013 (tp30) REVERT: A 455 LEU cc_start: 0.8387 (tp) cc_final: 0.8050 (tt) outliers start: 97 outliers final: 72 residues processed: 1196 average time/residue: 0.1729 time to fit residues: 321.0684 Evaluate side-chains 1234 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 1154 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 319 GLN Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 375 ASN Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain F residue 253 ASN Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain F residue 304 GLN Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 190 GLN Chi-restraints excluded: chain H residue 51 ASN Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain I residue 247 GLU Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 450 MET Chi-restraints excluded: chain I residue 587 LYS Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain I residue 684 ILE Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 217 ARG Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 236 ASN Chi-restraints excluded: chain M residue 240 CYS Chi-restraints excluded: chain M residue 258 LEU Chi-restraints excluded: chain M residue 275 GLN Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 408 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 72 optimal weight: 0.5980 chunk 321 optimal weight: 0.7980 chunk 239 optimal weight: 0.9990 chunk 328 optimal weight: 0.9990 chunk 241 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 295 optimal weight: 0.6980 chunk 253 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 GLN B 334 HIS C 105 HIS D 75 ASN D 140 ASN ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 HIS E 321 GLN F 225 HIS F 303 ASN G 98 HIS ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 564 GLN ** J 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 229 ASN ** M 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.137904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.111997 restraints weight = 60166.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.115762 restraints weight = 30836.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.118234 restraints weight = 18929.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.119869 restraints weight = 13194.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.121019 restraints weight = 10096.357| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26963 Z= 0.136 Angle : 0.640 13.955 36489 Z= 0.331 Chirality : 0.041 0.239 4207 Planarity : 0.004 0.060 4645 Dihedral : 4.937 55.811 3635 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.86 % Favored : 95.11 % Rotamer: Outliers : 3.93 % Allowed : 21.93 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.15), residues: 3290 helix: 1.66 (0.12), residues: 2158 sheet: -0.79 (0.47), residues: 132 loop : -1.92 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 193 TYR 0.024 0.001 TYR A 91 PHE 0.039 0.001 PHE A 446 TRP 0.027 0.001 TRP I 545 HIS 0.005 0.001 HIS M 339 Details of bonding type rmsd covalent geometry : bond 0.00287 (26952) covalent geometry : angle 0.63947 (36484) SS BOND : bond 0.00083 ( 1) SS BOND : angle 1.90467 ( 2) hydrogen bonds : bond 0.04452 ( 1569) hydrogen bonds : angle 4.13653 ( 4605) metal coordination : bond 0.00424 ( 10) metal coordination : angle 1.30704 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1266 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 1155 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 GLN cc_start: 0.8480 (mp10) cc_final: 0.7876 (mp10) REVERT: B 56 LYS cc_start: 0.8868 (mptt) cc_final: 0.8649 (tptt) REVERT: B 66 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7098 (mm-30) REVERT: B 70 LYS cc_start: 0.8953 (tmtt) cc_final: 0.8716 (tmtt) REVERT: B 72 LEU cc_start: 0.8721 (mt) cc_final: 0.7834 (mt) REVERT: B 74 GLN cc_start: 0.8570 (tp40) cc_final: 0.7619 (tp40) REVERT: B 75 MET cc_start: 0.7709 (ppp) cc_final: 0.6999 (ppp) REVERT: B 109 GLU cc_start: 0.8010 (tp30) cc_final: 0.7316 (tp30) REVERT: B 115 ILE cc_start: 0.8648 (mt) cc_final: 0.8364 (tp) REVERT: B 124 GLN cc_start: 0.8004 (tt0) cc_final: 0.7514 (tt0) REVERT: B 133 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8500 (tp30) REVERT: B 136 LEU cc_start: 0.8588 (mt) cc_final: 0.7889 (mt) REVERT: B 140 LYS cc_start: 0.8646 (ptpp) cc_final: 0.8199 (ptpp) REVERT: B 149 PHE cc_start: 0.7951 (t80) cc_final: 0.7603 (t80) REVERT: B 152 ASN cc_start: 0.8050 (t0) cc_final: 0.7613 (t0) REVERT: B 158 LEU cc_start: 0.8801 (tp) cc_final: 0.8486 (tt) REVERT: B 161 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7274 (tm-30) REVERT: B 165 TYR cc_start: 0.8511 (m-10) cc_final: 0.8232 (m-80) REVERT: B 176 HIS cc_start: 0.7322 (m170) cc_final: 0.6545 (m170) REVERT: B 198 TYR cc_start: 0.8315 (m-10) cc_final: 0.8026 (m-80) REVERT: B 201 GLU cc_start: 0.8027 (pp20) cc_final: 0.7734 (tm-30) REVERT: B 225 LYS cc_start: 0.8762 (mptt) cc_final: 0.8528 (mptt) REVERT: B 226 SER cc_start: 0.8440 (m) cc_final: 0.8223 (p) REVERT: B 234 MET cc_start: 0.7791 (mmm) cc_final: 0.7529 (mmm) REVERT: B 250 GLU cc_start: 0.8390 (tt0) cc_final: 0.7996 (tm-30) REVERT: B 253 LYS cc_start: 0.7851 (mmtp) cc_final: 0.7002 (mtmm) REVERT: B 257 ASP cc_start: 0.8411 (m-30) cc_final: 0.7820 (m-30) REVERT: B 260 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7822 (mm-30) REVERT: B 291 ILE cc_start: 0.9285 (mp) cc_final: 0.8699 (tp) REVERT: B 322 ASP cc_start: 0.8403 (t0) cc_final: 0.8003 (t0) REVERT: B 325 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7448 (mm-30) REVERT: B 328 LYS cc_start: 0.9103 (ttpp) cc_final: 0.8766 (ttmm) REVERT: B 338 MET cc_start: 0.7254 (tpt) cc_final: 0.6269 (tpt) REVERT: B 347 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8289 (mm) REVERT: B 358 VAL cc_start: 0.9009 (t) cc_final: 0.8756 (p) REVERT: B 361 LYS cc_start: 0.8728 (tptp) cc_final: 0.8335 (tptp) REVERT: B 363 ILE cc_start: 0.8910 (pt) cc_final: 0.8562 (tp) REVERT: B 368 ARG cc_start: 0.8347 (mtp-110) cc_final: 0.8039 (mtp-110) REVERT: B 391 GLN cc_start: 0.8224 (tm-30) cc_final: 0.7532 (tm-30) REVERT: B 410 GLU cc_start: 0.7636 (pp20) cc_final: 0.7256 (pp20) REVERT: B 411 LEU cc_start: 0.8179 (mp) cc_final: 0.7571 (mp) REVERT: B 415 LYS cc_start: 0.8390 (tttp) cc_final: 0.8092 (tttp) REVERT: B 433 SER cc_start: 0.9094 (m) cc_final: 0.8757 (p) REVERT: C 78 PHE cc_start: 0.8843 (t80) cc_final: 0.8513 (t80) REVERT: C 82 GLN cc_start: 0.8560 (mt0) cc_final: 0.7991 (mt0) REVERT: C 94 ARG cc_start: 0.8752 (ttp-110) cc_final: 0.8506 (ttp-170) REVERT: C 98 ASP cc_start: 0.8557 (t0) cc_final: 0.8257 (m-30) REVERT: C 100 PHE cc_start: 0.7564 (t80) cc_final: 0.7044 (t80) REVERT: C 104 CYS cc_start: 0.8694 (m) cc_final: 0.8253 (m) REVERT: C 105 HIS cc_start: 0.7746 (OUTLIER) cc_final: 0.7546 (m90) REVERT: C 106 GLN cc_start: 0.8500 (mm-40) cc_final: 0.8006 (mm-40) REVERT: C 121 ILE cc_start: 0.8983 (mm) cc_final: 0.8757 (tp) REVERT: C 126 GLN cc_start: 0.8311 (mt0) cc_final: 0.7563 (mm110) REVERT: C 129 ASP cc_start: 0.7647 (m-30) cc_final: 0.7138 (m-30) REVERT: C 136 ASN cc_start: 0.8931 (p0) cc_final: 0.8076 (p0) REVERT: C 147 GLN cc_start: 0.8329 (tm-30) cc_final: 0.8027 (tm-30) REVERT: C 154 CYS cc_start: 0.8467 (t) cc_final: 0.8260 (t) REVERT: C 166 MET cc_start: 0.7682 (mpp) cc_final: 0.7464 (mpp) REVERT: C 190 MET cc_start: 0.7787 (ttm) cc_final: 0.7577 (tpp) REVERT: C 219 ILE cc_start: 0.7916 (mt) cc_final: 0.7578 (mm) REVERT: C 244 TYR cc_start: 0.7953 (p90) cc_final: 0.7726 (p90) REVERT: C 247 GLN cc_start: 0.7947 (pp30) cc_final: 0.7422 (tm-30) REVERT: C 271 ASN cc_start: 0.7684 (t0) cc_final: 0.6927 (t0) REVERT: C 291 ASN cc_start: 0.8271 (m110) cc_final: 0.8027 (m110) REVERT: C 292 MET cc_start: 0.7855 (tmm) cc_final: 0.7615 (tmm) REVERT: C 304 LYS cc_start: 0.8810 (mttp) cc_final: 0.8594 (mttp) REVERT: C 309 ARG cc_start: 0.8949 (ttm170) cc_final: 0.8596 (ttp-170) REVERT: C 320 GLN cc_start: 0.8181 (tp-100) cc_final: 0.7766 (tp40) REVERT: C 365 GLU cc_start: 0.8192 (tp30) cc_final: 0.7984 (tp30) REVERT: C 366 LYS cc_start: 0.8718 (mmmm) cc_final: 0.8388 (mtpp) REVERT: C 379 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7356 (mm-30) REVERT: C 380 MET cc_start: 0.8398 (mtt) cc_final: 0.7748 (mtt) REVERT: C 383 CYS cc_start: 0.8292 (t) cc_final: 0.7869 (p) REVERT: C 385 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7376 (tm-30) REVERT: C 393 MET cc_start: 0.7539 (tpp) cc_final: 0.7170 (tpp) REVERT: C 405 GLN cc_start: 0.8453 (tm-30) cc_final: 0.8136 (tm-30) REVERT: C 406 LYS cc_start: 0.9035 (mttp) cc_final: 0.8495 (mttp) REVERT: D 28 GLN cc_start: 0.8222 (mp10) cc_final: 0.7822 (mm-40) REVERT: D 50 GLU cc_start: 0.8265 (pt0) cc_final: 0.7824 (pt0) REVERT: D 53 VAL cc_start: 0.7498 (m) cc_final: 0.7266 (p) REVERT: D 56 ASN cc_start: 0.8134 (p0) cc_final: 0.7914 (t0) REVERT: D 62 SER cc_start: 0.8369 (m) cc_final: 0.7836 (p) REVERT: D 90 GLU cc_start: 0.7887 (tp30) cc_final: 0.6819 (tp30) REVERT: D 91 LYS cc_start: 0.8520 (mmpt) cc_final: 0.7998 (mmpt) REVERT: D 141 VAL cc_start: 0.7976 (p) cc_final: 0.7667 (t) REVERT: D 144 LYS cc_start: 0.8165 (mtmt) cc_final: 0.7609 (mtmt) REVERT: D 145 LEU cc_start: 0.8187 (tp) cc_final: 0.7702 (mm) REVERT: D 146 GLU cc_start: 0.7938 (tp30) cc_final: 0.7127 (tp30) REVERT: D 149 LEU cc_start: 0.8036 (mt) cc_final: 0.7600 (mt) REVERT: D 150 LYS cc_start: 0.8623 (ttmm) cc_final: 0.8256 (ttmm) REVERT: D 160 ASP cc_start: 0.8136 (t0) cc_final: 0.7916 (t0) REVERT: D 203 GLU cc_start: 0.7923 (mp0) cc_final: 0.7385 (mp0) REVERT: D 226 LEU cc_start: 0.8898 (tp) cc_final: 0.8580 (tp) REVERT: D 227 LYS cc_start: 0.8987 (ttpp) cc_final: 0.8592 (ttpp) REVERT: D 241 GLN cc_start: 0.8048 (tp40) cc_final: 0.7656 (tp40) REVERT: D 245 MET cc_start: 0.8671 (tpp) cc_final: 0.8293 (tpp) REVERT: D 266 LYS cc_start: 0.8915 (mttt) cc_final: 0.8575 (mttt) REVERT: D 268 TYR cc_start: 0.8706 (t80) cc_final: 0.8424 (t80) REVERT: D 286 MET cc_start: 0.8281 (tpp) cc_final: 0.7184 (mpp) REVERT: D 289 GLN cc_start: 0.8827 (mt0) cc_final: 0.8364 (mt0) REVERT: D 301 ASP cc_start: 0.7416 (m-30) cc_final: 0.6990 (m-30) REVERT: D 302 ARG cc_start: 0.7875 (tpp80) cc_final: 0.6957 (tpp80) REVERT: D 306 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7674 (mt-10) REVERT: D 319 ILE cc_start: 0.8041 (tt) cc_final: 0.7783 (tp) REVERT: D 322 GLU cc_start: 0.8438 (mp0) cc_final: 0.8205 (mp0) REVERT: D 329 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7124 (mm-30) REVERT: D 336 GLU cc_start: 0.8613 (tt0) cc_final: 0.8254 (tt0) REVERT: D 342 MET cc_start: 0.8550 (ttp) cc_final: 0.8235 (mtp) REVERT: D 354 GLN cc_start: 0.8486 (tt0) cc_final: 0.8143 (tt0) REVERT: D 358 ILE cc_start: 0.8441 (mt) cc_final: 0.8098 (mm) REVERT: D 359 VAL cc_start: 0.8449 (t) cc_final: 0.8191 (p) REVERT: D 372 LYS cc_start: 0.8642 (tptt) cc_final: 0.8206 (tptt) REVERT: D 379 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.7974 (m-10) REVERT: D 380 GLN cc_start: 0.8404 (mm110) cc_final: 0.8080 (mm-40) REVERT: D 383 ASN cc_start: 0.7988 (m-40) cc_final: 0.7598 (m-40) REVERT: D 387 LYS cc_start: 0.9190 (tttt) cc_final: 0.8846 (tttt) REVERT: D 400 MET cc_start: 0.8702 (mtt) cc_final: 0.8487 (mtt) REVERT: E 252 SER cc_start: 0.8194 (m) cc_final: 0.7955 (m) REVERT: E 258 ASN cc_start: 0.8643 (m-40) cc_final: 0.8045 (m-40) REVERT: E 262 THR cc_start: 0.9164 (m) cc_final: 0.8837 (p) REVERT: E 272 LYS cc_start: 0.8937 (mtpt) cc_final: 0.8620 (mttt) REVERT: E 305 ARG cc_start: 0.8301 (mtp-110) cc_final: 0.7788 (mtp-110) REVERT: E 308 CYS cc_start: 0.8708 (m) cc_final: 0.8392 (m) REVERT: E 309 LYS cc_start: 0.8883 (tttt) cc_final: 0.8423 (tttt) REVERT: E 313 GLU cc_start: 0.8469 (tp30) cc_final: 0.7839 (tp30) REVERT: E 321 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8606 (mm-40) REVERT: F 230 MET cc_start: 0.8456 (mmt) cc_final: 0.8097 (mmt) REVERT: F 240 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7464 (mt-10) REVERT: F 241 TYR cc_start: 0.8738 (t80) cc_final: 0.8400 (t80) REVERT: F 258 ARG cc_start: 0.8321 (mtt180) cc_final: 0.8094 (mtt180) REVERT: F 270 LEU cc_start: 0.8571 (tp) cc_final: 0.8069 (tp) REVERT: F 278 ASP cc_start: 0.8287 (m-30) cc_final: 0.7828 (m-30) REVERT: F 279 PHE cc_start: 0.8724 (t80) cc_final: 0.8130 (t80) REVERT: F 283 CYS cc_start: 0.9158 (m) cc_final: 0.8650 (m) REVERT: F 301 THR cc_start: 0.8770 (m) cc_final: 0.8271 (p) REVERT: F 302 MET cc_start: 0.8119 (ttt) cc_final: 0.7560 (mmm) REVERT: G 14 GLN cc_start: 0.8092 (mt0) cc_final: 0.7612 (mt0) REVERT: G 36 GLU cc_start: 0.7906 (pt0) cc_final: 0.7695 (pt0) REVERT: G 65 GLN cc_start: 0.8114 (tp-100) cc_final: 0.7154 (tp-100) REVERT: G 66 LEU cc_start: 0.8745 (tt) cc_final: 0.8512 (tt) REVERT: G 92 GLN cc_start: 0.8732 (mt0) cc_final: 0.8379 (mt0) REVERT: G 93 GLN cc_start: 0.8549 (pt0) cc_final: 0.8307 (pt0) REVERT: G 97 LYS cc_start: 0.8716 (mttt) cc_final: 0.8131 (mmtp) REVERT: G 99 LEU cc_start: 0.8761 (mt) cc_final: 0.8484 (mt) REVERT: G 120 LEU cc_start: 0.8453 (mt) cc_final: 0.8172 (mm) REVERT: G 125 LEU cc_start: 0.8481 (mt) cc_final: 0.7825 (mt) REVERT: G 129 GLU cc_start: 0.8483 (mt-10) cc_final: 0.7887 (mt-10) REVERT: G 133 ILE cc_start: 0.8311 (mm) cc_final: 0.8063 (mm) REVERT: G 150 GLN cc_start: 0.8415 (mm-40) cc_final: 0.7989 (mm-40) REVERT: G 155 ASP cc_start: 0.8457 (m-30) cc_final: 0.8236 (m-30) REVERT: G 181 CYS cc_start: 0.8508 (m) cc_final: 0.8273 (m) REVERT: G 188 ILE cc_start: 0.8336 (mt) cc_final: 0.8052 (tp) REVERT: G 193 LEU cc_start: 0.8990 (tp) cc_final: 0.8746 (tp) REVERT: G 197 GLN cc_start: 0.8495 (tm-30) cc_final: 0.8076 (tm-30) REVERT: G 202 HIS cc_start: 0.8185 (t70) cc_final: 0.7850 (t70) REVERT: G 204 ARG cc_start: 0.8823 (ttm170) cc_final: 0.8511 (ttm170) REVERT: G 210 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7645 (mm-30) REVERT: H 17 LEU cc_start: 0.8455 (tp) cc_final: 0.8002 (tp) REVERT: H 18 ASP cc_start: 0.7799 (m-30) cc_final: 0.7546 (m-30) REVERT: H 21 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7923 (mt-10) REVERT: H 23 GLN cc_start: 0.8581 (tt0) cc_final: 0.8342 (tt0) REVERT: H 58 LYS cc_start: 0.8575 (ttmt) cc_final: 0.8343 (ttmt) REVERT: H 79 GLN cc_start: 0.8061 (tt0) cc_final: 0.7535 (mt0) REVERT: H 123 GLN cc_start: 0.8633 (tp-100) cc_final: 0.8279 (tp-100) REVERT: H 129 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7531 (mt) REVERT: I 22 ASP cc_start: 0.7604 (p0) cc_final: 0.7285 (p0) REVERT: I 121 GLN cc_start: 0.8797 (tm-30) cc_final: 0.8532 (tm-30) REVERT: I 142 ARG cc_start: 0.8284 (tpp80) cc_final: 0.7868 (tpm170) REVERT: I 247 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.7038 (mp0) REVERT: I 262 LYS cc_start: 0.8488 (pttp) cc_final: 0.8155 (pttp) REVERT: I 287 LEU cc_start: 0.8813 (tp) cc_final: 0.8502 (tt) REVERT: I 322 MET cc_start: 0.8132 (ttm) cc_final: 0.7840 (ttm) REVERT: I 374 HIS cc_start: 0.8789 (t-90) cc_final: 0.8532 (t-170) REVERT: I 381 VAL cc_start: 0.8928 (m) cc_final: 0.8728 (p) REVERT: I 420 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7768 (tm-30) REVERT: I 428 SER cc_start: 0.8894 (t) cc_final: 0.8506 (p) REVERT: I 429 LEU cc_start: 0.8381 (tp) cc_final: 0.8050 (tp) REVERT: I 464 LYS cc_start: 0.8348 (tptm) cc_final: 0.7960 (tptm) REVERT: I 466 TYR cc_start: 0.7979 (t80) cc_final: 0.7717 (t80) REVERT: I 468 LYS cc_start: 0.8614 (tppt) cc_final: 0.8064 (tppt) REVERT: I 503 LYS cc_start: 0.8396 (ttmm) cc_final: 0.8085 (ttmm) REVERT: I 522 LYS cc_start: 0.8292 (tppp) cc_final: 0.7872 (tppp) REVERT: I 540 LEU cc_start: 0.8114 (mp) cc_final: 0.7692 (mp) REVERT: I 548 GLN cc_start: 0.8461 (tp-100) cc_final: 0.8233 (tp40) REVERT: I 564 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8309 (mt0) REVERT: I 580 THR cc_start: 0.8021 (OUTLIER) cc_final: 0.7809 (p) REVERT: I 586 SER cc_start: 0.8460 (OUTLIER) cc_final: 0.7741 (m) REVERT: I 602 GLN cc_start: 0.6910 (tp40) cc_final: 0.6597 (tp40) REVERT: I 607 GLN cc_start: 0.7873 (mp10) cc_final: 0.7398 (mp10) REVERT: I 608 MET cc_start: 0.7617 (tpp) cc_final: 0.7253 (tpp) REVERT: I 630 GLN cc_start: 0.7488 (tm-30) cc_final: 0.7122 (tm-30) REVERT: I 638 GLN cc_start: 0.8887 (mp10) cc_final: 0.8506 (mp10) REVERT: I 642 ILE cc_start: 0.8894 (mt) cc_final: 0.8536 (tt) REVERT: I 643 LEU cc_start: 0.8923 (mp) cc_final: 0.8435 (tp) REVERT: I 721 MET cc_start: 0.8619 (mtm) cc_final: 0.8348 (mtm) REVERT: J 50 MET cc_start: 0.1847 (mtt) cc_final: 0.1237 (mtt) REVERT: L 57 LYS cc_start: 0.8446 (ptpt) cc_final: 0.8175 (ptpt) REVERT: L 126 MET cc_start: 0.8003 (mmp) cc_final: 0.7562 (mmp) REVERT: M 102 ASP cc_start: 0.7513 (p0) cc_final: 0.7190 (p0) REVERT: M 118 LEU cc_start: 0.9048 (mp) cc_final: 0.8294 (tt) REVERT: M 161 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7289 (tp) REVERT: M 167 ARG cc_start: 0.7709 (mpp80) cc_final: 0.7436 (mpp80) REVERT: M 184 GLN cc_start: 0.7955 (mp10) cc_final: 0.7684 (mp10) REVERT: M 208 LEU cc_start: 0.8578 (mt) cc_final: 0.8259 (mm) REVERT: M 217 ARG cc_start: 0.5859 (OUTLIER) cc_final: 0.3935 (ptp90) REVERT: M 251 LEU cc_start: 0.8767 (tt) cc_final: 0.8406 (pp) REVERT: M 259 ASP cc_start: 0.7937 (p0) cc_final: 0.7533 (p0) REVERT: M 323 LEU cc_start: 0.8624 (mp) cc_final: 0.7984 (pp) REVERT: N 23 MET cc_start: 0.7250 (ttm) cc_final: 0.6956 (ttm) REVERT: N 36 HIS cc_start: 0.7774 (p90) cc_final: 0.7481 (p-80) REVERT: N 58 MET cc_start: 0.7528 (mtp) cc_final: 0.7118 (mtp) REVERT: P 43 PHE cc_start: 0.8513 (p90) cc_final: 0.8102 (p90) REVERT: P 44 PHE cc_start: 0.7819 (t80) cc_final: 0.7566 (t80) REVERT: P 52 ASP cc_start: 0.7521 (t0) cc_final: 0.7007 (t0) REVERT: A 90 MET cc_start: 0.8186 (tpt) cc_final: 0.7452 (tpt) REVERT: A 98 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8904 (mm) REVERT: A 130 TRP cc_start: 0.7439 (t60) cc_final: 0.6839 (t60) REVERT: A 132 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7969 (pm20) REVERT: A 148 ASP cc_start: 0.8500 (p0) cc_final: 0.8058 (p0) REVERT: A 152 TYR cc_start: 0.8258 (m-10) cc_final: 0.7922 (m-80) REVERT: A 165 HIS cc_start: 0.9011 (m-70) cc_final: 0.8317 (m90) REVERT: A 172 TYR cc_start: 0.8335 (m-10) cc_final: 0.8027 (m-80) REVERT: A 174 ASP cc_start: 0.8932 (m-30) cc_final: 0.8417 (t0) REVERT: A 196 LYS cc_start: 0.8689 (mptt) cc_final: 0.8374 (mptt) REVERT: A 262 LYS cc_start: 0.8663 (ttpp) cc_final: 0.8194 (ttpt) REVERT: A 288 ASN cc_start: 0.7478 (m110) cc_final: 0.6909 (m110) REVERT: A 296 CYS cc_start: 0.8294 (m) cc_final: 0.7933 (m) REVERT: A 304 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7484 (mm-40) REVERT: A 317 LYS cc_start: 0.8390 (ptpt) cc_final: 0.8091 (ptpt) REVERT: A 321 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7728 (mt-10) REVERT: A 322 LEU cc_start: 0.8860 (mt) cc_final: 0.8478 (tp) REVERT: A 323 GLU cc_start: 0.7516 (mp0) cc_final: 0.7102 (mp0) REVERT: A 348 MET cc_start: 0.7476 (tmm) cc_final: 0.7205 (tmm) REVERT: A 355 ASP cc_start: 0.8367 (t0) cc_final: 0.8089 (t0) REVERT: A 358 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7634 (mp) REVERT: A 386 MET cc_start: 0.8632 (mtp) cc_final: 0.8282 (mtp) REVERT: A 408 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8469 (tp) REVERT: A 437 GLU cc_start: 0.8208 (tp30) cc_final: 0.7999 (tp30) REVERT: A 451 LYS cc_start: 0.8493 (mtmt) cc_final: 0.7868 (mtmt) outliers start: 111 outliers final: 78 residues processed: 1188 average time/residue: 0.1654 time to fit residues: 304.9965 Evaluate side-chains 1228 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 1136 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 334 HIS Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 105 HIS Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 375 ASN Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 288 HIS Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain F residue 253 ASN Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain F residue 304 GLN Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 190 GLN Chi-restraints excluded: chain H residue 51 ASN Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 228 TYR Chi-restraints excluded: chain I residue 247 GLU Chi-restraints excluded: chain I residue 431 LYS Chi-restraints excluded: chain I residue 450 MET Chi-restraints excluded: chain I residue 564 GLN Chi-restraints excluded: chain I residue 580 THR Chi-restraints excluded: chain I residue 586 SER Chi-restraints excluded: chain I residue 587 LYS Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain I residue 684 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 161 ILE Chi-restraints excluded: chain M residue 217 ARG Chi-restraints excluded: chain M residue 236 ASN Chi-restraints excluded: chain M residue 240 CYS Chi-restraints excluded: chain M residue 258 LEU Chi-restraints excluded: chain M residue 275 GLN Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 408 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 1 optimal weight: 5.9990 chunk 300 optimal weight: 0.9990 chunk 204 optimal weight: 4.9990 chunk 19 optimal weight: 0.3980 chunk 249 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 162 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 180 HIS D 75 ASN D 180 ASN ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 HIS F 225 HIS G 98 HIS H 94 ASN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 564 GLN ** J 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS A 447 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.136142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.110311 restraints weight = 59522.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.114014 restraints weight = 30589.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.116444 restraints weight = 18834.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.118091 restraints weight = 13167.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.119216 restraints weight = 10092.937| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26963 Z= 0.167 Angle : 0.681 15.720 36489 Z= 0.350 Chirality : 0.043 0.285 4207 Planarity : 0.004 0.058 4645 Dihedral : 5.021 58.082 3635 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.14 % Favored : 94.83 % Rotamer: Outliers : 4.10 % Allowed : 23.06 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.15), residues: 3290 helix: 1.61 (0.12), residues: 2151 sheet: -0.88 (0.50), residues: 122 loop : -1.90 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 193 TYR 0.024 0.001 TYR B 218 PHE 0.038 0.001 PHE A 446 TRP 0.028 0.002 TRP I 545 HIS 0.024 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00351 (26952) covalent geometry : angle 0.68028 (36484) SS BOND : bond 0.00357 ( 1) SS BOND : angle 2.18095 ( 2) hydrogen bonds : bond 0.04778 ( 1569) hydrogen bonds : angle 4.24761 ( 4605) metal coordination : bond 0.00491 ( 10) metal coordination : angle 1.45752 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1254 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 1138 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 GLN cc_start: 0.8533 (mp10) cc_final: 0.7929 (mp10) REVERT: B 56 LYS cc_start: 0.8875 (mptt) cc_final: 0.8653 (tptt) REVERT: B 66 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7231 (mm-30) REVERT: B 70 LYS cc_start: 0.8956 (tmtt) cc_final: 0.8705 (tmtt) REVERT: B 72 LEU cc_start: 0.8738 (mt) cc_final: 0.7976 (mt) REVERT: B 74 GLN cc_start: 0.8656 (tp40) cc_final: 0.7737 (tp40) REVERT: B 75 MET cc_start: 0.7752 (ppp) cc_final: 0.7146 (ppp) REVERT: B 76 ILE cc_start: 0.8434 (mt) cc_final: 0.8146 (tp) REVERT: B 109 GLU cc_start: 0.8015 (tp30) cc_final: 0.7351 (tp30) REVERT: B 115 ILE cc_start: 0.8663 (mt) cc_final: 0.8372 (tp) REVERT: B 149 PHE cc_start: 0.7992 (t80) cc_final: 0.7661 (t80) REVERT: B 152 ASN cc_start: 0.8052 (t0) cc_final: 0.7634 (t0) REVERT: B 158 LEU cc_start: 0.8924 (tp) cc_final: 0.8613 (tt) REVERT: B 161 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7313 (tm-30) REVERT: B 163 GLU cc_start: 0.7771 (tp30) cc_final: 0.7336 (tp30) REVERT: B 164 GLU cc_start: 0.8012 (tp30) cc_final: 0.7437 (tm-30) REVERT: B 165 TYR cc_start: 0.8394 (m-10) cc_final: 0.8089 (m-10) REVERT: B 176 HIS cc_start: 0.7370 (m170) cc_final: 0.6594 (m170) REVERT: B 226 SER cc_start: 0.8480 (m) cc_final: 0.8243 (p) REVERT: B 234 MET cc_start: 0.7850 (mmm) cc_final: 0.7531 (mmm) REVERT: B 250 GLU cc_start: 0.8370 (tt0) cc_final: 0.8047 (tt0) REVERT: B 257 ASP cc_start: 0.8396 (m-30) cc_final: 0.7797 (m-30) REVERT: B 260 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7827 (mm-30) REVERT: B 291 ILE cc_start: 0.9284 (mp) cc_final: 0.8683 (tp) REVERT: B 322 ASP cc_start: 0.8465 (t0) cc_final: 0.8040 (t0) REVERT: B 325 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7439 (mm-30) REVERT: B 328 LYS cc_start: 0.9087 (ttpp) cc_final: 0.8786 (ttmm) REVERT: B 338 MET cc_start: 0.7398 (tpt) cc_final: 0.6433 (tpt) REVERT: B 347 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8302 (mm) REVERT: B 361 LYS cc_start: 0.8737 (tptp) cc_final: 0.8343 (tptp) REVERT: B 363 ILE cc_start: 0.8933 (pt) cc_final: 0.8523 (tp) REVERT: B 368 ARG cc_start: 0.8369 (mtp-110) cc_final: 0.7940 (mtp180) REVERT: B 391 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7733 (tm-30) REVERT: B 410 GLU cc_start: 0.7628 (pp20) cc_final: 0.7218 (pp20) REVERT: B 411 LEU cc_start: 0.8228 (mp) cc_final: 0.7534 (mp) REVERT: B 415 LYS cc_start: 0.8395 (tttp) cc_final: 0.8112 (tttp) REVERT: B 433 SER cc_start: 0.9077 (m) cc_final: 0.8717 (p) REVERT: C 78 PHE cc_start: 0.8866 (t80) cc_final: 0.8512 (t80) REVERT: C 82 GLN cc_start: 0.8539 (mt0) cc_final: 0.7998 (mt0) REVERT: C 94 ARG cc_start: 0.8757 (ttp-110) cc_final: 0.8532 (ttp-170) REVERT: C 98 ASP cc_start: 0.8530 (t0) cc_final: 0.8203 (m-30) REVERT: C 100 PHE cc_start: 0.7600 (t80) cc_final: 0.7056 (t80) REVERT: C 104 CYS cc_start: 0.8800 (m) cc_final: 0.8350 (m) REVERT: C 106 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8012 (mm110) REVERT: C 121 ILE cc_start: 0.8988 (mm) cc_final: 0.8739 (tp) REVERT: C 126 GLN cc_start: 0.8379 (mt0) cc_final: 0.7617 (mm-40) REVERT: C 129 ASP cc_start: 0.7708 (m-30) cc_final: 0.7243 (m-30) REVERT: C 136 ASN cc_start: 0.8967 (p0) cc_final: 0.8181 (p0) REVERT: C 147 GLN cc_start: 0.8328 (tm-30) cc_final: 0.8038 (tm-30) REVERT: C 166 MET cc_start: 0.7728 (mpp) cc_final: 0.7395 (mpp) REVERT: C 176 TYR cc_start: 0.8268 (t80) cc_final: 0.8067 (t80) REVERT: C 190 MET cc_start: 0.7804 (ttm) cc_final: 0.7576 (tpp) REVERT: C 219 ILE cc_start: 0.7992 (mt) cc_final: 0.7662 (mm) REVERT: C 247 GLN cc_start: 0.7957 (pp30) cc_final: 0.7439 (tm-30) REVERT: C 271 ASN cc_start: 0.7699 (t0) cc_final: 0.6927 (t0) REVERT: C 280 ASN cc_start: 0.8440 (m-40) cc_final: 0.8112 (m110) REVERT: C 291 ASN cc_start: 0.8287 (m110) cc_final: 0.8040 (m110) REVERT: C 292 MET cc_start: 0.7818 (tmm) cc_final: 0.7480 (tmm) REVERT: C 304 LYS cc_start: 0.8832 (mttp) cc_final: 0.8616 (mttp) REVERT: C 309 ARG cc_start: 0.8971 (ttm170) cc_final: 0.8556 (ttp-170) REVERT: C 320 GLN cc_start: 0.8229 (tp-100) cc_final: 0.7816 (tp40) REVERT: C 366 LYS cc_start: 0.8714 (mmmm) cc_final: 0.8346 (mtpp) REVERT: C 379 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7387 (mm-30) REVERT: C 380 MET cc_start: 0.8429 (mtt) cc_final: 0.7782 (mtt) REVERT: C 383 CYS cc_start: 0.8297 (t) cc_final: 0.7888 (p) REVERT: C 385 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7394 (tm-30) REVERT: C 393 MET cc_start: 0.7514 (tpp) cc_final: 0.7138 (tpp) REVERT: C 405 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8122 (tm-30) REVERT: C 406 LYS cc_start: 0.9038 (mttp) cc_final: 0.8486 (mttp) REVERT: D 28 GLN cc_start: 0.8195 (mp10) cc_final: 0.7798 (mm-40) REVERT: D 50 GLU cc_start: 0.8279 (pt0) cc_final: 0.7842 (pt0) REVERT: D 53 VAL cc_start: 0.7507 (m) cc_final: 0.7279 (p) REVERT: D 62 SER cc_start: 0.8523 (m) cc_final: 0.8059 (p) REVERT: D 90 GLU cc_start: 0.7911 (tp30) cc_final: 0.6867 (tp30) REVERT: D 91 LYS cc_start: 0.8581 (mmpt) cc_final: 0.8067 (mmpt) REVERT: D 141 VAL cc_start: 0.8058 (p) cc_final: 0.7805 (t) REVERT: D 144 LYS cc_start: 0.8204 (mtmt) cc_final: 0.7666 (mtmt) REVERT: D 146 GLU cc_start: 0.7964 (tp30) cc_final: 0.7209 (tp30) REVERT: D 150 LYS cc_start: 0.8650 (ttmm) cc_final: 0.8300 (ttmm) REVERT: D 160 ASP cc_start: 0.8209 (t0) cc_final: 0.8006 (t0) REVERT: D 203 GLU cc_start: 0.7943 (mp0) cc_final: 0.7463 (mp0) REVERT: D 226 LEU cc_start: 0.8938 (tp) cc_final: 0.8635 (tp) REVERT: D 227 LYS cc_start: 0.9012 (ttpp) cc_final: 0.8659 (ttpp) REVERT: D 240 GLN cc_start: 0.7677 (tm-30) cc_final: 0.7039 (tm-30) REVERT: D 241 GLN cc_start: 0.8089 (tp40) cc_final: 0.7708 (tp40) REVERT: D 245 MET cc_start: 0.8661 (tpp) cc_final: 0.8150 (tpp) REVERT: D 266 LYS cc_start: 0.8933 (mttt) cc_final: 0.8651 (mttt) REVERT: D 268 TYR cc_start: 0.8707 (t80) cc_final: 0.8410 (t80) REVERT: D 286 MET cc_start: 0.8293 (tpp) cc_final: 0.7150 (mpp) REVERT: D 289 GLN cc_start: 0.8831 (mt0) cc_final: 0.8334 (mt0) REVERT: D 301 ASP cc_start: 0.7431 (m-30) cc_final: 0.7068 (m-30) REVERT: D 302 ARG cc_start: 0.7923 (tpp80) cc_final: 0.7015 (tpp80) REVERT: D 306 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7683 (mt-10) REVERT: D 322 GLU cc_start: 0.8450 (mp0) cc_final: 0.8106 (mp0) REVERT: D 329 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7141 (mm-30) REVERT: D 336 GLU cc_start: 0.8617 (tt0) cc_final: 0.8266 (tt0) REVERT: D 342 MET cc_start: 0.8573 (ttp) cc_final: 0.8246 (mtp) REVERT: D 354 GLN cc_start: 0.8508 (tt0) cc_final: 0.8167 (tt0) REVERT: D 358 ILE cc_start: 0.8464 (mt) cc_final: 0.8114 (mm) REVERT: D 359 VAL cc_start: 0.8445 (t) cc_final: 0.8157 (p) REVERT: D 372 LYS cc_start: 0.8626 (tptt) cc_final: 0.8194 (tptt) REVERT: D 379 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.7997 (m-10) REVERT: D 380 GLN cc_start: 0.8404 (mm110) cc_final: 0.8006 (mm110) REVERT: D 383 ASN cc_start: 0.8037 (m-40) cc_final: 0.7636 (m-40) REVERT: D 387 LYS cc_start: 0.9191 (tttt) cc_final: 0.8794 (tttt) REVERT: E 252 SER cc_start: 0.8282 (m) cc_final: 0.8053 (m) REVERT: E 258 ASN cc_start: 0.8683 (m-40) cc_final: 0.8067 (m-40) REVERT: E 262 THR cc_start: 0.9178 (m) cc_final: 0.8877 (p) REVERT: E 305 ARG cc_start: 0.8291 (mtp-110) cc_final: 0.7788 (mtp-110) REVERT: E 308 CYS cc_start: 0.8733 (m) cc_final: 0.8422 (m) REVERT: E 309 LYS cc_start: 0.8901 (tttt) cc_final: 0.8448 (tttt) REVERT: E 313 GLU cc_start: 0.8480 (tp30) cc_final: 0.7846 (tp30) REVERT: E 321 GLN cc_start: 0.8947 (mm-40) cc_final: 0.8604 (mm-40) REVERT: F 230 MET cc_start: 0.8497 (mmt) cc_final: 0.8135 (mmt) REVERT: F 241 TYR cc_start: 0.8723 (t80) cc_final: 0.8363 (t80) REVERT: F 258 ARG cc_start: 0.8322 (mtt180) cc_final: 0.8092 (mtt180) REVERT: F 270 LEU cc_start: 0.8565 (tp) cc_final: 0.8079 (tp) REVERT: F 278 ASP cc_start: 0.8305 (m-30) cc_final: 0.7840 (m-30) REVERT: F 279 PHE cc_start: 0.8715 (t80) cc_final: 0.8030 (t80) REVERT: F 283 CYS cc_start: 0.9158 (m) cc_final: 0.8542 (m) REVERT: F 301 THR cc_start: 0.8844 (m) cc_final: 0.8350 (p) REVERT: F 302 MET cc_start: 0.8131 (ttt) cc_final: 0.7558 (mmm) REVERT: G 14 GLN cc_start: 0.8080 (mt0) cc_final: 0.7598 (mt0) REVERT: G 36 GLU cc_start: 0.7922 (pt0) cc_final: 0.7691 (pt0) REVERT: G 65 GLN cc_start: 0.8128 (tp-100) cc_final: 0.7186 (tp-100) REVERT: G 66 LEU cc_start: 0.8751 (tt) cc_final: 0.8516 (tt) REVERT: G 92 GLN cc_start: 0.8795 (mt0) cc_final: 0.8339 (mt0) REVERT: G 93 GLN cc_start: 0.8574 (pt0) cc_final: 0.8317 (pt0) REVERT: G 97 LYS cc_start: 0.8721 (mttt) cc_final: 0.8135 (mmtp) REVERT: G 99 LEU cc_start: 0.8781 (mt) cc_final: 0.8505 (mt) REVERT: G 120 LEU cc_start: 0.8522 (mt) cc_final: 0.8219 (mm) REVERT: G 125 LEU cc_start: 0.8521 (mt) cc_final: 0.7923 (mt) REVERT: G 129 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7972 (mt-10) REVERT: G 133 ILE cc_start: 0.8346 (mm) cc_final: 0.8085 (mm) REVERT: G 150 GLN cc_start: 0.8456 (mm-40) cc_final: 0.7904 (mm-40) REVERT: G 155 ASP cc_start: 0.8444 (m-30) cc_final: 0.8212 (m-30) REVERT: G 181 CYS cc_start: 0.8537 (m) cc_final: 0.8310 (m) REVERT: G 193 LEU cc_start: 0.8990 (tp) cc_final: 0.8756 (tp) REVERT: G 197 GLN cc_start: 0.8507 (tm-30) cc_final: 0.8083 (tm-30) REVERT: G 202 HIS cc_start: 0.8213 (t70) cc_final: 0.7828 (t70) REVERT: G 204 ARG cc_start: 0.8826 (ttm170) cc_final: 0.8507 (ttm170) REVERT: G 210 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7710 (mm-30) REVERT: H 14 LYS cc_start: 0.8804 (mppt) cc_final: 0.7883 (mppt) REVERT: H 17 LEU cc_start: 0.8442 (tp) cc_final: 0.7989 (tp) REVERT: H 18 ASP cc_start: 0.7847 (m-30) cc_final: 0.7593 (m-30) REVERT: H 21 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7949 (mt-10) REVERT: H 23 GLN cc_start: 0.8614 (tt0) cc_final: 0.8358 (tt0) REVERT: H 52 ASN cc_start: 0.8702 (m-40) cc_final: 0.8424 (m110) REVERT: H 58 LYS cc_start: 0.8594 (ttmt) cc_final: 0.8355 (ttmt) REVERT: H 79 GLN cc_start: 0.8082 (tt0) cc_final: 0.7558 (mt0) REVERT: H 123 GLN cc_start: 0.8644 (tp-100) cc_final: 0.8278 (tp-100) REVERT: H 129 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7547 (mt) REVERT: I 43 MET cc_start: 0.7563 (ppp) cc_final: 0.7345 (ppp) REVERT: I 95 PHE cc_start: 0.7112 (t80) cc_final: 0.6761 (t80) REVERT: I 121 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8525 (tm-30) REVERT: I 243 PHE cc_start: 0.8011 (t80) cc_final: 0.7656 (t80) REVERT: I 262 LYS cc_start: 0.8500 (pttp) cc_final: 0.8179 (pttp) REVERT: I 287 LEU cc_start: 0.8823 (tp) cc_final: 0.8601 (tt) REVERT: I 322 MET cc_start: 0.8132 (ttm) cc_final: 0.7830 (ttm) REVERT: I 374 HIS cc_start: 0.8780 (t-90) cc_final: 0.8538 (t-170) REVERT: I 381 VAL cc_start: 0.8956 (m) cc_final: 0.8754 (p) REVERT: I 420 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7764 (tm-30) REVERT: I 428 SER cc_start: 0.8911 (t) cc_final: 0.8504 (p) REVERT: I 464 LYS cc_start: 0.8348 (tptm) cc_final: 0.7979 (tptm) REVERT: I 468 LYS cc_start: 0.8647 (tppt) cc_final: 0.8115 (tppt) REVERT: I 503 LYS cc_start: 0.8510 (ttmm) cc_final: 0.8196 (ttmm) REVERT: I 522 LYS cc_start: 0.8283 (tppp) cc_final: 0.7888 (tppp) REVERT: I 548 GLN cc_start: 0.8482 (tp-100) cc_final: 0.8154 (tp40) REVERT: I 564 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8331 (mt0) REVERT: I 580 THR cc_start: 0.8043 (OUTLIER) cc_final: 0.7796 (p) REVERT: I 602 GLN cc_start: 0.6930 (tp40) cc_final: 0.6590 (tp40) REVERT: I 607 GLN cc_start: 0.7955 (mp10) cc_final: 0.7467 (mp10) REVERT: I 608 MET cc_start: 0.7746 (tpp) cc_final: 0.7380 (tpp) REVERT: I 630 GLN cc_start: 0.7450 (tm-30) cc_final: 0.7112 (tm-30) REVERT: I 638 GLN cc_start: 0.8892 (mp10) cc_final: 0.8489 (mp10) REVERT: I 643 LEU cc_start: 0.8937 (mp) cc_final: 0.8456 (tp) REVERT: I 721 MET cc_start: 0.8612 (mtm) cc_final: 0.8332 (mtm) REVERT: L 32 GLU cc_start: 0.7897 (tp30) cc_final: 0.7557 (tp30) REVERT: L 57 LYS cc_start: 0.8403 (ptpt) cc_final: 0.8133 (ptpt) REVERT: L 126 MET cc_start: 0.7971 (mmp) cc_final: 0.7450 (mmp) REVERT: M 118 LEU cc_start: 0.9058 (mp) cc_final: 0.8307 (tt) REVERT: M 161 ILE cc_start: 0.7676 (OUTLIER) cc_final: 0.7428 (tp) REVERT: M 208 LEU cc_start: 0.8565 (mt) cc_final: 0.8278 (mm) REVERT: M 217 ARG cc_start: 0.6002 (OUTLIER) cc_final: 0.4108 (ptp90) REVERT: M 251 LEU cc_start: 0.8718 (tt) cc_final: 0.8369 (pp) REVERT: M 259 ASP cc_start: 0.7922 (p0) cc_final: 0.7488 (p0) REVERT: M 323 LEU cc_start: 0.8682 (mp) cc_final: 0.8018 (pp) REVERT: N 23 MET cc_start: 0.7264 (ttm) cc_final: 0.6838 (ttm) REVERT: N 34 LYS cc_start: 0.8604 (mppt) cc_final: 0.8338 (mppt) REVERT: N 58 MET cc_start: 0.7597 (mtp) cc_final: 0.7157 (mtp) REVERT: P 43 PHE cc_start: 0.8483 (p90) cc_final: 0.8120 (p90) REVERT: P 44 PHE cc_start: 0.7961 (t80) cc_final: 0.7713 (t80) REVERT: P 52 ASP cc_start: 0.7545 (t0) cc_final: 0.7046 (t0) REVERT: A 90 MET cc_start: 0.8222 (tpt) cc_final: 0.7480 (tpt) REVERT: A 98 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8946 (mm) REVERT: A 130 TRP cc_start: 0.7567 (t60) cc_final: 0.6912 (t60) REVERT: A 132 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7973 (pm20) REVERT: A 148 ASP cc_start: 0.8486 (p0) cc_final: 0.7943 (p0) REVERT: A 152 TYR cc_start: 0.8170 (m-10) cc_final: 0.7820 (m-10) REVERT: A 165 HIS cc_start: 0.9003 (m-70) cc_final: 0.8324 (m90) REVERT: A 172 TYR cc_start: 0.8345 (m-10) cc_final: 0.8100 (m-80) REVERT: A 174 ASP cc_start: 0.9005 (m-30) cc_final: 0.8408 (t0) REVERT: A 196 LYS cc_start: 0.8713 (mptt) cc_final: 0.8427 (mptt) REVERT: A 262 LYS cc_start: 0.8697 (ttpp) cc_final: 0.8206 (ttpt) REVERT: A 288 ASN cc_start: 0.7462 (m110) cc_final: 0.6922 (m110) REVERT: A 296 CYS cc_start: 0.8294 (m) cc_final: 0.7886 (m) REVERT: A 304 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7500 (mm-40) REVERT: A 317 LYS cc_start: 0.8392 (ptpt) cc_final: 0.8039 (ptpt) REVERT: A 321 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7697 (mt-10) REVERT: A 322 LEU cc_start: 0.8871 (mt) cc_final: 0.8494 (tp) REVERT: A 323 GLU cc_start: 0.7525 (mp0) cc_final: 0.7147 (mp0) REVERT: A 348 MET cc_start: 0.7522 (tmm) cc_final: 0.7248 (tmm) REVERT: A 355 ASP cc_start: 0.8449 (t0) cc_final: 0.8227 (t0) REVERT: A 358 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7661 (mp) REVERT: A 367 THR cc_start: 0.8444 (t) cc_final: 0.8064 (p) REVERT: A 386 MET cc_start: 0.8651 (mtp) cc_final: 0.8295 (mtp) REVERT: A 451 LYS cc_start: 0.8487 (mtmt) cc_final: 0.7742 (mtmt) outliers start: 116 outliers final: 86 residues processed: 1175 average time/residue: 0.1663 time to fit residues: 303.2179 Evaluate side-chains 1225 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 1129 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 319 GLN Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 375 ASN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 244 ARG Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain F residue 253 ASN Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain F residue 304 GLN Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 175 HIS Chi-restraints excluded: chain G residue 190 GLN Chi-restraints excluded: chain H residue 51 ASN Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 247 GLU Chi-restraints excluded: chain I residue 431 LYS Chi-restraints excluded: chain I residue 450 MET Chi-restraints excluded: chain I residue 564 GLN Chi-restraints excluded: chain I residue 580 THR Chi-restraints excluded: chain I residue 586 SER Chi-restraints excluded: chain I residue 587 LYS Chi-restraints excluded: chain I residue 629 THR Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain I residue 684 ILE Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 161 ILE Chi-restraints excluded: chain M residue 217 ARG Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 236 ASN Chi-restraints excluded: chain M residue 240 CYS Chi-restraints excluded: chain M residue 258 LEU Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 447 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 54 optimal weight: 2.9990 chunk 321 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 204 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 134 optimal weight: 0.0050 chunk 208 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 HIS B 435 ASN C 105 HIS C 116 GLN D 56 ASN D 75 ASN ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 HIS F 225 HIS G 98 HIS ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 564 GLN ** J 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.137750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.111954 restraints weight = 59828.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.115703 restraints weight = 30562.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.118168 restraints weight = 18786.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.119789 restraints weight = 13082.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.120947 restraints weight = 10038.230| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26963 Z= 0.137 Angle : 0.688 16.013 36489 Z= 0.349 Chirality : 0.042 0.291 4207 Planarity : 0.004 0.054 4645 Dihedral : 4.965 59.134 3635 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.71 % Favored : 95.26 % Rotamer: Outliers : 3.78 % Allowed : 25.04 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.15), residues: 3290 helix: 1.64 (0.12), residues: 2154 sheet: -0.70 (0.48), residues: 134 loop : -1.91 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 193 TYR 0.043 0.001 TYR A 211 PHE 0.028 0.001 PHE D 48 TRP 0.027 0.001 TRP I 21 HIS 0.006 0.001 HIS D 307 Details of bonding type rmsd covalent geometry : bond 0.00295 (26952) covalent geometry : angle 0.68758 (36484) SS BOND : bond 0.00243 ( 1) SS BOND : angle 1.91879 ( 2) hydrogen bonds : bond 0.04471 ( 1569) hydrogen bonds : angle 4.18057 ( 4605) metal coordination : bond 0.00410 ( 10) metal coordination : angle 1.48208 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1249 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 1142 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 GLN cc_start: 0.8486 (mp10) cc_final: 0.7892 (mp10) REVERT: B 56 LYS cc_start: 0.8850 (mptt) cc_final: 0.8621 (tptt) REVERT: B 66 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7091 (mm-30) REVERT: B 70 LYS cc_start: 0.8942 (tmtt) cc_final: 0.8700 (tmtt) REVERT: B 72 LEU cc_start: 0.8750 (mt) cc_final: 0.8026 (mt) REVERT: B 74 GLN cc_start: 0.8613 (tp40) cc_final: 0.7657 (tp40) REVERT: B 75 MET cc_start: 0.7667 (ppp) cc_final: 0.7073 (ppp) REVERT: B 76 ILE cc_start: 0.8401 (mt) cc_final: 0.8105 (tp) REVERT: B 100 ARG cc_start: 0.8026 (ttt180) cc_final: 0.7765 (ttt180) REVERT: B 109 GLU cc_start: 0.8048 (tp30) cc_final: 0.7684 (tp30) REVERT: B 115 ILE cc_start: 0.8651 (mt) cc_final: 0.8350 (tp) REVERT: B 149 PHE cc_start: 0.7951 (t80) cc_final: 0.7602 (t80) REVERT: B 152 ASN cc_start: 0.8021 (t0) cc_final: 0.7584 (t0) REVERT: B 158 LEU cc_start: 0.8894 (tp) cc_final: 0.8589 (tt) REVERT: B 161 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7326 (tm-30) REVERT: B 163 GLU cc_start: 0.7750 (tp30) cc_final: 0.7282 (tp30) REVERT: B 164 GLU cc_start: 0.7996 (tp30) cc_final: 0.7345 (tm-30) REVERT: B 165 TYR cc_start: 0.8364 (m-10) cc_final: 0.8023 (m-10) REVERT: B 176 HIS cc_start: 0.7256 (m170) cc_final: 0.6692 (m170) REVERT: B 201 GLU cc_start: 0.8059 (pp20) cc_final: 0.7713 (tm-30) REVERT: B 226 SER cc_start: 0.8417 (m) cc_final: 0.8185 (p) REVERT: B 234 MET cc_start: 0.7765 (mmm) cc_final: 0.7450 (mmm) REVERT: B 250 GLU cc_start: 0.8308 (tt0) cc_final: 0.7190 (tt0) REVERT: B 253 LYS cc_start: 0.7779 (mmtp) cc_final: 0.6651 (mmtp) REVERT: B 257 ASP cc_start: 0.8380 (m-30) cc_final: 0.7759 (m-30) REVERT: B 260 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7857 (mm-30) REVERT: B 291 ILE cc_start: 0.9269 (mp) cc_final: 0.8677 (tp) REVERT: B 322 ASP cc_start: 0.8430 (t0) cc_final: 0.8022 (t0) REVERT: B 325 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7442 (mm-30) REVERT: B 328 LYS cc_start: 0.9101 (ttpp) cc_final: 0.8858 (ttpp) REVERT: B 338 MET cc_start: 0.7203 (tpt) cc_final: 0.6272 (tpt) REVERT: B 347 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8308 (mm) REVERT: B 361 LYS cc_start: 0.8720 (tptp) cc_final: 0.8328 (tptp) REVERT: B 363 ILE cc_start: 0.8897 (pt) cc_final: 0.8507 (tp) REVERT: B 368 ARG cc_start: 0.8351 (mtp-110) cc_final: 0.7909 (mtp180) REVERT: B 391 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7699 (tm-30) REVERT: B 410 GLU cc_start: 0.7603 (pp20) cc_final: 0.7139 (pp20) REVERT: B 411 LEU cc_start: 0.8195 (mp) cc_final: 0.7510 (mp) REVERT: B 415 LYS cc_start: 0.8392 (tttp) cc_final: 0.8077 (tttp) REVERT: B 433 SER cc_start: 0.9047 (m) cc_final: 0.8676 (p) REVERT: C 78 PHE cc_start: 0.8856 (t80) cc_final: 0.8477 (t80) REVERT: C 82 GLN cc_start: 0.8503 (mt0) cc_final: 0.7968 (mt0) REVERT: C 94 ARG cc_start: 0.8757 (ttp-110) cc_final: 0.8344 (ttp-170) REVERT: C 98 ASP cc_start: 0.8526 (t0) cc_final: 0.8218 (m-30) REVERT: C 100 PHE cc_start: 0.7624 (t80) cc_final: 0.7133 (t80) REVERT: C 104 CYS cc_start: 0.8670 (m) cc_final: 0.8303 (m) REVERT: C 106 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8044 (mm-40) REVERT: C 121 ILE cc_start: 0.8984 (mm) cc_final: 0.8770 (tp) REVERT: C 126 GLN cc_start: 0.8299 (mt0) cc_final: 0.7594 (mm110) REVERT: C 129 ASP cc_start: 0.7645 (m-30) cc_final: 0.7146 (m-30) REVERT: C 136 ASN cc_start: 0.8963 (p0) cc_final: 0.8111 (p0) REVERT: C 147 GLN cc_start: 0.8333 (tm-30) cc_final: 0.8017 (tm-30) REVERT: C 166 MET cc_start: 0.7737 (mpp) cc_final: 0.7294 (mpp) REVERT: C 219 ILE cc_start: 0.7898 (mt) cc_final: 0.7586 (mm) REVERT: C 247 GLN cc_start: 0.7957 (pp30) cc_final: 0.7437 (tm-30) REVERT: C 271 ASN cc_start: 0.7632 (t0) cc_final: 0.6927 (t0) REVERT: C 276 ARG cc_start: 0.8695 (ttp-170) cc_final: 0.8495 (ttp-170) REVERT: C 292 MET cc_start: 0.7792 (tmm) cc_final: 0.7515 (tpp) REVERT: C 304 LYS cc_start: 0.8830 (mttp) cc_final: 0.8583 (mttp) REVERT: C 309 ARG cc_start: 0.8943 (ttm170) cc_final: 0.8557 (ttp-170) REVERT: C 320 GLN cc_start: 0.8183 (tp-100) cc_final: 0.7752 (tp40) REVERT: C 335 GLU cc_start: 0.8149 (tp30) cc_final: 0.7882 (tp30) REVERT: C 351 ILE cc_start: 0.8100 (mp) cc_final: 0.7772 (mm) REVERT: C 366 LYS cc_start: 0.8719 (mmmm) cc_final: 0.8353 (mtpp) REVERT: C 379 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7358 (mm-30) REVERT: C 380 MET cc_start: 0.8427 (mtt) cc_final: 0.7785 (mtt) REVERT: C 383 CYS cc_start: 0.8154 (t) cc_final: 0.7781 (p) REVERT: C 385 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7387 (tm-30) REVERT: C 393 MET cc_start: 0.7476 (tpp) cc_final: 0.7139 (tpp) REVERT: C 405 GLN cc_start: 0.8420 (tm-30) cc_final: 0.8097 (tm-30) REVERT: C 406 LYS cc_start: 0.9039 (mttp) cc_final: 0.8477 (mttp) REVERT: D 28 GLN cc_start: 0.8168 (mp10) cc_final: 0.7763 (mm-40) REVERT: D 50 GLU cc_start: 0.8265 (pt0) cc_final: 0.7799 (pt0) REVERT: D 53 VAL cc_start: 0.7538 (m) cc_final: 0.7296 (p) REVERT: D 62 SER cc_start: 0.8556 (m) cc_final: 0.8125 (p) REVERT: D 90 GLU cc_start: 0.7914 (tp30) cc_final: 0.6875 (tp30) REVERT: D 91 LYS cc_start: 0.8594 (mmpt) cc_final: 0.8065 (mmpt) REVERT: D 141 VAL cc_start: 0.7973 (p) cc_final: 0.7686 (t) REVERT: D 144 LYS cc_start: 0.8093 (mtmt) cc_final: 0.7565 (mtmt) REVERT: D 146 GLU cc_start: 0.7912 (tp30) cc_final: 0.7109 (tp30) REVERT: D 150 LYS cc_start: 0.8588 (ttmm) cc_final: 0.8218 (ttmm) REVERT: D 158 ASP cc_start: 0.7926 (t70) cc_final: 0.7550 (t0) REVERT: D 160 ASP cc_start: 0.8198 (t0) cc_final: 0.7860 (t0) REVERT: D 175 GLN cc_start: 0.7356 (pp30) cc_final: 0.6862 (pp30) REVERT: D 203 GLU cc_start: 0.7921 (mp0) cc_final: 0.7448 (mp0) REVERT: D 226 LEU cc_start: 0.8903 (tp) cc_final: 0.8595 (tp) REVERT: D 227 LYS cc_start: 0.8972 (ttpp) cc_final: 0.8620 (ttpp) REVERT: D 240 GLN cc_start: 0.7638 (tm-30) cc_final: 0.6963 (pp30) REVERT: D 241 GLN cc_start: 0.8052 (tp40) cc_final: 0.7668 (tp40) REVERT: D 245 MET cc_start: 0.8682 (tpp) cc_final: 0.8160 (tpp) REVERT: D 266 LYS cc_start: 0.8905 (mttt) cc_final: 0.8612 (mttt) REVERT: D 286 MET cc_start: 0.8267 (tpp) cc_final: 0.7147 (mpp) REVERT: D 289 GLN cc_start: 0.8817 (mt0) cc_final: 0.8309 (mt0) REVERT: D 301 ASP cc_start: 0.7418 (m-30) cc_final: 0.6988 (m-30) REVERT: D 302 ARG cc_start: 0.7896 (tpp80) cc_final: 0.7041 (tpp80) REVERT: D 306 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7656 (mt-10) REVERT: D 322 GLU cc_start: 0.8453 (mp0) cc_final: 0.8075 (mp0) REVERT: D 329 GLU cc_start: 0.7296 (mm-30) cc_final: 0.7050 (mm-30) REVERT: D 336 GLU cc_start: 0.8618 (tt0) cc_final: 0.8233 (tt0) REVERT: D 342 MET cc_start: 0.8543 (ttp) cc_final: 0.8234 (mtp) REVERT: D 354 GLN cc_start: 0.8500 (tt0) cc_final: 0.8178 (tt0) REVERT: D 358 ILE cc_start: 0.8457 (mt) cc_final: 0.8097 (mm) REVERT: D 359 VAL cc_start: 0.8419 (t) cc_final: 0.8162 (p) REVERT: D 372 LYS cc_start: 0.8633 (tptt) cc_final: 0.8215 (tptt) REVERT: D 379 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.7970 (m-10) REVERT: D 380 GLN cc_start: 0.8384 (mm110) cc_final: 0.8003 (mm110) REVERT: D 383 ASN cc_start: 0.8020 (m-40) cc_final: 0.7617 (m-40) REVERT: D 387 LYS cc_start: 0.9214 (tttt) cc_final: 0.8802 (tttt) REVERT: E 252 SER cc_start: 0.8188 (m) cc_final: 0.7951 (m) REVERT: E 258 ASN cc_start: 0.8684 (m-40) cc_final: 0.8057 (m-40) REVERT: E 262 THR cc_start: 0.9169 (m) cc_final: 0.8863 (p) REVERT: E 305 ARG cc_start: 0.8268 (mtp-110) cc_final: 0.7789 (mtp-110) REVERT: E 308 CYS cc_start: 0.8695 (m) cc_final: 0.8384 (m) REVERT: E 309 LYS cc_start: 0.8880 (tttt) cc_final: 0.8426 (tttt) REVERT: E 313 GLU cc_start: 0.8472 (tp30) cc_final: 0.7829 (tp30) REVERT: E 321 GLN cc_start: 0.8941 (mm-40) cc_final: 0.8610 (mm-40) REVERT: F 230 MET cc_start: 0.8432 (mmt) cc_final: 0.8077 (mmt) REVERT: F 241 TYR cc_start: 0.8725 (t80) cc_final: 0.8393 (t80) REVERT: F 258 ARG cc_start: 0.8335 (mtt180) cc_final: 0.8044 (mtt180) REVERT: F 270 LEU cc_start: 0.8554 (tp) cc_final: 0.8077 (tp) REVERT: F 278 ASP cc_start: 0.8295 (m-30) cc_final: 0.7833 (m-30) REVERT: F 301 THR cc_start: 0.8796 (m) cc_final: 0.8300 (p) REVERT: F 302 MET cc_start: 0.8100 (ttt) cc_final: 0.7553 (mmm) REVERT: G 14 GLN cc_start: 0.8070 (mt0) cc_final: 0.7580 (mt0) REVERT: G 45 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7430 (tp30) REVERT: G 65 GLN cc_start: 0.8120 (tp-100) cc_final: 0.7179 (tp-100) REVERT: G 66 LEU cc_start: 0.8719 (tt) cc_final: 0.8492 (tt) REVERT: G 92 GLN cc_start: 0.8739 (mt0) cc_final: 0.8345 (mt0) REVERT: G 93 GLN cc_start: 0.8578 (pt0) cc_final: 0.8325 (pt0) REVERT: G 97 LYS cc_start: 0.8677 (mttt) cc_final: 0.8080 (mmtp) REVERT: G 99 LEU cc_start: 0.8796 (mt) cc_final: 0.8511 (mt) REVERT: G 120 LEU cc_start: 0.8500 (mt) cc_final: 0.8190 (mt) REVERT: G 125 LEU cc_start: 0.8456 (mt) cc_final: 0.7868 (mt) REVERT: G 129 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8037 (mt-10) REVERT: G 133 ILE cc_start: 0.8287 (mm) cc_final: 0.8032 (mm) REVERT: G 150 GLN cc_start: 0.8446 (mm-40) cc_final: 0.7801 (mm-40) REVERT: G 155 ASP cc_start: 0.8421 (m-30) cc_final: 0.8172 (m-30) REVERT: G 181 CYS cc_start: 0.8540 (m) cc_final: 0.8314 (m) REVERT: G 188 ILE cc_start: 0.8402 (mt) cc_final: 0.8002 (tp) REVERT: G 193 LEU cc_start: 0.8927 (tp) cc_final: 0.8686 (tp) REVERT: G 197 GLN cc_start: 0.8460 (tm-30) cc_final: 0.8042 (tm-30) REVERT: G 202 HIS cc_start: 0.8181 (t70) cc_final: 0.7836 (t70) REVERT: G 204 ARG cc_start: 0.8806 (ttm170) cc_final: 0.8492 (ttm170) REVERT: G 210 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7662 (mm-30) REVERT: H 14 LYS cc_start: 0.8774 (mppt) cc_final: 0.7847 (mppt) REVERT: H 17 LEU cc_start: 0.8422 (tp) cc_final: 0.7939 (tp) REVERT: H 18 ASP cc_start: 0.7810 (m-30) cc_final: 0.7555 (m-30) REVERT: H 21 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7922 (mt-10) REVERT: H 23 GLN cc_start: 0.8617 (tt0) cc_final: 0.8351 (tt0) REVERT: H 52 ASN cc_start: 0.8670 (m-40) cc_final: 0.8391 (m110) REVERT: H 58 LYS cc_start: 0.8574 (ttmt) cc_final: 0.8332 (ttmt) REVERT: H 79 GLN cc_start: 0.8036 (tt0) cc_final: 0.7543 (mt0) REVERT: H 123 GLN cc_start: 0.8626 (tp-100) cc_final: 0.8266 (tp-100) REVERT: H 129 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7531 (mt) REVERT: I 121 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8519 (tm-30) REVERT: I 136 ILE cc_start: 0.8353 (mm) cc_final: 0.8096 (mm) REVERT: I 210 GLU cc_start: 0.8198 (tt0) cc_final: 0.7940 (tt0) REVERT: I 247 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6981 (mp0) REVERT: I 262 LYS cc_start: 0.8447 (pttp) cc_final: 0.8123 (pttp) REVERT: I 287 LEU cc_start: 0.8795 (tp) cc_final: 0.8475 (tt) REVERT: I 322 MET cc_start: 0.8085 (ttm) cc_final: 0.7773 (ttm) REVERT: I 330 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.6085 (mt0) REVERT: I 374 HIS cc_start: 0.8769 (t-90) cc_final: 0.8522 (t-170) REVERT: I 420 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7720 (tm-30) REVERT: I 428 SER cc_start: 0.8892 (t) cc_final: 0.8556 (p) REVERT: I 429 LEU cc_start: 0.8382 (tp) cc_final: 0.8047 (tp) REVERT: I 464 LYS cc_start: 0.8343 (tptm) cc_final: 0.7966 (tptm) REVERT: I 468 LYS cc_start: 0.8595 (tppt) cc_final: 0.8056 (tppt) REVERT: I 503 LYS cc_start: 0.8518 (ttmm) cc_final: 0.8159 (ttmm) REVERT: I 522 LYS cc_start: 0.8244 (tppp) cc_final: 0.7831 (tppp) REVERT: I 564 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8304 (mt0) REVERT: I 580 THR cc_start: 0.8029 (OUTLIER) cc_final: 0.7783 (p) REVERT: I 586 SER cc_start: 0.8370 (OUTLIER) cc_final: 0.7671 (m) REVERT: I 602 GLN cc_start: 0.6869 (tp40) cc_final: 0.6541 (tp40) REVERT: I 607 GLN cc_start: 0.7888 (mp10) cc_final: 0.7424 (mp10) REVERT: I 608 MET cc_start: 0.7634 (tpp) cc_final: 0.7256 (tpp) REVERT: I 614 TYR cc_start: 0.7553 (m-10) cc_final: 0.7291 (m-80) REVERT: I 630 GLN cc_start: 0.7444 (tm-30) cc_final: 0.7092 (tm-30) REVERT: I 638 GLN cc_start: 0.8891 (mp10) cc_final: 0.8468 (mp10) REVERT: I 643 LEU cc_start: 0.8927 (mp) cc_final: 0.8441 (tp) REVERT: I 721 MET cc_start: 0.8603 (mtm) cc_final: 0.8314 (mtm) REVERT: L 32 GLU cc_start: 0.7957 (tp30) cc_final: 0.7570 (tp30) REVERT: L 57 LYS cc_start: 0.8458 (ptpt) cc_final: 0.8189 (ptpt) REVERT: L 126 MET cc_start: 0.7907 (mmp) cc_final: 0.7397 (mmp) REVERT: L 142 LYS cc_start: 0.7324 (mppt) cc_final: 0.6994 (mppt) REVERT: M 118 LEU cc_start: 0.9060 (mp) cc_final: 0.8332 (tt) REVERT: M 161 ILE cc_start: 0.7538 (OUTLIER) cc_final: 0.7323 (tp) REVERT: M 208 LEU cc_start: 0.8533 (mt) cc_final: 0.8185 (mm) REVERT: M 217 ARG cc_start: 0.5972 (OUTLIER) cc_final: 0.4128 (ptp90) REVERT: M 251 LEU cc_start: 0.8700 (tt) cc_final: 0.8366 (pp) REVERT: M 259 ASP cc_start: 0.7908 (p0) cc_final: 0.7473 (p0) REVERT: M 323 LEU cc_start: 0.8674 (mp) cc_final: 0.8010 (pp) REVERT: N 23 MET cc_start: 0.7249 (ttm) cc_final: 0.6805 (ttm) REVERT: N 34 LYS cc_start: 0.8592 (mppt) cc_final: 0.8334 (mppt) REVERT: N 58 MET cc_start: 0.7551 (mtp) cc_final: 0.7124 (mtp) REVERT: P 43 PHE cc_start: 0.8399 (p90) cc_final: 0.8033 (p90) REVERT: P 44 PHE cc_start: 0.7927 (t80) cc_final: 0.7690 (t80) REVERT: P 52 ASP cc_start: 0.7536 (t0) cc_final: 0.6996 (t0) REVERT: A 90 MET cc_start: 0.8187 (tpt) cc_final: 0.7409 (tpt) REVERT: A 98 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8916 (mm) REVERT: A 132 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7929 (pm20) REVERT: A 152 TYR cc_start: 0.8152 (m-10) cc_final: 0.7789 (m-80) REVERT: A 165 HIS cc_start: 0.9002 (m-70) cc_final: 0.8325 (m90) REVERT: A 172 TYR cc_start: 0.8299 (m-10) cc_final: 0.8052 (m-80) REVERT: A 174 ASP cc_start: 0.9007 (m-30) cc_final: 0.8390 (t0) REVERT: A 196 LYS cc_start: 0.8702 (mptt) cc_final: 0.8403 (mptt) REVERT: A 255 LEU cc_start: 0.8849 (tp) cc_final: 0.8390 (tt) REVERT: A 262 LYS cc_start: 0.8673 (ttpp) cc_final: 0.8199 (ttpt) REVERT: A 288 ASN cc_start: 0.7456 (m110) cc_final: 0.6915 (m110) REVERT: A 296 CYS cc_start: 0.8274 (m) cc_final: 0.7863 (m) REVERT: A 304 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7549 (mm-40) REVERT: A 317 LYS cc_start: 0.8336 (ptpt) cc_final: 0.8030 (ptpt) REVERT: A 321 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7801 (mt-10) REVERT: A 348 MET cc_start: 0.7505 (tmm) cc_final: 0.7238 (tmm) REVERT: A 367 THR cc_start: 0.8446 (t) cc_final: 0.8069 (p) REVERT: A 386 MET cc_start: 0.8624 (mtp) cc_final: 0.8242 (mtp) REVERT: A 408 ILE cc_start: 0.8636 (tp) cc_final: 0.8365 (tp) REVERT: A 451 LYS cc_start: 0.8471 (mtmt) cc_final: 0.7708 (mtmt) outliers start: 107 outliers final: 76 residues processed: 1178 average time/residue: 0.1690 time to fit residues: 308.2001 Evaluate side-chains 1217 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 1129 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 334 HIS Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 244 ARG Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain F residue 304 GLN Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 175 HIS Chi-restraints excluded: chain G residue 190 GLN Chi-restraints excluded: chain H residue 51 ASN Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 247 GLU Chi-restraints excluded: chain I residue 330 GLN Chi-restraints excluded: chain I residue 431 LYS Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 450 MET Chi-restraints excluded: chain I residue 560 GLU Chi-restraints excluded: chain I residue 564 GLN Chi-restraints excluded: chain I residue 580 THR Chi-restraints excluded: chain I residue 586 SER Chi-restraints excluded: chain I residue 587 LYS Chi-restraints excluded: chain I residue 684 ILE Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain M residue 145 LYS Chi-restraints excluded: chain M residue 161 ILE Chi-restraints excluded: chain M residue 217 ARG Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 236 ASN Chi-restraints excluded: chain M residue 240 CYS Chi-restraints excluded: chain M residue 258 LEU Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 330 GLU Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 374 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 103 optimal weight: 3.9990 chunk 127 optimal weight: 0.0770 chunk 233 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 264 optimal weight: 0.4980 chunk 141 optimal weight: 2.9990 chunk 2 optimal weight: 0.2980 chunk 47 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 317 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 HIS B 319 GLN B 334 HIS C 105 HIS C 291 ASN D 75 ASN ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 HIS F 224 GLN F 225 HIS G 98 HIS ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 564 GLN ** J 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS A 368 GLN A 447 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.137942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.112277 restraints weight = 59432.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.116016 restraints weight = 30567.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.118500 restraints weight = 18806.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.120139 restraints weight = 13086.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.121283 restraints weight = 10026.403| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 26963 Z= 0.136 Angle : 0.718 18.436 36489 Z= 0.362 Chirality : 0.042 0.265 4207 Planarity : 0.004 0.059 4645 Dihedral : 4.906 59.693 3635 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.47 % Favored : 95.50 % Rotamer: Outliers : 3.64 % Allowed : 25.65 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.15), residues: 3290 helix: 1.65 (0.12), residues: 2150 sheet: -0.69 (0.48), residues: 138 loop : -1.91 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 193 TYR 0.028 0.001 TYR B 218 PHE 0.028 0.001 PHE D 48 TRP 0.023 0.001 TRP L 88 HIS 0.005 0.001 HIS C 282 Details of bonding type rmsd covalent geometry : bond 0.00295 (26952) covalent geometry : angle 0.71824 (36484) SS BOND : bond 0.00200 ( 1) SS BOND : angle 1.81816 ( 2) hydrogen bonds : bond 0.04312 ( 1569) hydrogen bonds : angle 4.18840 ( 4605) metal coordination : bond 0.00401 ( 10) metal coordination : angle 1.24842 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1231 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 1128 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 GLN cc_start: 0.8489 (mp10) cc_final: 0.7877 (mp10) REVERT: B 56 LYS cc_start: 0.8831 (mptt) cc_final: 0.8584 (tptt) REVERT: B 66 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7148 (mm-30) REVERT: B 70 LYS cc_start: 0.8918 (tmtt) cc_final: 0.8692 (tmtt) REVERT: B 72 LEU cc_start: 0.8766 (mt) cc_final: 0.8056 (mt) REVERT: B 74 GLN cc_start: 0.8642 (tp40) cc_final: 0.7676 (tp40) REVERT: B 75 MET cc_start: 0.7662 (ppp) cc_final: 0.7068 (ppp) REVERT: B 76 ILE cc_start: 0.8402 (mt) cc_final: 0.8107 (tp) REVERT: B 109 GLU cc_start: 0.8049 (tp30) cc_final: 0.7684 (tp30) REVERT: B 115 ILE cc_start: 0.8625 (mt) cc_final: 0.8319 (tp) REVERT: B 149 PHE cc_start: 0.7946 (t80) cc_final: 0.7632 (t80) REVERT: B 152 ASN cc_start: 0.8006 (t0) cc_final: 0.7588 (t0) REVERT: B 158 LEU cc_start: 0.8896 (tp) cc_final: 0.8557 (tt) REVERT: B 161 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7288 (tm-30) REVERT: B 163 GLU cc_start: 0.7777 (tp30) cc_final: 0.7271 (tp30) REVERT: B 176 HIS cc_start: 0.7334 (m170) cc_final: 0.7036 (m170) REVERT: B 220 GLN cc_start: 0.8150 (pt0) cc_final: 0.7472 (pp30) REVERT: B 225 LYS cc_start: 0.8691 (mptt) cc_final: 0.8361 (mptt) REVERT: B 234 MET cc_start: 0.7742 (mmm) cc_final: 0.7405 (mmm) REVERT: B 250 GLU cc_start: 0.8299 (tt0) cc_final: 0.7950 (tt0) REVERT: B 257 ASP cc_start: 0.8376 (m-30) cc_final: 0.7741 (m-30) REVERT: B 291 ILE cc_start: 0.9250 (mp) cc_final: 0.8662 (tp) REVERT: B 322 ASP cc_start: 0.8394 (t0) cc_final: 0.7986 (t0) REVERT: B 325 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7417 (mm-30) REVERT: B 328 LYS cc_start: 0.9093 (ttpp) cc_final: 0.8834 (ttpp) REVERT: B 338 MET cc_start: 0.7249 (tpt) cc_final: 0.6310 (tpt) REVERT: B 345 GLU cc_start: 0.8154 (pm20) cc_final: 0.7893 (pm20) REVERT: B 361 LYS cc_start: 0.8720 (tptp) cc_final: 0.8333 (tptp) REVERT: B 363 ILE cc_start: 0.8884 (pt) cc_final: 0.8541 (tp) REVERT: B 368 ARG cc_start: 0.8330 (mtp-110) cc_final: 0.7881 (mtp180) REVERT: B 391 GLN cc_start: 0.8180 (tm-30) cc_final: 0.7595 (tm-30) REVERT: B 410 GLU cc_start: 0.7579 (pp20) cc_final: 0.7128 (pp20) REVERT: B 411 LEU cc_start: 0.8259 (mp) cc_final: 0.7581 (mt) REVERT: B 415 LYS cc_start: 0.8376 (tttp) cc_final: 0.8060 (tttp) REVERT: B 431 LEU cc_start: 0.8592 (mm) cc_final: 0.8242 (mt) REVERT: B 433 SER cc_start: 0.8972 (m) cc_final: 0.8582 (p) REVERT: B 435 ASN cc_start: 0.8482 (t0) cc_final: 0.8066 (t0) REVERT: C 78 PHE cc_start: 0.8870 (t80) cc_final: 0.8511 (t80) REVERT: C 82 GLN cc_start: 0.8464 (mt0) cc_final: 0.7941 (mt0) REVERT: C 98 ASP cc_start: 0.8515 (t0) cc_final: 0.8222 (m-30) REVERT: C 100 PHE cc_start: 0.7567 (t80) cc_final: 0.7069 (t80) REVERT: C 104 CYS cc_start: 0.8662 (m) cc_final: 0.8268 (m) REVERT: C 105 HIS cc_start: 0.7836 (OUTLIER) cc_final: 0.7531 (m90) REVERT: C 106 GLN cc_start: 0.8458 (mm-40) cc_final: 0.7935 (mm-40) REVERT: C 121 ILE cc_start: 0.8987 (mm) cc_final: 0.8755 (tp) REVERT: C 129 ASP cc_start: 0.7632 (m-30) cc_final: 0.7202 (m-30) REVERT: C 136 ASN cc_start: 0.8952 (p0) cc_final: 0.8047 (p0) REVERT: C 147 GLN cc_start: 0.8308 (tm-30) cc_final: 0.8065 (tm-30) REVERT: C 166 MET cc_start: 0.7721 (mpp) cc_final: 0.7321 (mpp) REVERT: C 219 ILE cc_start: 0.7866 (mt) cc_final: 0.7535 (mm) REVERT: C 247 GLN cc_start: 0.7956 (pp30) cc_final: 0.7446 (pp30) REVERT: C 280 ASN cc_start: 0.8212 (m-40) cc_final: 0.7979 (m110) REVERT: C 292 MET cc_start: 0.7696 (tmm) cc_final: 0.7356 (tpp) REVERT: C 304 LYS cc_start: 0.8823 (mttp) cc_final: 0.8584 (mttp) REVERT: C 309 ARG cc_start: 0.8842 (ttm170) cc_final: 0.8471 (ttp-170) REVERT: C 335 GLU cc_start: 0.8122 (tp30) cc_final: 0.7840 (tp30) REVERT: C 351 ILE cc_start: 0.8097 (mp) cc_final: 0.7779 (mm) REVERT: C 366 LYS cc_start: 0.8719 (mmmm) cc_final: 0.8340 (mtpp) REVERT: C 378 GLN cc_start: 0.8100 (mm110) cc_final: 0.7865 (mm-40) REVERT: C 379 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7359 (mm-30) REVERT: C 380 MET cc_start: 0.8443 (mtt) cc_final: 0.7789 (mtt) REVERT: C 383 CYS cc_start: 0.8008 (t) cc_final: 0.7688 (p) REVERT: C 385 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7375 (tm-30) REVERT: C 393 MET cc_start: 0.7489 (tpp) cc_final: 0.7136 (tpp) REVERT: C 405 GLN cc_start: 0.8407 (tm-30) cc_final: 0.8108 (tm-30) REVERT: C 406 LYS cc_start: 0.9036 (mttp) cc_final: 0.8504 (mttt) REVERT: D 50 GLU cc_start: 0.8256 (pt0) cc_final: 0.7785 (pt0) REVERT: D 62 SER cc_start: 0.8506 (m) cc_final: 0.8038 (p) REVERT: D 90 GLU cc_start: 0.7910 (tp30) cc_final: 0.6891 (tp30) REVERT: D 91 LYS cc_start: 0.8612 (mmpt) cc_final: 0.8090 (mmpt) REVERT: D 141 VAL cc_start: 0.7960 (p) cc_final: 0.7630 (t) REVERT: D 144 LYS cc_start: 0.8041 (mtmt) cc_final: 0.7521 (mtmt) REVERT: D 146 GLU cc_start: 0.7920 (tp30) cc_final: 0.7123 (tp30) REVERT: D 150 LYS cc_start: 0.8574 (ttmm) cc_final: 0.8229 (ttmm) REVERT: D 158 ASP cc_start: 0.7896 (t70) cc_final: 0.7556 (t70) REVERT: D 160 ASP cc_start: 0.8161 (t0) cc_final: 0.7891 (t0) REVERT: D 175 GLN cc_start: 0.7345 (pp30) cc_final: 0.6886 (pp30) REVERT: D 203 GLU cc_start: 0.7883 (mp0) cc_final: 0.7386 (mp0) REVERT: D 222 ARG cc_start: 0.8284 (mtt-85) cc_final: 0.8010 (mtt-85) REVERT: D 240 GLN cc_start: 0.7602 (tm-30) cc_final: 0.6906 (pp30) REVERT: D 241 GLN cc_start: 0.8031 (tp40) cc_final: 0.7632 (tp40) REVERT: D 245 MET cc_start: 0.8663 (tpp) cc_final: 0.8211 (tpp) REVERT: D 266 LYS cc_start: 0.8909 (mttt) cc_final: 0.8610 (mttt) REVERT: D 268 TYR cc_start: 0.8518 (t80) cc_final: 0.8241 (t80) REVERT: D 286 MET cc_start: 0.8282 (tpp) cc_final: 0.7164 (mpp) REVERT: D 289 GLN cc_start: 0.8808 (mt0) cc_final: 0.8342 (mt0) REVERT: D 301 ASP cc_start: 0.7426 (m-30) cc_final: 0.7095 (m-30) REVERT: D 302 ARG cc_start: 0.7885 (tpp80) cc_final: 0.7044 (tpp80) REVERT: D 306 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7616 (mt-10) REVERT: D 321 PHE cc_start: 0.8949 (m-80) cc_final: 0.8725 (m-80) REVERT: D 322 GLU cc_start: 0.8439 (mp0) cc_final: 0.8095 (mp0) REVERT: D 329 GLU cc_start: 0.7304 (mm-30) cc_final: 0.7034 (mm-30) REVERT: D 336 GLU cc_start: 0.8625 (tt0) cc_final: 0.8245 (tt0) REVERT: D 354 GLN cc_start: 0.8500 (tt0) cc_final: 0.8168 (tt0) REVERT: D 358 ILE cc_start: 0.8466 (mt) cc_final: 0.8112 (mm) REVERT: D 362 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6906 (pp20) REVERT: D 372 LYS cc_start: 0.8649 (tptt) cc_final: 0.8251 (tptt) REVERT: D 379 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7977 (m-10) REVERT: D 380 GLN cc_start: 0.8369 (mm110) cc_final: 0.7990 (mm110) REVERT: D 383 ASN cc_start: 0.7984 (m-40) cc_final: 0.7593 (m-40) REVERT: D 387 LYS cc_start: 0.9162 (tttt) cc_final: 0.8775 (tttt) REVERT: E 252 SER cc_start: 0.8161 (m) cc_final: 0.7910 (m) REVERT: E 258 ASN cc_start: 0.8706 (m-40) cc_final: 0.8052 (m-40) REVERT: E 262 THR cc_start: 0.9179 (m) cc_final: 0.8851 (p) REVERT: E 305 ARG cc_start: 0.8245 (mtp-110) cc_final: 0.7764 (mtp-110) REVERT: E 308 CYS cc_start: 0.8677 (m) cc_final: 0.8349 (m) REVERT: E 309 LYS cc_start: 0.8860 (tttt) cc_final: 0.8411 (tttt) REVERT: E 313 GLU cc_start: 0.8467 (tp30) cc_final: 0.7823 (tp30) REVERT: E 321 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8617 (mm-40) REVERT: F 230 MET cc_start: 0.8418 (mmt) cc_final: 0.8102 (mmt) REVERT: F 232 HIS cc_start: 0.9134 (t-90) cc_final: 0.8155 (t70) REVERT: F 241 TYR cc_start: 0.8704 (t80) cc_final: 0.8364 (t80) REVERT: F 258 ARG cc_start: 0.8335 (mtt180) cc_final: 0.8054 (mtt180) REVERT: F 270 LEU cc_start: 0.8537 (tp) cc_final: 0.8093 (tp) REVERT: F 278 ASP cc_start: 0.8283 (m-30) cc_final: 0.7832 (m-30) REVERT: F 301 THR cc_start: 0.8710 (m) cc_final: 0.8205 (p) REVERT: G 14 GLN cc_start: 0.8066 (mt0) cc_final: 0.7570 (mt0) REVERT: G 45 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7439 (tp30) REVERT: G 65 GLN cc_start: 0.8130 (tp-100) cc_final: 0.7181 (tp-100) REVERT: G 66 LEU cc_start: 0.8750 (tt) cc_final: 0.8501 (tt) REVERT: G 92 GLN cc_start: 0.8745 (mt0) cc_final: 0.8363 (mt0) REVERT: G 93 GLN cc_start: 0.8572 (pt0) cc_final: 0.8304 (pt0) REVERT: G 97 LYS cc_start: 0.8655 (mttt) cc_final: 0.8068 (mmtp) REVERT: G 99 LEU cc_start: 0.8807 (mt) cc_final: 0.8524 (mt) REVERT: G 120 LEU cc_start: 0.8478 (mt) cc_final: 0.8213 (mt) REVERT: G 125 LEU cc_start: 0.8450 (mt) cc_final: 0.7881 (mt) REVERT: G 129 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8014 (mt-10) REVERT: G 133 ILE cc_start: 0.8244 (mm) cc_final: 0.7985 (mm) REVERT: G 150 GLN cc_start: 0.8441 (mm-40) cc_final: 0.7961 (mm-40) REVERT: G 155 ASP cc_start: 0.8407 (m-30) cc_final: 0.8180 (m-30) REVERT: G 181 CYS cc_start: 0.8524 (m) cc_final: 0.8275 (m) REVERT: G 182 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7364 (mm-30) REVERT: G 188 ILE cc_start: 0.8390 (mt) cc_final: 0.7976 (tp) REVERT: G 193 LEU cc_start: 0.8934 (tp) cc_final: 0.8702 (tp) REVERT: G 197 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8018 (tm-30) REVERT: G 202 HIS cc_start: 0.8164 (t70) cc_final: 0.7772 (t70) REVERT: G 204 ARG cc_start: 0.8807 (ttm170) cc_final: 0.8485 (ttm170) REVERT: G 210 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7650 (mm-30) REVERT: H 17 LEU cc_start: 0.8408 (tp) cc_final: 0.7917 (tp) REVERT: H 18 ASP cc_start: 0.7797 (m-30) cc_final: 0.7549 (m-30) REVERT: H 21 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7878 (mt-10) REVERT: H 23 GLN cc_start: 0.8594 (tt0) cc_final: 0.8332 (tt0) REVERT: H 52 ASN cc_start: 0.8652 (m-40) cc_final: 0.8396 (m110) REVERT: H 58 LYS cc_start: 0.8547 (ttmt) cc_final: 0.8327 (ttmt) REVERT: H 79 GLN cc_start: 0.8003 (tt0) cc_final: 0.7496 (mt0) REVERT: H 123 GLN cc_start: 0.8622 (tp-100) cc_final: 0.8267 (tp-100) REVERT: I 121 GLN cc_start: 0.8802 (tm-30) cc_final: 0.8521 (tm-30) REVERT: I 136 ILE cc_start: 0.8331 (mm) cc_final: 0.8074 (mm) REVERT: I 210 GLU cc_start: 0.8161 (tt0) cc_final: 0.7791 (tt0) REVERT: I 243 PHE cc_start: 0.8010 (t80) cc_final: 0.7595 (t80) REVERT: I 247 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6791 (mp0) REVERT: I 262 LYS cc_start: 0.8376 (pttp) cc_final: 0.8051 (pttp) REVERT: I 287 LEU cc_start: 0.8810 (tp) cc_final: 0.8583 (tt) REVERT: I 322 MET cc_start: 0.8074 (ttm) cc_final: 0.7715 (ttm) REVERT: I 330 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.6053 (mt0) REVERT: I 374 HIS cc_start: 0.8749 (t-90) cc_final: 0.8497 (t-170) REVERT: I 420 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7701 (tm-30) REVERT: I 428 SER cc_start: 0.8885 (t) cc_final: 0.8544 (p) REVERT: I 429 LEU cc_start: 0.8372 (tp) cc_final: 0.8044 (tp) REVERT: I 464 LYS cc_start: 0.8312 (tptm) cc_final: 0.7948 (tptm) REVERT: I 468 LYS cc_start: 0.8597 (tppt) cc_final: 0.8038 (tppt) REVERT: I 503 LYS cc_start: 0.8533 (ttmm) cc_final: 0.8150 (ttmm) REVERT: I 522 LYS cc_start: 0.8204 (tppp) cc_final: 0.7757 (tppp) REVERT: I 539 VAL cc_start: 0.8851 (p) cc_final: 0.8617 (m) REVERT: I 564 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8183 (mt0) REVERT: I 566 PHE cc_start: 0.8430 (t80) cc_final: 0.8214 (t80) REVERT: I 580 THR cc_start: 0.8007 (OUTLIER) cc_final: 0.7778 (p) REVERT: I 581 TRP cc_start: 0.8481 (m100) cc_final: 0.8145 (m-10) REVERT: I 586 SER cc_start: 0.8269 (OUTLIER) cc_final: 0.7503 (m) REVERT: I 602 GLN cc_start: 0.6865 (tp40) cc_final: 0.6564 (tp40) REVERT: I 607 GLN cc_start: 0.7837 (mp10) cc_final: 0.7378 (mp10) REVERT: I 608 MET cc_start: 0.7537 (tpp) cc_final: 0.7177 (tpp) REVERT: I 614 TYR cc_start: 0.7498 (m-10) cc_final: 0.7267 (m-80) REVERT: I 630 GLN cc_start: 0.7404 (tm-30) cc_final: 0.7063 (tm-30) REVERT: I 638 GLN cc_start: 0.8882 (mp10) cc_final: 0.8455 (mp10) REVERT: I 643 LEU cc_start: 0.8925 (mp) cc_final: 0.8449 (tp) REVERT: I 721 MET cc_start: 0.8602 (mtm) cc_final: 0.8318 (mtm) REVERT: L 32 GLU cc_start: 0.7924 (tp30) cc_final: 0.7563 (tp30) REVERT: L 57 LYS cc_start: 0.8448 (ptpt) cc_final: 0.8171 (ptpt) REVERT: L 126 MET cc_start: 0.7861 (mmp) cc_final: 0.7333 (mmp) REVERT: L 142 LYS cc_start: 0.7394 (mppt) cc_final: 0.7073 (mppt) REVERT: M 155 LEU cc_start: 0.8597 (mp) cc_final: 0.8366 (mp) REVERT: M 161 ILE cc_start: 0.7466 (OUTLIER) cc_final: 0.6940 (tp) REVERT: M 167 ARG cc_start: 0.7891 (mpp80) cc_final: 0.7637 (mpp80) REVERT: M 208 LEU cc_start: 0.8515 (mt) cc_final: 0.8153 (mm) REVERT: M 217 ARG cc_start: 0.5947 (OUTLIER) cc_final: 0.4035 (ptp90) REVERT: M 251 LEU cc_start: 0.8687 (tt) cc_final: 0.8355 (pp) REVERT: M 259 ASP cc_start: 0.7889 (p0) cc_final: 0.7441 (p0) REVERT: M 323 LEU cc_start: 0.8637 (mp) cc_final: 0.7957 (pp) REVERT: N 23 MET cc_start: 0.7210 (ttm) cc_final: 0.6809 (ttm) REVERT: N 34 LYS cc_start: 0.8600 (mppt) cc_final: 0.8336 (mppt) REVERT: N 58 MET cc_start: 0.7517 (mtp) cc_final: 0.7102 (mtp) REVERT: P 43 PHE cc_start: 0.8364 (p90) cc_final: 0.7994 (p90) REVERT: P 44 PHE cc_start: 0.7889 (t80) cc_final: 0.7677 (t80) REVERT: P 52 ASP cc_start: 0.7514 (t0) cc_final: 0.6999 (t0) REVERT: A 98 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8867 (mm) REVERT: A 132 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7877 (pm20) REVERT: A 165 HIS cc_start: 0.8991 (m-70) cc_final: 0.8339 (m90) REVERT: A 172 TYR cc_start: 0.8287 (m-10) cc_final: 0.8043 (m-80) REVERT: A 174 ASP cc_start: 0.9016 (m-30) cc_final: 0.8397 (t0) REVERT: A 196 LYS cc_start: 0.8695 (mptt) cc_final: 0.8400 (mptt) REVERT: A 226 GLU cc_start: 0.7815 (pt0) cc_final: 0.7430 (pt0) REVERT: A 262 LYS cc_start: 0.8643 (ttpp) cc_final: 0.8152 (ttpt) REVERT: A 288 ASN cc_start: 0.7292 (m110) cc_final: 0.6778 (m110) REVERT: A 296 CYS cc_start: 0.8267 (m) cc_final: 0.7858 (m) REVERT: A 304 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7440 (mm-40) REVERT: A 317 LYS cc_start: 0.8305 (ptpt) cc_final: 0.8002 (ptpt) REVERT: A 321 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7845 (mt-10) REVERT: A 348 MET cc_start: 0.7480 (tmm) cc_final: 0.7222 (tmm) REVERT: A 367 THR cc_start: 0.8436 (t) cc_final: 0.8067 (p) REVERT: A 386 MET cc_start: 0.8628 (mtp) cc_final: 0.8234 (mtp) REVERT: A 406 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7607 (mm-40) REVERT: A 408 ILE cc_start: 0.8570 (tp) cc_final: 0.8313 (tp) REVERT: A 451 LYS cc_start: 0.8509 (mtmt) cc_final: 0.7869 (mtmt) outliers start: 103 outliers final: 75 residues processed: 1161 average time/residue: 0.1724 time to fit residues: 307.7381 Evaluate side-chains 1200 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 1113 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 334 HIS Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 105 HIS Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 244 ARG Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain F residue 304 GLN Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 175 HIS Chi-restraints excluded: chain G residue 190 GLN Chi-restraints excluded: chain H residue 51 ASN Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 228 TYR Chi-restraints excluded: chain I residue 247 GLU Chi-restraints excluded: chain I residue 330 GLN Chi-restraints excluded: chain I residue 431 LYS Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 450 MET Chi-restraints excluded: chain I residue 560 GLU Chi-restraints excluded: chain I residue 564 GLN Chi-restraints excluded: chain I residue 580 THR Chi-restraints excluded: chain I residue 586 SER Chi-restraints excluded: chain I residue 587 LYS Chi-restraints excluded: chain I residue 592 THR Chi-restraints excluded: chain I residue 629 THR Chi-restraints excluded: chain I residue 684 ILE Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain M residue 161 ILE Chi-restraints excluded: chain M residue 217 ARG Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 236 ASN Chi-restraints excluded: chain M residue 240 CYS Chi-restraints excluded: chain M residue 258 LEU Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 322 MET Chi-restraints excluded: chain M residue 330 GLU Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 447 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 37 optimal weight: 3.9990 chunk 306 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 245 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN C 105 HIS C 239 GLN C 320 GLN D 75 ASN ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 HIS ** F 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 HIS ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 564 GLN ** J 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS A 368 GLN A 447 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.135582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.109883 restraints weight = 59567.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.113582 restraints weight = 30702.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.116030 restraints weight = 18966.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.117645 restraints weight = 13255.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.118781 restraints weight = 10187.116| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26963 Z= 0.189 Angle : 0.753 17.994 36489 Z= 0.387 Chirality : 0.044 0.265 4207 Planarity : 0.004 0.060 4645 Dihedral : 5.061 58.736 3635 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.44 % Favored : 94.53 % Rotamer: Outliers : 3.11 % Allowed : 26.42 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.15), residues: 3290 helix: 1.59 (0.12), residues: 2145 sheet: -0.68 (0.51), residues: 122 loop : -1.95 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 193 TYR 0.031 0.002 TYR A 152 PHE 0.026 0.001 PHE I 402 TRP 0.030 0.002 TRP D 395 HIS 0.006 0.001 HIS D 307 Details of bonding type rmsd covalent geometry : bond 0.00395 (26952) covalent geometry : angle 0.75301 (36484) SS BOND : bond 0.00444 ( 1) SS BOND : angle 1.89255 ( 2) hydrogen bonds : bond 0.04902 ( 1569) hydrogen bonds : angle 4.36917 ( 4605) metal coordination : bond 0.00563 ( 10) metal coordination : angle 1.56700 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1232 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 1144 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 GLN cc_start: 0.8497 (mp10) cc_final: 0.7855 (mp10) REVERT: B 56 LYS cc_start: 0.8855 (mptt) cc_final: 0.8601 (tptt) REVERT: B 66 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7295 (mm-30) REVERT: B 72 LEU cc_start: 0.8788 (mt) cc_final: 0.8082 (mt) REVERT: B 74 GLN cc_start: 0.8693 (tp40) cc_final: 0.7752 (tp40) REVERT: B 75 MET cc_start: 0.7732 (ppp) cc_final: 0.7142 (ppp) REVERT: B 76 ILE cc_start: 0.8439 (mt) cc_final: 0.8128 (tp) REVERT: B 109 GLU cc_start: 0.8036 (tp30) cc_final: 0.7689 (tp30) REVERT: B 115 ILE cc_start: 0.8650 (mt) cc_final: 0.8333 (tp) REVERT: B 149 PHE cc_start: 0.8025 (t80) cc_final: 0.7690 (t80) REVERT: B 152 ASN cc_start: 0.8036 (t0) cc_final: 0.7664 (t0) REVERT: B 158 LEU cc_start: 0.8970 (tp) cc_final: 0.8693 (tt) REVERT: B 161 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7339 (tm-30) REVERT: B 163 GLU cc_start: 0.7733 (tp30) cc_final: 0.7320 (tp30) REVERT: B 176 HIS cc_start: 0.7354 (m170) cc_final: 0.6794 (m170) REVERT: B 220 GLN cc_start: 0.8189 (pt0) cc_final: 0.7554 (pp30) REVERT: B 234 MET cc_start: 0.7890 (mmm) cc_final: 0.7538 (mmm) REVERT: B 243 LYS cc_start: 0.8505 (ttmm) cc_final: 0.8213 (ttmm) REVERT: B 250 GLU cc_start: 0.8228 (tt0) cc_final: 0.7889 (tt0) REVERT: B 260 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7873 (mm-30) REVERT: B 291 ILE cc_start: 0.9280 (mp) cc_final: 0.8630 (tp) REVERT: B 322 ASP cc_start: 0.8457 (t0) cc_final: 0.8042 (t0) REVERT: B 325 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7435 (mm-30) REVERT: B 328 LYS cc_start: 0.9125 (ttpp) cc_final: 0.8875 (ttpp) REVERT: B 338 MET cc_start: 0.7445 (tpt) cc_final: 0.6508 (tpt) REVERT: B 345 GLU cc_start: 0.8088 (pm20) cc_final: 0.7826 (pm20) REVERT: B 347 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8350 (mm) REVERT: B 361 LYS cc_start: 0.8718 (tptp) cc_final: 0.8355 (tptp) REVERT: B 363 ILE cc_start: 0.8954 (pt) cc_final: 0.8494 (tp) REVERT: B 368 ARG cc_start: 0.8359 (mtp-110) cc_final: 0.7890 (mtp180) REVERT: B 391 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7732 (tm-30) REVERT: B 410 GLU cc_start: 0.7572 (pp20) cc_final: 0.7149 (pp20) REVERT: B 411 LEU cc_start: 0.8279 (mp) cc_final: 0.7662 (mt) REVERT: B 415 LYS cc_start: 0.8393 (tttp) cc_final: 0.8087 (tttp) REVERT: B 431 LEU cc_start: 0.8584 (mm) cc_final: 0.8275 (mt) REVERT: B 433 SER cc_start: 0.9057 (m) cc_final: 0.8680 (p) REVERT: B 435 ASN cc_start: 0.8530 (t0) cc_final: 0.8114 (t0) REVERT: C 78 PHE cc_start: 0.8876 (t80) cc_final: 0.8531 (t80) REVERT: C 82 GLN cc_start: 0.8492 (mt0) cc_final: 0.7984 (mt0) REVERT: C 98 ASP cc_start: 0.8313 (t0) cc_final: 0.8095 (m-30) REVERT: C 100 PHE cc_start: 0.7560 (t80) cc_final: 0.7121 (t80) REVERT: C 104 CYS cc_start: 0.8766 (m) cc_final: 0.8370 (m) REVERT: C 105 HIS cc_start: 0.7996 (OUTLIER) cc_final: 0.7771 (m90) REVERT: C 106 GLN cc_start: 0.8434 (mm-40) cc_final: 0.8040 (mm110) REVERT: C 121 ILE cc_start: 0.9002 (mm) cc_final: 0.8765 (tp) REVERT: C 126 GLN cc_start: 0.8471 (mt0) cc_final: 0.7730 (mm110) REVERT: C 129 ASP cc_start: 0.7724 (m-30) cc_final: 0.7276 (m-30) REVERT: C 136 ASN cc_start: 0.8981 (p0) cc_final: 0.8139 (p0) REVERT: C 147 GLN cc_start: 0.8333 (tm-30) cc_final: 0.8062 (tm-30) REVERT: C 166 MET cc_start: 0.7771 (mpp) cc_final: 0.7185 (mpp) REVERT: C 186 TYR cc_start: 0.8349 (t80) cc_final: 0.8075 (t80) REVERT: C 190 MET cc_start: 0.7863 (tpp) cc_final: 0.7407 (tpp) REVERT: C 206 GLU cc_start: 0.8344 (tt0) cc_final: 0.8120 (tt0) REVERT: C 247 GLN cc_start: 0.7965 (pp30) cc_final: 0.7462 (tm-30) REVERT: C 271 ASN cc_start: 0.7675 (t0) cc_final: 0.6949 (t0) REVERT: C 280 ASN cc_start: 0.8327 (m-40) cc_final: 0.8091 (m110) REVERT: C 292 MET cc_start: 0.7801 (tmm) cc_final: 0.7454 (tpp) REVERT: C 309 ARG cc_start: 0.8882 (ttm170) cc_final: 0.8495 (ttp-170) REVERT: C 321 ASP cc_start: 0.8350 (m-30) cc_final: 0.8034 (m-30) REVERT: C 335 GLU cc_start: 0.8194 (tp30) cc_final: 0.7909 (tp30) REVERT: C 351 ILE cc_start: 0.8096 (mp) cc_final: 0.7770 (mm) REVERT: C 366 LYS cc_start: 0.8707 (mmmm) cc_final: 0.8331 (mtpp) REVERT: C 379 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7416 (mm-30) REVERT: C 380 MET cc_start: 0.8476 (mtt) cc_final: 0.7805 (mtt) REVERT: C 383 CYS cc_start: 0.8181 (t) cc_final: 0.7790 (p) REVERT: C 385 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7425 (tm-30) REVERT: C 393 MET cc_start: 0.7515 (tpp) cc_final: 0.6867 (tpp) REVERT: C 405 GLN cc_start: 0.8426 (tm-30) cc_final: 0.8142 (tm-30) REVERT: C 406 LYS cc_start: 0.9057 (mttp) cc_final: 0.8526 (mttt) REVERT: D 50 GLU cc_start: 0.8320 (pt0) cc_final: 0.7864 (pt0) REVERT: D 62 SER cc_start: 0.8614 (m) cc_final: 0.8148 (p) REVERT: D 90 GLU cc_start: 0.7912 (tp30) cc_final: 0.6943 (tp30) REVERT: D 91 LYS cc_start: 0.8640 (mmpt) cc_final: 0.8112 (mmpt) REVERT: D 141 VAL cc_start: 0.8062 (p) cc_final: 0.7731 (t) REVERT: D 144 LYS cc_start: 0.8134 (mtmt) cc_final: 0.7611 (mtmt) REVERT: D 146 GLU cc_start: 0.7937 (tp30) cc_final: 0.7173 (tp30) REVERT: D 150 LYS cc_start: 0.8604 (ttmm) cc_final: 0.8271 (ttmm) REVERT: D 158 ASP cc_start: 0.8040 (t70) cc_final: 0.7699 (t70) REVERT: D 160 ASP cc_start: 0.8182 (t0) cc_final: 0.7895 (t0) REVERT: D 175 GLN cc_start: 0.7426 (pp30) cc_final: 0.7029 (pp30) REVERT: D 203 GLU cc_start: 0.7935 (mp0) cc_final: 0.7547 (mp0) REVERT: D 218 HIS cc_start: 0.7539 (t70) cc_final: 0.6943 (t70) REVERT: D 227 LYS cc_start: 0.9029 (ttpp) cc_final: 0.8714 (ttpp) REVERT: D 240 GLN cc_start: 0.7648 (tm-30) cc_final: 0.6947 (pp30) REVERT: D 241 GLN cc_start: 0.8038 (tp40) cc_final: 0.7666 (tp40) REVERT: D 245 MET cc_start: 0.8684 (tpp) cc_final: 0.8193 (tpp) REVERT: D 266 LYS cc_start: 0.8923 (mttt) cc_final: 0.8617 (mttt) REVERT: D 268 TYR cc_start: 0.8631 (t80) cc_final: 0.8252 (t80) REVERT: D 271 ARG cc_start: 0.8108 (mmm160) cc_final: 0.7465 (mmm-85) REVERT: D 286 MET cc_start: 0.8304 (tpp) cc_final: 0.7111 (mpp) REVERT: D 289 GLN cc_start: 0.8805 (mt0) cc_final: 0.8286 (mt0) REVERT: D 301 ASP cc_start: 0.7459 (m-30) cc_final: 0.7018 (m-30) REVERT: D 302 ARG cc_start: 0.7942 (tpp80) cc_final: 0.7087 (tpp80) REVERT: D 306 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7662 (mt-10) REVERT: D 322 GLU cc_start: 0.8466 (mp0) cc_final: 0.8106 (mp0) REVERT: D 329 GLU cc_start: 0.7335 (mm-30) cc_final: 0.7078 (mm-30) REVERT: D 336 GLU cc_start: 0.8621 (tt0) cc_final: 0.8282 (tt0) REVERT: D 342 MET cc_start: 0.8687 (mtp) cc_final: 0.8293 (mtp) REVERT: D 354 GLN cc_start: 0.8522 (tt0) cc_final: 0.8177 (tt0) REVERT: D 358 ILE cc_start: 0.8478 (mt) cc_final: 0.8127 (mm) REVERT: D 359 VAL cc_start: 0.8496 (t) cc_final: 0.8181 (p) REVERT: D 362 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6924 (pp20) REVERT: D 372 LYS cc_start: 0.8667 (tptt) cc_final: 0.8259 (tptt) REVERT: D 374 ILE cc_start: 0.8934 (mt) cc_final: 0.8641 (pt) REVERT: D 379 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.8029 (m-10) REVERT: D 380 GLN cc_start: 0.8426 (mm110) cc_final: 0.8064 (mm110) REVERT: D 383 ASN cc_start: 0.8017 (m-40) cc_final: 0.7636 (m-40) REVERT: D 387 LYS cc_start: 0.9179 (tttt) cc_final: 0.8760 (tttt) REVERT: E 252 SER cc_start: 0.8248 (m) cc_final: 0.8010 (m) REVERT: E 258 ASN cc_start: 0.8778 (m-40) cc_final: 0.8083 (m110) REVERT: E 262 THR cc_start: 0.9175 (m) cc_final: 0.8835 (p) REVERT: E 305 ARG cc_start: 0.8295 (mtp-110) cc_final: 0.7814 (mtp-110) REVERT: E 308 CYS cc_start: 0.8735 (m) cc_final: 0.8423 (m) REVERT: E 309 LYS cc_start: 0.8948 (tttt) cc_final: 0.8523 (tttt) REVERT: E 313 GLU cc_start: 0.8483 (tp30) cc_final: 0.7821 (tp30) REVERT: E 321 GLN cc_start: 0.8968 (mm-40) cc_final: 0.8655 (mm-40) REVERT: F 230 MET cc_start: 0.8460 (mmt) cc_final: 0.8147 (mmt) REVERT: F 241 TYR cc_start: 0.8715 (t80) cc_final: 0.8399 (t80) REVERT: F 258 ARG cc_start: 0.8337 (mtt180) cc_final: 0.7953 (mtt180) REVERT: F 270 LEU cc_start: 0.8528 (tp) cc_final: 0.8118 (tp) REVERT: F 278 ASP cc_start: 0.8309 (m-30) cc_final: 0.7840 (m-30) REVERT: F 283 CYS cc_start: 0.9113 (m) cc_final: 0.8680 (m) REVERT: G 14 GLN cc_start: 0.8059 (mt0) cc_final: 0.7557 (mt0) REVERT: G 45 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7519 (tp30) REVERT: G 65 GLN cc_start: 0.8171 (tp-100) cc_final: 0.7218 (tp-100) REVERT: G 66 LEU cc_start: 0.8777 (tt) cc_final: 0.8512 (tt) REVERT: G 92 GLN cc_start: 0.8821 (mt0) cc_final: 0.8316 (mt0) REVERT: G 93 GLN cc_start: 0.8601 (pt0) cc_final: 0.8346 (pt0) REVERT: G 97 LYS cc_start: 0.8680 (mttt) cc_final: 0.8087 (mmtp) REVERT: G 99 LEU cc_start: 0.8771 (mt) cc_final: 0.8496 (mt) REVERT: G 120 LEU cc_start: 0.8570 (mt) cc_final: 0.8271 (mm) REVERT: G 125 LEU cc_start: 0.8564 (mt) cc_final: 0.8126 (mt) REVERT: G 129 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8100 (mt-10) REVERT: G 133 ILE cc_start: 0.8306 (mm) cc_final: 0.8052 (mm) REVERT: G 150 GLN cc_start: 0.8479 (mm-40) cc_final: 0.7991 (mm-40) REVERT: G 155 ASP cc_start: 0.8412 (m-30) cc_final: 0.8161 (m-30) REVERT: G 181 CYS cc_start: 0.8565 (m) cc_final: 0.8342 (m) REVERT: G 188 ILE cc_start: 0.8398 (mt) cc_final: 0.7985 (tp) REVERT: G 193 LEU cc_start: 0.8981 (tp) cc_final: 0.8749 (tp) REVERT: G 197 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8061 (tm-30) REVERT: G 202 HIS cc_start: 0.8224 (t70) cc_final: 0.7803 (t70) REVERT: G 204 ARG cc_start: 0.8828 (ttm170) cc_final: 0.8508 (ttm170) REVERT: G 210 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7702 (mm-30) REVERT: H 14 LYS cc_start: 0.8800 (mppt) cc_final: 0.7873 (mppt) REVERT: H 17 LEU cc_start: 0.8400 (tp) cc_final: 0.7914 (tp) REVERT: H 18 ASP cc_start: 0.7812 (m-30) cc_final: 0.7574 (m-30) REVERT: H 21 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7927 (mt-10) REVERT: H 23 GLN cc_start: 0.8619 (tt0) cc_final: 0.8358 (tt0) REVERT: H 58 LYS cc_start: 0.8571 (ttmt) cc_final: 0.8350 (ttmt) REVERT: H 79 GLN cc_start: 0.8083 (tt0) cc_final: 0.7549 (mt0) REVERT: H 110 ARG cc_start: 0.8201 (mtt180) cc_final: 0.7945 (mtt-85) REVERT: H 123 GLN cc_start: 0.8631 (tp-100) cc_final: 0.8274 (tp-100) REVERT: I 121 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8520 (tm-30) REVERT: I 136 ILE cc_start: 0.8275 (mm) cc_final: 0.8026 (mm) REVERT: I 210 GLU cc_start: 0.8140 (tt0) cc_final: 0.7874 (tt0) REVERT: I 243 PHE cc_start: 0.8021 (t80) cc_final: 0.7594 (t80) REVERT: I 247 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: I 262 LYS cc_start: 0.8439 (pttp) cc_final: 0.8129 (pttp) REVERT: I 287 LEU cc_start: 0.8819 (tp) cc_final: 0.8593 (tt) REVERT: I 322 MET cc_start: 0.8049 (ttm) cc_final: 0.7735 (ttm) REVERT: I 330 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.6114 (mt0) REVERT: I 374 HIS cc_start: 0.8771 (t-90) cc_final: 0.8521 (t-170) REVERT: I 420 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7748 (tm-30) REVERT: I 428 SER cc_start: 0.8893 (t) cc_final: 0.8552 (p) REVERT: I 429 LEU cc_start: 0.8410 (tp) cc_final: 0.8130 (tp) REVERT: I 464 LYS cc_start: 0.8364 (tptm) cc_final: 0.7974 (tptm) REVERT: I 468 LYS cc_start: 0.8662 (tppt) cc_final: 0.8101 (tppt) REVERT: I 503 LYS cc_start: 0.8580 (ttmm) cc_final: 0.8189 (ttmm) REVERT: I 522 LYS cc_start: 0.8280 (tppp) cc_final: 0.7885 (tppp) REVERT: I 539 VAL cc_start: 0.8860 (p) cc_final: 0.8632 (m) REVERT: I 564 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8229 (mt0) REVERT: I 580 THR cc_start: 0.8083 (OUTLIER) cc_final: 0.7807 (p) REVERT: I 581 TRP cc_start: 0.8529 (m100) cc_final: 0.8188 (m-10) REVERT: I 602 GLN cc_start: 0.6999 (tp40) cc_final: 0.6674 (tp40) REVERT: I 607 GLN cc_start: 0.8016 (mp10) cc_final: 0.7547 (mp10) REVERT: I 608 MET cc_start: 0.7780 (tpp) cc_final: 0.7495 (tpp) REVERT: I 614 TYR cc_start: 0.7547 (m-10) cc_final: 0.7326 (m-80) REVERT: I 630 GLN cc_start: 0.7342 (tm-30) cc_final: 0.7012 (tm-30) REVERT: I 638 GLN cc_start: 0.8912 (mp10) cc_final: 0.8488 (mp10) REVERT: I 643 LEU cc_start: 0.8956 (mp) cc_final: 0.8476 (tp) REVERT: I 672 TYR cc_start: 0.6878 (t80) cc_final: 0.6674 (t80) REVERT: I 721 MET cc_start: 0.8681 (mtm) cc_final: 0.8407 (mtm) REVERT: L 32 GLU cc_start: 0.7990 (tp30) cc_final: 0.7585 (tp30) REVERT: L 57 LYS cc_start: 0.8409 (ptpt) cc_final: 0.8146 (ptpt) REVERT: L 126 MET cc_start: 0.7836 (mmp) cc_final: 0.7346 (mmp) REVERT: M 155 LEU cc_start: 0.8627 (mp) cc_final: 0.8398 (mp) REVERT: M 208 LEU cc_start: 0.8533 (mt) cc_final: 0.8296 (mm) REVERT: M 217 ARG cc_start: 0.5844 (OUTLIER) cc_final: 0.3729 (ptp90) REVERT: M 241 SER cc_start: 0.8022 (p) cc_final: 0.7474 (m) REVERT: M 251 LEU cc_start: 0.8677 (tt) cc_final: 0.8350 (pp) REVERT: M 259 ASP cc_start: 0.7912 (p0) cc_final: 0.7448 (p0) REVERT: M 323 LEU cc_start: 0.8639 (mp) cc_final: 0.8092 (pp) REVERT: N 23 MET cc_start: 0.7257 (ttm) cc_final: 0.6777 (ttm) REVERT: N 34 LYS cc_start: 0.8602 (mppt) cc_final: 0.8340 (mppt) REVERT: N 58 MET cc_start: 0.7604 (mtp) cc_final: 0.7173 (mtp) REVERT: P 40 HIS cc_start: 0.8707 (m90) cc_final: 0.8228 (m90) REVERT: P 52 ASP cc_start: 0.7557 (t0) cc_final: 0.7051 (t0) REVERT: A 98 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.9029 (mm) REVERT: A 132 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7920 (pm20) REVERT: A 165 HIS cc_start: 0.9019 (m-70) cc_final: 0.8327 (m90) REVERT: A 172 TYR cc_start: 0.8367 (m-10) cc_final: 0.8125 (m-80) REVERT: A 174 ASP cc_start: 0.9073 (m-30) cc_final: 0.8448 (t0) REVERT: A 196 LYS cc_start: 0.8716 (mptt) cc_final: 0.8417 (mptt) REVERT: A 226 GLU cc_start: 0.7871 (pt0) cc_final: 0.7465 (pt0) REVERT: A 257 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7480 (mt-10) REVERT: A 262 LYS cc_start: 0.8701 (ttpp) cc_final: 0.8066 (ttpt) REVERT: A 288 ASN cc_start: 0.7374 (m110) cc_final: 0.6846 (m110) REVERT: A 296 CYS cc_start: 0.8307 (m) cc_final: 0.7800 (m) REVERT: A 304 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7543 (mm-40) REVERT: A 317 LYS cc_start: 0.8337 (ptpt) cc_final: 0.7990 (ptpt) REVERT: A 321 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7791 (mt-10) REVERT: A 322 LEU cc_start: 0.8862 (tp) cc_final: 0.8528 (tp) REVERT: A 348 MET cc_start: 0.7520 (tmm) cc_final: 0.7268 (tmm) REVERT: A 386 MET cc_start: 0.8670 (mtp) cc_final: 0.8275 (mtp) REVERT: A 451 LYS cc_start: 0.8536 (mtmt) cc_final: 0.7821 (mtmt) outliers start: 88 outliers final: 68 residues processed: 1172 average time/residue: 0.1682 time to fit residues: 304.9599 Evaluate side-chains 1215 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 1136 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain C residue 105 HIS Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 375 ASN Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 244 ARG Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain F residue 304 GLN Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 175 HIS Chi-restraints excluded: chain G residue 190 GLN Chi-restraints excluded: chain H residue 51 ASN Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 247 GLU Chi-restraints excluded: chain I residue 330 GLN Chi-restraints excluded: chain I residue 431 LYS Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 450 MET Chi-restraints excluded: chain I residue 564 GLN Chi-restraints excluded: chain I residue 580 THR Chi-restraints excluded: chain I residue 586 SER Chi-restraints excluded: chain I residue 587 LYS Chi-restraints excluded: chain I residue 629 THR Chi-restraints excluded: chain I residue 684 ILE Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain M residue 217 ARG Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 236 ASN Chi-restraints excluded: chain M residue 240 CYS Chi-restraints excluded: chain M residue 258 LEU Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 330 GLU Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 460 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 53 optimal weight: 0.0270 chunk 215 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 266 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 326 optimal weight: 3.9990 chunk 156 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 193 optimal weight: 0.9980 chunk 254 optimal weight: 6.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 HIS C 105 HIS C 239 GLN D 56 ASN D 75 ASN ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 HIS G 98 HIS ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 564 GLN ** J 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.138083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.112387 restraints weight = 59149.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.116151 restraints weight = 30483.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.118644 restraints weight = 18803.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.120311 restraints weight = 13071.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.121446 restraints weight = 10015.460| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26963 Z= 0.141 Angle : 0.755 17.940 36489 Z= 0.380 Chirality : 0.043 0.269 4207 Planarity : 0.004 0.061 4645 Dihedral : 4.978 58.217 3635 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.62 % Favored : 95.35 % Rotamer: Outliers : 2.90 % Allowed : 27.38 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.15), residues: 3290 helix: 1.58 (0.12), residues: 2151 sheet: -0.59 (0.49), residues: 138 loop : -1.89 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 193 TYR 0.041 0.001 TYR A 152 PHE 0.029 0.001 PHE D 48 TRP 0.054 0.002 TRP M 410 HIS 0.008 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00309 (26952) covalent geometry : angle 0.75494 (36484) SS BOND : bond 0.00176 ( 1) SS BOND : angle 1.76089 ( 2) hydrogen bonds : bond 0.04380 ( 1569) hydrogen bonds : angle 4.21307 ( 4605) metal coordination : bond 0.00412 ( 10) metal coordination : angle 1.24025 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6429.53 seconds wall clock time: 110 minutes 46.42 seconds (6646.42 seconds total)