Starting phenix.real_space_refine on Thu Aug 6 21:39:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28jl_56543/08_2026/28jl_56543_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/28jl_56543/08_2026/28jl_56543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/28jl_56543/08_2026/28jl_56543_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28jl_56543/08_2026/28jl_56543_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/28jl_56543/08_2026/28jl_56543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28jl_56543/08_2026/28jl_56543.map" } resolution = 3.6 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= 0.003 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 55 5.16 5 C 10705 2.51 5 N 2995 2.21 5 O 3348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17104 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 6050 Classifications: {'peptide': 774} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 28, 'TRANS': 745} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 77 Planarities with less than four sites: {'GLU:plan': 2, 'TYR:plan': 4, 'HIS:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 2737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2737 Classifications: {'peptide': 365} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 353} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2274 Classifications: {'peptide': 319} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 16, 'TRANS': 302} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 2, 'GLU:plan': 3, 'ASP:plan': 7, 'ASN:plan1': 1, 'TRP:plan': 1, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 81 Chain: "D" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1755 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "E" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "F" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3569 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 440} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.59, per 1000 atoms: 0.21 Number of scatterers: 17104 At special positions: 0 Unit cell: (132.24, 153.52, 156.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 55 16.00 O 3348 8.00 N 2995 7.00 C 10705 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 Simple disulfide: pdb=" SG CYS A 723 " - pdb=" SG CYS F 186 " 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: 1.50 Conformation dependent library (CDL) restraints added in 715.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F 601 " pdb="ZN ZN F 601 " - pdb=" ND1 HIS F 246 " pdb="ZN ZN F 601 " - pdb=" NE2 HIS F 140 " pdb="ZN ZN F 601 " - pdb=" NE2 HIS F 136 " 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4104 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 21 sheets defined 36.6% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 38 through 45 Processing helix chain 'A' and resid 55 through 69 removed outlier: 3.754A pdb=" N THR A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 118 removed outlier: 3.573A pdb=" N LEU A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 129 Processing helix chain 'A' and resid 130 through 143 removed outlier: 3.906A pdb=" N GLU A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER A 143 " --> pdb=" O ASP A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.542A pdb=" N LEU A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 232 removed outlier: 3.517A pdb=" N LEU A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 288 removed outlier: 3.675A pdb=" N GLU A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLN A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 313 removed outlier: 3.709A pdb=" N VAL A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 308 " --> pdb=" O MET A 304 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.988A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 393 removed outlier: 3.970A pdb=" N GLY A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 542 through 552 removed outlier: 3.622A pdb=" N TYR A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 729 through 731 No H-bonds generated for 'chain 'A' and resid 729 through 731' Processing helix chain 'A' and resid 750 through 755 removed outlier: 4.171A pdb=" N TYR A 754 " --> pdb=" O ASP A 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 33 removed outlier: 3.615A pdb=" N LYS C 32 " --> pdb=" O SER C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 removed outlier: 3.608A pdb=" N GLU C 43 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA C 44 " --> pdb=" O TYR C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.814A pdb=" N LEU C 80 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 114 removed outlier: 4.335A pdb=" N ASN C 114 " --> pdb=" O GLY C 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 111 through 114' Processing helix chain 'C' and resid 115 through 128 Processing helix chain 'C' and resid 190 through 215 removed outlier: 4.265A pdb=" N MET C 201 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET C 202 " --> pdb=" O SER C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 263 Proline residue: C 256 - end of helix removed outlier: 3.710A pdb=" N GLU C 260 " --> pdb=" O PRO C 256 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 292 Processing helix chain 'C' and resid 327 through 342 removed outlier: 4.040A pdb=" N VAL C 335 " --> pdb=" O ASN C 331 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ALA C 336 " --> pdb=" O ASP C 332 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL C 337 " --> pdb=" O ALA C 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 67 through 82 removed outlier: 3.779A pdb=" N TYR D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 119 removed outlier: 3.657A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU D 119 " --> pdb=" O THR D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 137 through 154 removed outlier: 3.624A pdb=" N ARG D 141 " --> pdb=" O PRO D 137 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA D 142 " --> pdb=" O GLN D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 189 removed outlier: 3.656A pdb=" N LYS D 165 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 202 removed outlier: 3.534A pdb=" N MET D 201 " --> pdb=" O ARG D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 214 Processing helix chain 'D' and resid 214 through 225 removed outlier: 3.898A pdb=" N MET D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU D 219 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 241 removed outlier: 3.774A pdb=" N ASN D 241 " --> pdb=" O ILE D 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 25 removed outlier: 3.733A pdb=" N ARG E 25 " --> pdb=" O SER E 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 21 through 25' Processing helix chain 'E' and resid 39 through 45 removed outlier: 3.824A pdb=" N SER E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS E 45 " --> pdb=" O ASN E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'F' and resid 45 through 63 removed outlier: 3.643A pdb=" N ARG F 58 " --> pdb=" O ASP F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 86 removed outlier: 4.118A pdb=" N HIS F 86 " --> pdb=" O ARG F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 124 removed outlier: 3.625A pdb=" N TYR F 123 " --> pdb=" O ALA F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 143 removed outlier: 3.552A pdb=" N LEU F 130 " --> pdb=" O ASN F 126 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL F 133 " --> pdb=" O GLN F 129 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET F 134 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN F 143 " --> pdb=" O SER F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 172 removed outlier: 3.673A pdb=" N ALA F 157 " --> pdb=" O GLN F 153 " (cutoff:3.500A) Proline residue: F 158 - end of helix removed outlier: 3.561A pdb=" N TRP F 161 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N MET F 172 " --> pdb=" O ILE F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 215 removed outlier: 3.908A pdb=" N GLN F 199 " --> pdb=" O SER F 195 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN F 200 " --> pdb=" O PHE F 196 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU F 201 " --> pdb=" O THR F 197 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLN F 210 " --> pdb=" O ARG F 206 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER F 215 " --> pdb=" O VAL F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 232 removed outlier: 3.626A pdb=" N THR F 224 " --> pdb=" O GLN F 220 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN F 232 " --> pdb=" O LYS F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 235 No H-bonds generated for 'chain 'F' and resid 233 through 235' Processing helix chain 'F' and resid 240 through 245 Processing helix chain 'F' and resid 251 through 261 removed outlier: 3.859A pdb=" N ARG F 259 " --> pdb=" O ASP F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 285 removed outlier: 4.312A pdb=" N TYR F 275 " --> pdb=" O SER F 271 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU F 276 " --> pdb=" O GLU F 272 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR F 285 " --> pdb=" O THR F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 302 removed outlier: 3.782A pdb=" N LEU F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS F 302 " --> pdb=" O ASP F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 322 Processing helix chain 'F' and resid 324 through 339 Proline residue: F 334 - end of helix Processing helix chain 'F' and resid 342 through 356 removed outlier: 3.907A pdb=" N LEU F 348 " --> pdb=" O TRP F 344 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN F 356 " --> pdb=" O ILE F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 368 removed outlier: 4.480A pdb=" N ASN F 364 " --> pdb=" O ASN F 360 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ARG F 365 " --> pdb=" O GLU F 361 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU F 366 " --> pdb=" O ALA F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 390 Processing helix chain 'F' and resid 391 through 404 removed outlier: 3.758A pdb=" N ALA F 395 " --> pdb=" O GLN F 391 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN F 397 " --> pdb=" O GLN F 393 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE F 398 " --> pdb=" O GLU F 394 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 422 removed outlier: 4.295A pdb=" N TRP F 413 " --> pdb=" O ASP F 409 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP F 414 " --> pdb=" O SER F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 440 removed outlier: 3.768A pdb=" N GLU F 435 " --> pdb=" O ALA F 431 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY F 436 " --> pdb=" O ALA F 432 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR F 437 " --> pdb=" O ARG F 433 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA F 440 " --> pdb=" O GLY F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 455 removed outlier: 3.698A pdb=" N ALA F 446 " --> pdb=" O ARG F 442 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER F 448 " --> pdb=" O ASP F 444 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER F 455 " --> pdb=" O SER F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 487 removed outlier: 3.590A pdb=" N LYS F 482 " --> pdb=" O GLN F 478 " (cutoff:3.500A) Proline residue: F 483 - end of helix removed outlier: 4.253A pdb=" N LYS F 486 " --> pdb=" O LYS F 482 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N MET F 487 " --> pdb=" O PRO F 483 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 32 removed outlier: 4.599A pdb=" N ASP A 74 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 6.647A pdb=" N THR A 93 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LEU A 165 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ALA A 95 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 13.064A pdb=" N LEU A 167 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N ILE A 97 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 12.999A pdb=" N PHE A 169 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 10.683A pdb=" N PHE A 99 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 177 through 183 removed outlier: 7.596A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ILE A 182 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ILE A 260 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR A 255 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL A 245 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N THR A 257 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N THR A 243 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASN A 259 " --> pdb=" O ASP A 241 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN A 239 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER B 193 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 272 through 273 removed outlier: 6.155A pdb=" N GLU A 272 " --> pdb=" O VAL A 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 355 removed outlier: 6.067A pdb=" N VAL A 412 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS A 351 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 419 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 426 removed outlier: 3.568A pdb=" N PHE A 440 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN A 459 " --> pdb=" O GLU A 470 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 486 " --> pdb=" O THR A 514 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY A 510 " --> pdb=" O PHE A 490 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 505 " --> pdb=" O SER A 537 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A 537 " --> pdb=" O THR A 505 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 517 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A 519 " --> pdb=" O ASN A 523 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASN A 523 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 524 " --> pdb=" O THR A 577 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A 577 " --> pdb=" O SER A 524 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 526 " --> pdb=" O GLY A 575 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY A 575 " --> pdb=" O ARG A 526 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY A 590 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR A 600 " --> pdb=" O TYR A 608 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU A 613 " --> pdb=" O TRP A 635 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A 617 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 619 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 785 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.475A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.622A pdb=" N SER B 389 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER B 49 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL B 387 " --> pdb=" O SER B 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 68 removed outlier: 3.828A pdb=" N TRP B 93 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 111 through 118 removed outlier: 3.812A pdb=" N GLY B 125 " --> pdb=" O GLY B 113 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL B 115 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR B 123 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL B 117 " --> pdb=" O HIS B 121 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N HIS B 121 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.536A pdb=" N ALA B 173 " --> pdb=" O TRP B 183 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TRP B 183 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN B 175 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL B 181 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 203 removed outlier: 4.160A pdb=" N TRP B 228 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU B 220 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N MET B 226 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 254 removed outlier: 4.018A pdb=" N TRP B 279 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP B 271 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ILE B 277 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 290 through 292 removed outlier: 4.079A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR B 309 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N THR B 315 " --> pdb=" O THR B 309 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 332 removed outlier: 6.909A pdb=" N LEU B 346 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLN B 359 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TRP B 348 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 96 through 100 removed outlier: 4.032A pdb=" N ARG C 96 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ARG C 160 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU C 181 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ARG C 158 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYR C 161 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ASP C 144 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE C 163 " --> pdb=" O THR C 142 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N THR C 142 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL C 165 " --> pdb=" O THR C 140 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N THR C 140 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN C 133 " --> pdb=" O THR C 142 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASP C 144 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE C 131 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 96 through 100 removed outlier: 4.032A pdb=" N ARG C 96 " --> pdb=" O LEU C 107 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 230 through 234 removed outlier: 3.739A pdb=" N ALA C 233 " --> pdb=" O MET C 241 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N PHE C 318 " --> pdb=" O PRO C 240 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN C 275 " --> pdb=" O SER C 269 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SER C 269 " --> pdb=" O ASN C 275 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA C 277 " --> pdb=" O THR C 267 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 33 through 35 removed outlier: 3.556A pdb=" N GLN E 34 " --> pdb=" O ARG E 78 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG E 78 " --> pdb=" O GLN E 34 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 33 through 35 removed outlier: 3.556A pdb=" N GLN E 34 " --> pdb=" O ARG E 78 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG E 78 " --> pdb=" O GLN E 34 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR E 90 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN E 103 " --> pdb=" O THR E 94 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 95 through 99 removed outlier: 3.699A pdb=" N ASN F 113 " --> pdb=" O PHE F 109 " (cutoff:3.500A) 778 hydrogen bonds defined for protein. 2214 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.33 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5835 1.35 - 1.46: 3857 1.46 - 1.58: 7638 1.58 - 1.70: 0 1.70 - 1.82: 105 Bond restraints: 17435 Sorted by residual: bond pdb=" N VAL B 29 " pdb=" CA VAL B 29 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.08e-02 8.57e+03 1.22e+01 bond pdb=" N VAL A 611 " pdb=" CA VAL A 611 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.07e-02 8.73e+03 1.10e+01 bond pdb=" N VAL D 198 " pdb=" CA VAL D 198 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.34e-02 5.57e+03 9.86e+00 bond pdb=" N VAL A 54 " pdb=" CA VAL A 54 " ideal model delta sigma weight residual 1.454 1.494 -0.040 1.28e-02 6.10e+03 9.83e+00 bond pdb=" N ASP A 797 " pdb=" CA ASP A 797 " ideal model delta sigma weight residual 1.453 1.493 -0.040 1.31e-02 5.83e+03 9.56e+00 ... (remaining 17430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 22907 1.81 - 3.62: 670 3.62 - 5.42: 104 5.42 - 7.23: 11 7.23 - 9.04: 3 Bond angle restraints: 23695 Sorted by residual: angle pdb=" N PRO A 763 " pdb=" CA PRO A 763 " pdb=" C PRO A 763 " ideal model delta sigma weight residual 114.18 106.44 7.74 1.39e+00 5.18e-01 3.10e+01 angle pdb=" N GLN A 678 " pdb=" CA GLN A 678 " pdb=" C GLN A 678 " ideal model delta sigma weight residual 113.72 106.51 7.21 1.30e+00 5.92e-01 3.08e+01 angle pdb=" CA GLN A 265 " pdb=" C GLN A 265 " pdb=" O GLN A 265 " ideal model delta sigma weight residual 121.55 116.23 5.32 1.06e+00 8.90e-01 2.52e+01 angle pdb=" CA VAL A 611 " pdb=" C VAL A 611 " pdb=" O VAL A 611 " ideal model delta sigma weight residual 121.09 117.20 3.89 8.20e-01 1.49e+00 2.25e+01 angle pdb=" N PHE A 347 " pdb=" CA PHE A 347 " pdb=" CB PHE A 347 " ideal model delta sigma weight residual 110.36 103.60 6.76 1.43e+00 4.89e-01 2.23e+01 ... (remaining 23690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9262 17.97 - 35.95: 852 35.95 - 53.92: 223 53.92 - 71.89: 37 71.89 - 89.86: 39 Dihedral angle restraints: 10413 sinusoidal: 3999 harmonic: 6414 Sorted by residual: dihedral pdb=" CD ARG A 321 " pdb=" NE ARG A 321 " pdb=" CZ ARG A 321 " pdb=" NH1 ARG A 321 " ideal model delta sinusoidal sigma weight residual 0.00 -84.39 84.39 1 1.00e+01 1.00e-02 8.66e+01 dihedral pdb=" CB CYS A 690 " pdb=" SG CYS A 690 " pdb=" SG CYS A 700 " pdb=" CB CYS A 700 " ideal model delta sinusoidal sigma weight residual -86.00 -161.77 75.77 1 1.00e+01 1.00e-02 7.24e+01 dihedral pdb=" CD ARG A 632 " pdb=" NE ARG A 632 " pdb=" CZ ARG A 632 " pdb=" NH1 ARG A 632 " ideal model delta sinusoidal sigma weight residual 0.00 52.42 -52.42 1 1.00e+01 1.00e-02 3.75e+01 ... (remaining 10410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2051 0.044 - 0.088: 339 0.088 - 0.132: 202 0.132 - 0.176: 26 0.176 - 0.220: 9 Chirality restraints: 2627 Sorted by residual: chirality pdb=" CA VAL C 146 " pdb=" N VAL C 146 " pdb=" C VAL C 146 " pdb=" CB VAL C 146 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB VAL A 322 " pdb=" CA VAL A 322 " pdb=" CG1 VAL A 322 " pdb=" CG2 VAL A 322 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE A 352 " pdb=" N ILE A 352 " pdb=" C ILE A 352 " pdb=" CB ILE A 352 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2624 not shown) Planarity restraints: 3146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 321 " -1.094 9.50e-02 1.11e+02 4.90e-01 1.45e+02 pdb=" NE ARG A 321 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG A 321 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 321 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 321 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 632 " -0.868 9.50e-02 1.11e+02 3.89e-01 9.18e+01 pdb=" NE ARG A 632 " 0.052 2.00e-02 2.50e+03 pdb=" CZ ARG A 632 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 632 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 632 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 634 " 0.836 9.50e-02 1.11e+02 3.75e-01 8.53e+01 pdb=" NE ARG A 634 " -0.049 2.00e-02 2.50e+03 pdb=" CZ ARG A 634 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 634 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 634 " 0.025 2.00e-02 2.50e+03 ... (remaining 3143 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 212 2.65 - 3.21: 15783 3.21 - 3.78: 24043 3.78 - 4.34: 31109 4.34 - 4.90: 52952 Nonbonded interactions: 124099 Sorted by model distance: nonbonded pdb=" OD2 ASP E 66 " pdb=" OG1 THR E 70 " model vdw 2.088 3.040 nonbonded pdb=" OG1 THR E 51 " pdb=" OE1 GLN E 54 " model vdw 2.110 3.040 nonbonded pdb=" O ALA A 672 " pdb=" OG SER A 702 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR A 230 " pdb=" OE1 GLU A 262 " model vdw 2.202 3.040 nonbonded pdb=" OG SER B 33 " pdb=" O LEU B 323 " model vdw 2.213 3.040 ... (remaining 124094 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: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 18.430 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 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 : 0.004 0.046 17440 Z= 0.291 Angle : 0.679 9.040 23699 Z= 0.447 Chirality : 0.046 0.220 2627 Planarity : 0.015 0.490 3146 Dihedral : 15.952 89.863 6303 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.45 % Allowed : 3.85 % Favored : 95.70 % Rotamer: Outliers : 3.25 % Allowed : 14.90 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.19), residues: 2208 helix: 2.16 (0.20), residues: 712 sheet: -0.23 (0.24), residues: 483 loop : -0.95 (0.20), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 127 TYR 0.024 0.001 TYR A 266 PHE 0.012 0.001 PHE A 648 TRP 0.011 0.001 TRP A 776 HIS 0.004 0.001 HIS F 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.29 (17435) covalent geometry : angle 0.67915 / 0.45 (23695) SS BOND : bond 0.00061 / 0.03 ( 2) SS BOND : angle 1.47697 / 0.86 ( 4) hydrogen bonds : bond 0.22864 / 15.06 ( 763) hydrogen bonds : angle 7.01645 / 4.95 ( 2214) metal coordination : bond 0.00941 / 0.47 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 429 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.7128 (t70) cc_final: 0.6887 (t0) REVERT: A 252 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7554 (ttmt) REVERT: A 537 SER cc_start: 0.8309 (OUTLIER) cc_final: 0.7940 (p) REVERT: A 539 MET cc_start: 0.7303 (ttm) cc_final: 0.7083 (tpt) REVERT: A 626 LYS cc_start: 0.8285 (mmtp) cc_final: 0.7792 (mtmt) REVERT: A 648 PHE cc_start: 0.7391 (p90) cc_final: 0.6945 (p90) REVERT: A 728 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8654 (tttm) REVERT: A 741 MET cc_start: 0.7177 (ptm) cc_final: 0.6945 (ptp) REVERT: A 753 GLN cc_start: 0.7065 (mm-40) cc_final: 0.6803 (tm-30) REVERT: B 23 PHE cc_start: 0.3292 (OUTLIER) cc_final: 0.3031 (m-10) REVERT: B 31 LYS cc_start: 0.4524 (OUTLIER) cc_final: 0.4141 (mmtt) REVERT: B 215 ARG cc_start: 0.7413 (mtt180) cc_final: 0.6755 (mpt180) REVERT: B 229 GLN cc_start: 0.7343 (mt0) cc_final: 0.7130 (mt0) REVERT: B 231 ARG cc_start: 0.7597 (ttt180) cc_final: 0.7348 (ttt90) REVERT: B 233 SER cc_start: 0.8891 (t) cc_final: 0.7363 (t) REVERT: B 236 THR cc_start: 0.7058 (m) cc_final: 0.6851 (p) REVERT: B 314 VAL cc_start: 0.7087 (t) cc_final: 0.6850 (p) REVERT: B 360 GLN cc_start: 0.7334 (pt0) cc_final: 0.6528 (pm20) REVERT: B 377 LYS cc_start: 0.7318 (mttt) cc_final: 0.7009 (tppt) REVERT: B 378 LEU cc_start: 0.8296 (tp) cc_final: 0.8024 (mt) REVERT: C 186 LYS cc_start: 0.7990 (tppt) cc_final: 0.7739 (mptt) REVERT: C 202 MET cc_start: 0.6340 (tpt) cc_final: 0.5846 (tpp) REVERT: C 261 LYS cc_start: 0.8753 (ttmt) cc_final: 0.8499 (ttpt) REVERT: D 112 ARG cc_start: 0.7292 (ttt-90) cc_final: 0.7066 (ttp80) REVERT: D 146 ASP cc_start: 0.6888 (m-30) cc_final: 0.6500 (t0) REVERT: E 50 MET cc_start: 0.7232 (tpp) cc_final: 0.6835 (ttm) REVERT: F 442 ARG cc_start: 0.8428 (mtp85) cc_final: 0.7883 (ttm110) outliers start: 58 outliers final: 17 residues processed: 475 average time/residue: 0.1612 time to fit residues: 109.8685 Evaluate side-chains 248 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 226 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain B residue 23 PHE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 237 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 7.9990 chunk 212 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 HIS A 61 ASN A 71 ASN A 87 GLN A 765 ASN B 165 HIS ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN C 168 GLN C 231 GLN D 104 ASN D 125 GLN D 230 GLN E 54 GLN E 103 ASN ** F 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 360 ASN F 428 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.151295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.116732 restraints weight = 25162.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.114212 restraints weight = 37063.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.116786 restraints weight = 25988.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.117606 restraints weight = 15270.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.118223 restraints weight = 13882.469| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.075 17440 Z= 0.396 Angle : 0.818 10.238 23699 Z= 0.431 Chirality : 0.052 0.204 2627 Planarity : 0.006 0.058 3146 Dihedral : 6.061 58.671 2473 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.98 % Favored : 93.89 % Rotamer: Outliers : 4.99 % Allowed : 16.86 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.17), residues: 2208 helix: 1.09 (0.18), residues: 744 sheet: -0.44 (0.22), residues: 510 loop : -1.27 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 767 TYR 0.032 0.003 TYR D 77 PHE 0.025 0.003 PHE D 147 TRP 0.024 0.002 TRP B 93 HIS 0.013 0.003 HIS F 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00977 / 0.40 (17435) covalent geometry : angle 0.81738 / 0.43 (23695) SS BOND : bond 0.00888 / 0.42 ( 2) SS BOND : angle 1.39199 / 0.77 ( 4) hydrogen bonds : bond 0.08537 / 5.78 ( 763) hydrogen bonds : angle 5.28773 / 3.72 ( 2214) metal coordination : bond 0.03360 / 1.68 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 219 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8814 (mm) REVERT: A 222 ASP cc_start: 0.7845 (t70) cc_final: 0.7639 (t0) REVERT: A 328 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7931 (mt) REVERT: A 377 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8984 (tp) REVERT: A 537 SER cc_start: 0.9207 (OUTLIER) cc_final: 0.8490 (m) REVERT: A 650 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7801 (tt0) REVERT: B 23 PHE cc_start: 0.3390 (OUTLIER) cc_final: 0.2855 (m-10) REVERT: B 31 LYS cc_start: 0.5488 (OUTLIER) cc_final: 0.5068 (mmtt) REVERT: B 233 SER cc_start: 0.8861 (t) cc_final: 0.7994 (t) REVERT: B 355 ARG cc_start: 0.6832 (mmp80) cc_final: 0.6428 (mmp80) REVERT: B 360 GLN cc_start: 0.7771 (pt0) cc_final: 0.7435 (pm20) REVERT: C 211 LYS cc_start: 0.8703 (tppt) cc_final: 0.7969 (ttpt) REVERT: D 98 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8162 (mt) REVERT: D 202 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8753 (mp) REVERT: D 207 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7925 (p0) REVERT: F 420 GLU cc_start: 0.8795 (tp30) cc_final: 0.8550 (mm-30) outliers start: 89 outliers final: 52 residues processed: 294 average time/residue: 0.1529 time to fit residues: 65.5848 Evaluate side-chains 231 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 169 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 650 GLU Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 769 SER Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain B residue 23 PHE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 371 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 53 optimal weight: 4.9990 chunk 167 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 chunk 156 optimal weight: 0.9990 chunk 189 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 218 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 8 optimal weight: 0.0970 chunk 206 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN A 87 GLN B 175 ASN B 229 GLN C 231 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.158085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.125120 restraints weight = 25420.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.122453 restraints weight = 28341.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.124698 restraints weight = 23330.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.124546 restraints weight = 14226.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.126734 restraints weight = 12752.454| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.089 17440 Z= 0.120 Angle : 0.530 7.557 23699 Z= 0.282 Chirality : 0.042 0.177 2627 Planarity : 0.004 0.051 3146 Dihedral : 5.022 59.598 2447 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.49 % Favored : 96.42 % Rotamer: Outliers : 3.59 % Allowed : 18.32 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.06 (0.18), residues: 2208 helix: 1.65 (0.19), residues: 749 sheet: -0.14 (0.22), residues: 517 loop : -1.17 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 29 TYR 0.018 0.001 TYR A 794 PHE 0.015 0.001 PHE D 127 TRP 0.011 0.001 TRP B 93 HIS 0.005 0.001 HIS F 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (17435) covalent geometry : angle 0.52714 / 0.28 (23695) SS BOND : bond 0.00548 / 0.29 ( 2) SS BOND : angle 4.39833 / 2.39 ( 4) hydrogen bonds : bond 0.05336 / 3.62 ( 763) hydrogen bonds : angle 4.54166 / 3.19 ( 2214) metal coordination : bond 0.01168 / 0.56 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 204 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.7256 (t70) cc_final: 0.7027 (t0) REVERT: A 289 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8250 (tmmt) REVERT: A 328 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7873 (mt) REVERT: A 546 TRP cc_start: 0.7380 (m100) cc_final: 0.6190 (m100) REVERT: A 753 GLN cc_start: 0.6644 (tm-30) cc_final: 0.6399 (tm-30) REVERT: B 31 LYS cc_start: 0.5320 (OUTLIER) cc_final: 0.5001 (mmtt) REVERT: B 197 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7324 (mm-30) REVERT: B 360 GLN cc_start: 0.7846 (pt0) cc_final: 0.7390 (pm20) REVERT: C 202 MET cc_start: 0.7544 (tpp) cc_final: 0.7049 (tpp) REVERT: D 98 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8027 (mt) REVERT: D 207 ASP cc_start: 0.8090 (p0) cc_final: 0.7752 (p0) REVERT: F 331 THR cc_start: 0.8226 (m) cc_final: 0.7974 (m) REVERT: F 420 GLU cc_start: 0.8767 (tp30) cc_final: 0.8551 (mm-30) outliers start: 64 outliers final: 33 residues processed: 256 average time/residue: 0.1541 time to fit residues: 57.6550 Evaluate side-chains 221 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 361 GLU Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 371 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 218 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 207 optimal weight: 9.9990 chunk 193 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 123 optimal weight: 50.0000 chunk 185 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN E 34 GLN F 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.154494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.122112 restraints weight = 25436.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.121643 restraints weight = 35020.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.123149 restraints weight = 25428.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.123875 restraints weight = 15101.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.124802 restraints weight = 13031.231| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17440 Z= 0.174 Angle : 0.553 7.183 23699 Z= 0.292 Chirality : 0.043 0.159 2627 Planarity : 0.004 0.039 3146 Dihedral : 4.614 57.643 2440 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.30 % Favored : 95.61 % Rotamer: Outliers : 4.48 % Allowed : 17.98 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.01 (0.18), residues: 2208 helix: 1.61 (0.19), residues: 750 sheet: -0.12 (0.22), residues: 518 loop : -1.25 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 29 TYR 0.016 0.001 TYR D 77 PHE 0.019 0.002 PHE D 127 TRP 0.011 0.001 TRP A 745 HIS 0.004 0.001 HIS B 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 (17435) covalent geometry : angle 0.55246 / 0.29 (23695) SS BOND : bond 0.00433 / 0.21 ( 2) SS BOND : angle 2.61922 / 1.42 ( 4) hydrogen bonds : bond 0.05982 / 4.06 ( 763) hydrogen bonds : angle 4.41036 / 3.10 ( 2214) metal coordination : bond 0.00171 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 184 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8352 (tmmt) REVERT: A 328 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.8010 (mt) REVERT: A 546 TRP cc_start: 0.7409 (m100) cc_final: 0.6876 (m100) REVERT: A 650 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7487 (tt0) REVERT: B 31 LYS cc_start: 0.5567 (OUTLIER) cc_final: 0.5104 (tptp) REVERT: B 272 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7915 (mp) REVERT: C 181 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7395 (mp) REVERT: C 202 MET cc_start: 0.7670 (tpp) cc_final: 0.7232 (tpp) REVERT: C 211 LYS cc_start: 0.8525 (tppt) cc_final: 0.7811 (ttpt) REVERT: D 98 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8193 (mt) REVERT: D 207 ASP cc_start: 0.8235 (p0) cc_final: 0.7862 (p0) REVERT: E 25 ARG cc_start: 0.8191 (mmt180) cc_final: 0.7945 (mtt180) outliers start: 80 outliers final: 46 residues processed: 247 average time/residue: 0.1408 time to fit residues: 52.2158 Evaluate side-chains 228 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 175 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 650 GLU Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 371 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 130 optimal weight: 6.9990 chunk 191 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 136 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN C 34 GLN C 168 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.154161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.121208 restraints weight = 25260.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.119867 restraints weight = 26405.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.120790 restraints weight = 23451.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.121418 restraints weight = 12740.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.123117 restraints weight = 11269.309| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17440 Z= 0.173 Angle : 0.545 7.921 23699 Z= 0.288 Chirality : 0.042 0.150 2627 Planarity : 0.004 0.040 3146 Dihedral : 4.556 56.935 2440 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.03 % Favored : 95.88 % Rotamer: Outliers : 4.71 % Allowed : 18.04 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.18), residues: 2208 helix: 1.61 (0.19), residues: 750 sheet: -0.03 (0.23), residues: 520 loop : -1.29 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 231 TYR 0.016 0.001 TYR D 77 PHE 0.016 0.001 PHE F 109 TRP 0.010 0.001 TRP A 749 HIS 0.004 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (17435) covalent geometry : angle 0.54463 / 0.29 (23695) SS BOND : bond 0.00380 / 0.18 ( 2) SS BOND : angle 1.90253 / 1.03 ( 4) hydrogen bonds : bond 0.05720 / 3.88 ( 763) hydrogen bonds : angle 4.26435 / 2.99 ( 2214) metal coordination : bond 0.01672 / 0.84 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 181 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7688 (mt-10) REVERT: A 289 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8440 (tmmt) REVERT: A 328 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.7973 (mt) REVERT: A 369 MET cc_start: 0.8622 (mmp) cc_final: 0.8391 (mmm) REVERT: A 539 MET cc_start: 0.7869 (tpt) cc_final: 0.7400 (tpt) REVERT: A 650 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7424 (tt0) REVERT: B 31 LYS cc_start: 0.5687 (OUTLIER) cc_final: 0.5306 (tptp) REVERT: B 272 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7772 (mp) REVERT: B 278 MET cc_start: 0.7540 (mtm) cc_final: 0.7269 (mtt) REVERT: B 377 LYS cc_start: 0.8265 (ptpp) cc_final: 0.7681 (pttm) REVERT: C 181 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7243 (mp) REVERT: D 98 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8267 (mt) REVERT: D 207 ASP cc_start: 0.8201 (p0) cc_final: 0.7812 (p0) REVERT: F 363 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8308 (mt) outliers start: 84 outliers final: 53 residues processed: 249 average time/residue: 0.1391 time to fit residues: 52.4740 Evaluate side-chains 233 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 172 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 650 GLU Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain F residue 361 GLU Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 371 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 85 optimal weight: 0.9990 chunk 52 optimal weight: 20.0000 chunk 38 optimal weight: 0.0570 chunk 167 optimal weight: 4.9990 chunk 79 optimal weight: 30.0000 chunk 146 optimal weight: 8.9990 chunk 154 optimal weight: 0.0570 chunk 177 optimal weight: 0.5980 chunk 160 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 overall best weight: 0.5420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN F 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.158757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.125959 restraints weight = 25264.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.125217 restraints weight = 24820.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.126061 restraints weight = 21230.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.126710 restraints weight = 12038.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.127913 restraints weight = 10809.908| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17440 Z= 0.096 Angle : 0.484 7.644 23699 Z= 0.253 Chirality : 0.040 0.152 2627 Planarity : 0.003 0.045 3146 Dihedral : 4.234 56.309 2440 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.94 % Favored : 96.97 % Rotamer: Outliers : 2.58 % Allowed : 20.45 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.18), residues: 2208 helix: 1.94 (0.19), residues: 748 sheet: 0.14 (0.22), residues: 537 loop : -1.22 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 29 TYR 0.013 0.001 TYR D 184 PHE 0.023 0.001 PHE D 127 TRP 0.009 0.001 TRP B 93 HIS 0.004 0.001 HIS F 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.10 (17435) covalent geometry : angle 0.48389 / 0.25 (23695) SS BOND : bond 0.00191 / 0.10 ( 2) SS BOND : angle 1.63218 / 0.88 ( 4) hydrogen bonds : bond 0.04017 / 2.73 ( 763) hydrogen bonds : angle 3.92103 / 2.74 ( 2214) metal coordination : bond 0.00946 / 0.48 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 184 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.7896 (OUTLIER) cc_final: 0.7371 (t0) REVERT: A 213 LYS cc_start: 0.8623 (mtmt) cc_final: 0.8193 (mmtt) REVERT: A 289 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8326 (tmmt) REVERT: A 775 GLN cc_start: 0.7992 (tt0) cc_final: 0.7517 (mt0) REVERT: B 31 LYS cc_start: 0.5592 (OUTLIER) cc_final: 0.5281 (tptp) REVERT: B 231 ARG cc_start: 0.8126 (ttt90) cc_final: 0.7694 (mtp180) REVERT: B 272 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7856 (mp) REVERT: B 377 LYS cc_start: 0.8181 (ptpp) cc_final: 0.7657 (pttm) REVERT: C 181 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7256 (mp) REVERT: C 211 LYS cc_start: 0.8585 (tppt) cc_final: 0.7687 (ttpt) REVERT: D 98 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8067 (mt) REVERT: D 207 ASP cc_start: 0.8030 (p0) cc_final: 0.7584 (p0) REVERT: F 241 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7355 (mm-30) outliers start: 46 outliers final: 31 residues processed: 220 average time/residue: 0.1331 time to fit residues: 43.5480 Evaluate side-chains 211 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 371 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 35 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 chunk 96 optimal weight: 20.0000 chunk 47 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 78 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 54 GLN F 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.152945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.120580 restraints weight = 25212.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.119719 restraints weight = 34037.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.121252 restraints weight = 26117.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.121855 restraints weight = 15577.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.123036 restraints weight = 13381.976| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17440 Z= 0.212 Angle : 0.575 7.115 23699 Z= 0.303 Chirality : 0.043 0.161 2627 Planarity : 0.004 0.035 3146 Dihedral : 4.271 55.688 2437 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.21 % Favored : 95.70 % Rotamer: Outliers : 3.42 % Allowed : 20.00 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.18), residues: 2208 helix: 1.70 (0.19), residues: 747 sheet: -0.04 (0.22), residues: 528 loop : -1.26 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 127 TYR 0.017 0.002 TYR D 77 PHE 0.020 0.002 PHE F 109 TRP 0.011 0.001 TRP A 745 HIS 0.005 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.21 (17435) covalent geometry : angle 0.57427 / 0.30 (23695) SS BOND : bond 0.00439 / 0.21 ( 2) SS BOND : angle 1.71939 / 0.92 ( 4) hydrogen bonds : bond 0.06170 / 4.19 ( 763) hydrogen bonds : angle 4.18825 / 2.94 ( 2214) metal coordination : bond 0.00647 / 0.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 170 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.8018 (t0) cc_final: 0.7784 (t0) REVERT: A 289 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8462 (tmmt) REVERT: B 31 LYS cc_start: 0.5925 (OUTLIER) cc_final: 0.5568 (tptp) REVERT: B 231 ARG cc_start: 0.8099 (ttt90) cc_final: 0.7678 (mtp180) REVERT: B 272 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7973 (mp) REVERT: B 377 LYS cc_start: 0.8170 (ptpp) cc_final: 0.7719 (pttm) REVERT: C 181 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7380 (mp) REVERT: D 98 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8336 (mt) REVERT: D 207 ASP cc_start: 0.8333 (p0) cc_final: 0.7875 (p0) outliers start: 61 outliers final: 46 residues processed: 224 average time/residue: 0.1231 time to fit residues: 41.6558 Evaluate side-chains 214 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 163 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 366 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 149 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 38 optimal weight: 0.2980 chunk 60 optimal weight: 2.9990 chunk 185 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 141 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.155882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.123950 restraints weight = 25329.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.123043 restraints weight = 33380.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.124599 restraints weight = 25573.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.125298 restraints weight = 15192.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.126164 restraints weight = 13035.719| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17440 Z= 0.115 Angle : 0.499 7.387 23699 Z= 0.262 Chirality : 0.041 0.156 2627 Planarity : 0.003 0.034 3146 Dihedral : 4.086 54.870 2437 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.31 % Favored : 96.60 % Rotamer: Outliers : 2.69 % Allowed : 20.78 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.18), residues: 2208 helix: 1.89 (0.19), residues: 749 sheet: 0.09 (0.23), residues: 519 loop : -1.26 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 127 TYR 0.014 0.001 TYR D 184 PHE 0.018 0.001 PHE D 127 TRP 0.008 0.001 TRP B 93 HIS 0.003 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (17435) covalent geometry : angle 0.49817 / 0.26 (23695) SS BOND : bond 0.00265 / 0.13 ( 2) SS BOND : angle 1.60745 / 0.87 ( 4) hydrogen bonds : bond 0.04726 / 3.21 ( 763) hydrogen bonds : angle 3.95845 / 2.78 ( 2214) metal coordination : bond 0.00457 / 0.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 176 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 LYS cc_start: 0.8693 (mtmt) cc_final: 0.8242 (mmtt) REVERT: A 289 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8409 (tmmt) REVERT: A 650 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7106 (tt0) REVERT: B 31 LYS cc_start: 0.5868 (OUTLIER) cc_final: 0.5531 (tptp) REVERT: B 231 ARG cc_start: 0.8098 (ttt90) cc_final: 0.7681 (mtp180) REVERT: B 272 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7951 (mp) REVERT: B 377 LYS cc_start: 0.8104 (ptpp) cc_final: 0.7719 (pttm) REVERT: C 181 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7386 (mp) REVERT: C 202 MET cc_start: 0.7167 (tpp) cc_final: 0.6805 (ttt) REVERT: C 211 LYS cc_start: 0.8511 (tppt) cc_final: 0.7607 (ttpt) REVERT: D 98 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8243 (mt) REVERT: D 207 ASP cc_start: 0.8181 (p0) cc_final: 0.7658 (p0) outliers start: 48 outliers final: 37 residues processed: 217 average time/residue: 0.1249 time to fit residues: 40.4421 Evaluate side-chains 214 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 171 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 650 GLU Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 371 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 2 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 213 optimal weight: 0.8980 chunk 151 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 58 optimal weight: 0.0980 chunk 83 optimal weight: 30.0000 chunk 127 optimal weight: 9.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 223 GLN D 125 GLN F 360 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.154197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.122434 restraints weight = 25261.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.120880 restraints weight = 36506.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.122718 restraints weight = 27243.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.123400 restraints weight = 15944.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.124440 restraints weight = 13443.679| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17440 Z= 0.129 Angle : 0.506 7.417 23699 Z= 0.265 Chirality : 0.041 0.147 2627 Planarity : 0.003 0.031 3146 Dihedral : 4.035 54.062 2437 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.67 % Favored : 96.24 % Rotamer: Outliers : 2.97 % Allowed : 20.95 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.18), residues: 2208 helix: 1.96 (0.19), residues: 747 sheet: 0.13 (0.22), residues: 524 loop : -1.26 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 355 TYR 0.023 0.001 TYR A 504 PHE 0.017 0.001 PHE D 127 TRP 0.008 0.001 TRP A 376 HIS 0.004 0.001 HIS F 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (17435) covalent geometry : angle 0.50592 / 0.26 (23695) SS BOND : bond 0.00324 / 0.16 ( 2) SS BOND : angle 1.57730 / 0.85 ( 4) hydrogen bonds : bond 0.04846 / 3.29 ( 763) hydrogen bonds : angle 3.92258 / 2.76 ( 2214) metal coordination : bond 0.00378 / 0.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 173 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 LYS cc_start: 0.8674 (mtmt) cc_final: 0.8227 (mmtt) REVERT: A 650 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7096 (tt0) REVERT: B 31 LYS cc_start: 0.5923 (OUTLIER) cc_final: 0.5579 (tptp) REVERT: B 272 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7851 (mp) REVERT: B 377 LYS cc_start: 0.8066 (ptpp) cc_final: 0.7678 (pttm) REVERT: C 177 LYS cc_start: 0.7874 (tptm) cc_final: 0.7164 (tptt) REVERT: C 181 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7408 (mp) REVERT: C 202 MET cc_start: 0.7201 (tpp) cc_final: 0.6824 (ttt) REVERT: D 98 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8257 (mt) REVERT: D 207 ASP cc_start: 0.8191 (p0) cc_final: 0.7657 (p0) outliers start: 53 outliers final: 43 residues processed: 218 average time/residue: 0.1316 time to fit residues: 42.8821 Evaluate side-chains 217 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 169 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 546 TRP Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 650 GLU Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 371 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 153 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 13 optimal weight: 0.0570 chunk 200 optimal weight: 4.9990 chunk 78 optimal weight: 0.0040 chunk 126 optimal weight: 10.0000 chunk 213 optimal weight: 0.6980 chunk 117 optimal weight: 0.0980 chunk 74 optimal weight: 0.0670 overall best weight: 0.1848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 651 ASN F 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.158612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.125999 restraints weight = 25164.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.123959 restraints weight = 21549.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.124921 restraints weight = 20503.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.125578 restraints weight = 12215.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.126618 restraints weight = 10857.160| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17440 Z= 0.093 Angle : 0.482 7.717 23699 Z= 0.250 Chirality : 0.040 0.147 2627 Planarity : 0.003 0.033 3146 Dihedral : 3.802 53.417 2437 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.85 % Favored : 97.06 % Rotamer: Outliers : 2.46 % Allowed : 21.23 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.48 (0.18), residues: 2208 helix: 2.11 (0.19), residues: 754 sheet: 0.24 (0.22), residues: 538 loop : -1.19 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 355 TYR 0.017 0.001 TYR A 649 PHE 0.020 0.001 PHE D 127 TRP 0.010 0.001 TRP A 627 HIS 0.012 0.001 HIS F 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.09 (17435) covalent geometry : angle 0.48163 / 0.25 (23695) SS BOND : bond 0.01138 / 0.60 ( 2) SS BOND : angle 2.13078 / 1.14 ( 4) hydrogen bonds : bond 0.03377 / 2.29 ( 763) hydrogen bonds : angle 3.68522 / 2.59 ( 2214) metal coordination : bond 0.00392 / 0.20 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 188 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 LYS cc_start: 0.8652 (mtmt) cc_final: 0.8244 (mmtt) REVERT: A 622 ASP cc_start: 0.8656 (p0) cc_final: 0.8390 (p0) REVERT: A 651 ASN cc_start: 0.8985 (OUTLIER) cc_final: 0.8297 (m110) REVERT: B 31 LYS cc_start: 0.5802 (OUTLIER) cc_final: 0.5551 (tptp) REVERT: B 231 ARG cc_start: 0.8155 (ttt90) cc_final: 0.7721 (mtp180) REVERT: B 272 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7648 (mp) REVERT: B 377 LYS cc_start: 0.8020 (ptpp) cc_final: 0.7552 (pttm) REVERT: C 177 LYS cc_start: 0.7538 (tptm) cc_final: 0.6782 (tptt) REVERT: C 181 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7209 (mp) REVERT: C 202 MET cc_start: 0.6943 (tpp) cc_final: 0.6527 (ttt) REVERT: C 211 LYS cc_start: 0.8516 (tppt) cc_final: 0.7316 (tmtt) REVERT: D 98 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8067 (mt) REVERT: D 207 ASP cc_start: 0.7906 (p0) cc_final: 0.7466 (p0) REVERT: F 241 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7442 (mm-30) outliers start: 44 outliers final: 35 residues processed: 220 average time/residue: 0.1344 time to fit residues: 44.0218 Evaluate side-chains 216 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 546 TRP Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 104 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 97 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 129 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 203 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.154681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.121812 restraints weight = 25251.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.121081 restraints weight = 33190.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.122500 restraints weight = 25847.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.123310 restraints weight = 15339.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.124085 restraints weight = 13220.682| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17440 Z= 0.193 Angle : 0.559 7.011 23699 Z= 0.293 Chirality : 0.043 0.153 2627 Planarity : 0.004 0.032 3146 Dihedral : 3.987 52.309 2435 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.71 % Favored : 96.20 % Rotamer: Outliers : 2.75 % Allowed : 21.01 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.18), residues: 2208 helix: 1.86 (0.19), residues: 753 sheet: 0.07 (0.22), residues: 534 loop : -1.23 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 79 TYR 0.020 0.002 TYR A 504 PHE 0.020 0.002 PHE F 109 TRP 0.010 0.001 TRP A 635 HIS 0.007 0.001 HIS F 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.19 (17435) covalent geometry : angle 0.55817 / 0.29 (23695) SS BOND : bond 0.00574 / 0.29 ( 2) SS BOND : angle 2.25025 / 1.22 ( 4) hydrogen bonds : bond 0.05664 / 3.85 ( 763) hydrogen bonds : angle 3.98424 / 2.80 ( 2214) metal coordination : bond 0.01263 / 0.62 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2709.62 seconds wall clock time: 47 minutes 25.17 seconds (2845.17 seconds total)