Starting phenix.real_space_refine on Fri Feb 6 12:08:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eg8_47986/02_2026/9eg8_47986.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eg8_47986/02_2026/9eg8_47986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9eg8_47986/02_2026/9eg8_47986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eg8_47986/02_2026/9eg8_47986.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9eg8_47986/02_2026/9eg8_47986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eg8_47986/02_2026/9eg8_47986.map" } resolution = 3.39 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= 0.005 sd= 0.023 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 3 6.06 5 S 144 5.16 5 C 15731 2.51 5 N 4243 2.21 5 O 4624 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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24745 Number of models: 1 Model: "" Number of chains: 12 Chain: "E" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2330 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 8, 'TRANS': 285} Chain breaks: 2 Chain: "I" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 599 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "J" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2754 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 329} Chain breaks: 2 Chain: "A" Number of atoms: 3271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3271 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 8, 'TRANS': 400} Chain breaks: 1 Chain: "B" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3342 Classifications: {'peptide': 408} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 396} Chain breaks: 1 Chain: "C" Number of atoms: 3222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3222 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 13, 'TRANS': 391} Chain: "D" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3241 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 9, 'TRANS': 395} Chain: "F" Number of atoms: 2229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2229 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain: "G" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1687 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 4, 'TRANS': 208} Chain: "H" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1374 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 161} Chain breaks: 1 Chain: "K" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 693 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain breaks: 1 Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 24341 SG CYS K 53 77.536 60.230 80.749 1.00 42.23 S ATOM 24364 SG CYS K 56 75.865 57.026 81.976 1.00 57.69 S ATOM 24410 SG CYS K 68 75.039 58.484 78.498 1.00 72.32 S ATOM 24255 SG CYS K 42 82.536 63.070 74.522 1.00 31.46 S ATOM 24274 SG CYS K 45 83.692 63.107 78.053 1.00 30.84 S ATOM 24460 SG CYS K 75 78.917 75.298 68.405 1.00 45.69 S ATOM 24627 SG CYS K 94 80.434 74.852 71.876 1.00 33.72 S Time building chain proxies: 5.74, per 1000 atoms: 0.23 Number of scatterers: 24745 At special positions: 0 Unit cell: (137.76, 162.12, 200.76, 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 3 29.99 S 144 16.00 O 4624 8.00 N 4243 7.00 C 15731 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" ND1 HIS K 82 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 53 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 68 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 56 " pdb=" ZN K 202 " pdb="ZN ZN K 202 " - pdb=" SG CYS K 45 " pdb="ZN ZN K 202 " - pdb=" ND1 HIS K 80 " pdb="ZN ZN K 202 " - pdb=" SG CYS K 42 " pdb=" ZN K 203 " pdb="ZN ZN K 203 " - pdb=" SG CYS K 94 " pdb="ZN ZN K 203 " - pdb=" ND1 HIS K 77 " pdb="ZN ZN K 203 " - pdb=" SG CYS K 75 " Number of angles added : 3 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5888 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 11 sheets defined 66.9% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'E' and resid 26 through 30 Processing helix chain 'E' and resid 32 through 43 Processing helix chain 'E' and resid 59 through 72 Processing helix chain 'E' and resid 111 through 128 removed outlier: 3.940A pdb=" N GLU E 115 " --> pdb=" O ALA E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 162 removed outlier: 3.661A pdb=" N SER E 153 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 179 Processing helix chain 'E' and resid 208 through 213 Processing helix chain 'E' and resid 231 through 240 removed outlier: 3.960A pdb=" N LEU E 240 " --> pdb=" O LYS E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 251 Processing helix chain 'E' and resid 258 through 281 Processing helix chain 'E' and resid 299 through 329 removed outlier: 3.646A pdb=" N ALA E 303 " --> pdb=" O LYS E 299 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 34 removed outlier: 3.645A pdb=" N ILE I 26 " --> pdb=" O LYS I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 41 removed outlier: 3.828A pdb=" N GLN I 41 " --> pdb=" O PRO I 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 410 through 418 Processing helix chain 'J' and resid 420 through 424 Processing helix chain 'J' and resid 426 through 441 removed outlier: 3.844A pdb=" N GLU J 430 " --> pdb=" O ASP J 426 " (cutoff:3.500A) Processing helix chain 'J' and resid 445 through 463 removed outlier: 3.822A pdb=" N PHE J 449 " --> pdb=" O GLY J 445 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL J 463 " --> pdb=" O LYS J 459 " (cutoff:3.500A) Processing helix chain 'J' and resid 468 through 481 removed outlier: 3.593A pdb=" N GLU J 472 " --> pdb=" O SER J 468 " (cutoff:3.500A) Processing helix chain 'J' and resid 484 through 489 removed outlier: 3.569A pdb=" N THR J 488 " --> pdb=" O GLY J 484 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER J 489 " --> pdb=" O ALA J 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 484 through 489' Processing helix chain 'J' and resid 489 through 515 Processing helix chain 'J' and resid 544 through 562 removed outlier: 3.628A pdb=" N ILE J 548 " --> pdb=" O THR J 544 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS J 549 " --> pdb=" O PRO J 545 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU J 550 " --> pdb=" O GLU J 546 " (cutoff:3.500A) Processing helix chain 'J' and resid 593 through 604 removed outlier: 3.886A pdb=" N GLU J 604 " --> pdb=" O LEU J 600 " (cutoff:3.500A) Processing helix chain 'J' and resid 609 through 618 Processing helix chain 'J' and resid 620 through 630 removed outlier: 3.705A pdb=" N SER J 630 " --> pdb=" O ARG J 626 " (cutoff:3.500A) Processing helix chain 'J' and resid 633 through 637 removed outlier: 3.952A pdb=" N ARG J 637 " --> pdb=" O GLY J 634 " (cutoff:3.500A) Processing helix chain 'J' and resid 670 through 674 removed outlier: 4.244A pdb=" N GLN J 673 " --> pdb=" O ASN J 670 " (cutoff:3.500A) Processing helix chain 'J' and resid 690 through 704 Processing helix chain 'J' and resid 712 through 723 Processing helix chain 'J' and resid 728 through 742 removed outlier: 3.504A pdb=" N LEU J 732 " --> pdb=" O LYS J 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.987A pdb=" N ALA A 49 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 65 removed outlier: 4.146A pdb=" N ILE A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 removed outlier: 4.454A pdb=" N ALA A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 102 Processing helix chain 'A' and resid 128 through 156 Processing helix chain 'A' and resid 157 through 174 Processing helix chain 'A' and resid 178 through 188 Processing helix chain 'A' and resid 189 through 191 No H-bonds generated for 'chain 'A' and resid 189 through 191' Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.767A pdb=" N TYR A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 228 Processing helix chain 'A' and resid 229 through 234 Processing helix chain 'A' and resid 238 through 243 removed outlier: 3.963A pdb=" N THR A 242 " --> pdb=" O ARG A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 260 removed outlier: 4.482A pdb=" N LYS A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 271 removed outlier: 3.536A pdb=" N CYS A 269 " --> pdb=" O GLN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 removed outlier: 3.579A pdb=" N CYS A 278 " --> pdb=" O PHE A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 301 removed outlier: 4.072A pdb=" N ALA A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 Processing helix chain 'A' and resid 314 through 323 removed outlier: 4.213A pdb=" N LEU A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU A 323 " --> pdb=" O PHE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 335 removed outlier: 3.760A pdb=" N ARG A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 355 removed outlier: 4.425A pdb=" N ASP A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASN A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 379 removed outlier: 4.543A pdb=" N ARG A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N THR A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 393 Processing helix chain 'A' and resid 396 through 410 Processing helix chain 'A' and resid 430 through 463 removed outlier: 3.693A pdb=" N LEU A 455 " --> pdb=" O LYS A 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 4.083A pdb=" N TYR B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR B 37 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 42 " --> pdb=" O ASN B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 60 Processing helix chain 'B' and resid 65 through 82 removed outlier: 3.623A pdb=" N PHE B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 99 removed outlier: 3.611A pdb=" N MET B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 121 Processing helix chain 'B' and resid 124 through 142 removed outlier: 3.565A pdb=" N LEU B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 163 removed outlier: 3.513A pdb=" N ARG B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 180 Processing helix chain 'B' and resid 190 through 209 removed outlier: 3.745A pdb=" N LEU B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 207 " --> pdb=" O GLN B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 222 Processing helix chain 'B' and resid 230 through 249 removed outlier: 3.568A pdb=" N CYS B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY B 241 " --> pdb=" O ILE B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 268 removed outlier: 3.823A pdb=" N GLU B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER B 268 " --> pdb=" O ASN B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 Processing helix chain 'B' and resid 292 through 296 removed outlier: 3.824A pdb=" N SER B 296 " --> pdb=" O PRO B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 305 removed outlier: 4.242A pdb=" N ASN B 304 " --> pdb=" O PRO B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 319 Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 352 through 363 Processing helix chain 'B' and resid 371 through 379 Processing helix chain 'B' and resid 381 through 395 Processing helix chain 'B' and resid 418 through 440 removed outlier: 3.748A pdb=" N THR B 422 " --> pdb=" O GLY B 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 18 Processing helix chain 'C' and resid 20 through 32 Processing helix chain 'C' and resid 45 through 51 removed outlier: 3.873A pdb=" N LEU C 49 " --> pdb=" O VAL C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 66 removed outlier: 3.799A pdb=" N VAL C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 87 Processing helix chain 'C' and resid 91 through 96 removed outlier: 3.858A pdb=" N ARG C 94 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 109 removed outlier: 3.931A pdb=" N GLY C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 132 removed outlier: 3.675A pdb=" N LYS C 125 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS C 130 " --> pdb=" O GLN C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 152 removed outlier: 4.189A pdb=" N ALA C 143 " --> pdb=" O THR C 139 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 164 removed outlier: 4.225A pdb=" N VAL C 164 " --> pdb=" O PRO C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 177 through 195 removed outlier: 3.762A pdb=" N PHE C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY C 189 " --> pdb=" O TYR C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 210 Processing helix chain 'C' and resid 217 through 235 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.612A pdb=" N LEU C 256 " --> pdb=" O PHE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 269 Processing helix chain 'C' and resid 271 through 282 removed outlier: 3.709A pdb=" N ARG C 276 " --> pdb=" O PRO C 272 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN C 277 " --> pdb=" O SER C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 289 removed outlier: 3.506A pdb=" N PHE C 286 " --> pdb=" O HIS C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 312 removed outlier: 4.036A pdb=" N TYR C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS C 304 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 326 Processing helix chain 'C' and resid 330 through 345 Processing helix chain 'C' and resid 369 through 398 removed outlier: 3.723A pdb=" N LEU C 373 " --> pdb=" O ASN C 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 14 removed outlier: 3.518A pdb=" N LEU D 9 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA D 10 " --> pdb=" O ARG D 6 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN D 11 " --> pdb=" O GLN D 7 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET D 13 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN D 14 " --> pdb=" O ALA D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 35 removed outlier: 4.135A pdb=" N ALA D 23 " --> pdb=" O HIS D 19 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN D 35 " --> pdb=" O GLU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 53 Processing helix chain 'D' and resid 58 through 73 Processing helix chain 'D' and resid 77 through 92 Processing helix chain 'D' and resid 93 through 96 removed outlier: 3.500A pdb=" N VAL D 96 " --> pdb=" O GLN D 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 93 through 96' Processing helix chain 'D' and resid 99 through 117 removed outlier: 3.526A pdb=" N VAL D 103 " --> pdb=" O PHE D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 129 removed outlier: 3.689A pdb=" N GLN D 125 " --> pdb=" O ARG D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 157 Processing helix chain 'D' and resid 160 through 176 removed outlier: 3.903A pdb=" N LEU D 174 " --> pdb=" O ARG D 170 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASN D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 198 removed outlier: 3.608A pdb=" N ILE D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 213 removed outlier: 3.719A pdb=" N TYR D 213 " --> pdb=" O ASN D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 236 Processing helix chain 'D' and resid 239 through 251 removed outlier: 3.513A pdb=" N SER D 243 " --> pdb=" O GLY D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.775A pdb=" N GLN D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 269 removed outlier: 3.694A pdb=" N LEU D 269 " --> pdb=" O GLU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 280 removed outlier: 4.029A pdb=" N GLU D 280 " --> pdb=" O GLN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 285 removed outlier: 3.545A pdb=" N LEU D 285 " --> pdb=" O ALA D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 291 removed outlier: 3.560A pdb=" N LYS D 290 " --> pdb=" O PRO D 287 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA D 291 " --> pdb=" O HIS D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 313 Processing helix chain 'D' and resid 321 through 329 Processing helix chain 'D' and resid 334 through 343 Processing helix chain 'D' and resid 366 through 392 Processing helix chain 'D' and resid 392 through 405 removed outlier: 3.501A pdb=" N ALA D 405 " --> pdb=" O GLU D 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 63 Processing helix chain 'F' and resid 102 through 113 removed outlier: 3.635A pdb=" N LYS F 113 " --> pdb=" O GLU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 143 Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 215 through 248 removed outlier: 3.520A pdb=" N GLU F 219 " --> pdb=" O SER F 215 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN F 224 " --> pdb=" O HIS F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 265 removed outlier: 3.593A pdb=" N ARG F 258 " --> pdb=" O HIS F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 313 removed outlier: 4.164A pdb=" N GLY F 293 " --> pdb=" O MET F 289 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR F 296 " --> pdb=" O LEU F 292 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS F 297 " --> pdb=" O GLY F 293 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL F 311 " --> pdb=" O ASN F 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 20 removed outlier: 3.743A pdb=" N PHE G 15 " --> pdb=" O LEU G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 37 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 49 through 55 Processing helix chain 'G' and resid 60 through 72 removed outlier: 3.920A pdb=" N LEU G 64 " --> pdb=" O ASN G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 81 removed outlier: 3.650A pdb=" N ASN G 81 " --> pdb=" O ASP G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 108 removed outlier: 3.595A pdb=" N ARG G 107 " --> pdb=" O SER G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 121 Processing helix chain 'G' and resid 124 through 138 removed outlier: 3.505A pdb=" N THR G 138 " --> pdb=" O GLU G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 165 No H-bonds generated for 'chain 'G' and resid 163 through 165' Processing helix chain 'G' and resid 166 through 222 removed outlier: 3.542A pdb=" N ILE G 170 " --> pdb=" O ASP G 166 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU G 212 " --> pdb=" O GLN G 208 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL G 213 " --> pdb=" O VAL G 209 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN G 215 " --> pdb=" O ALA G 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 26 Processing helix chain 'H' and resid 33 through 47 Processing helix chain 'H' and resid 49 through 60 Processing helix chain 'H' and resid 61 through 68 removed outlier: 3.961A pdb=" N ASN H 68 " --> pdb=" O ILE H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 83 removed outlier: 4.235A pdb=" N GLY H 72 " --> pdb=" O ASN H 68 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN H 83 " --> pdb=" O GLN H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 93 Processing helix chain 'H' and resid 99 through 101 No H-bonds generated for 'chain 'H' and resid 99 through 101' Processing helix chain 'H' and resid 102 through 124 removed outlier: 3.849A pdb=" N GLU H 107 " --> pdb=" O GLN H 103 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA H 108 " --> pdb=" O PRO H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 138 Processing helix chain 'H' and resid 140 through 152 Processing helix chain 'H' and resid 196 through 209 removed outlier: 3.607A pdb=" N ASN H 209 " --> pdb=" O ALA H 205 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 60 Processing helix chain 'K' and resid 81 through 91 removed outlier: 3.811A pdb=" N THR K 90 " --> pdb=" O ARG K 86 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 221 through 223 removed outlier: 8.139A pdb=" N VAL E 168 " --> pdb=" O ILE E 134 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TRP E 136 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ILE E 170 " --> pdb=" O TRP E 136 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N HIS E 138 " --> pdb=" O ILE E 170 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ALA E 133 " --> pdb=" O GLY E 83 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLY E 83 " --> pdb=" O ALA E 133 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N MET E 78 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ALA E 97 " --> pdb=" O MET E 78 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU E 80 " --> pdb=" O SER E 95 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N SER E 95 " --> pdb=" O LEU E 80 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU E 82 " --> pdb=" O MET E 93 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TYR E 54 " --> pdb=" O MET E 90 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE E 92 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LYS E 56 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ASP E 94 " --> pdb=" O LYS E 56 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N SER E 58 " --> pdb=" O ASP E 94 " (cutoff:3.500A) removed outlier: 10.985A pdb=" N PHE E 96 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N CYS E 55 " --> pdb=" O SER E 227 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N PHE E 229 " --> pdb=" O CYS E 55 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE E 57 " --> pdb=" O PHE E 229 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 12 through 15 removed outlier: 6.739A pdb=" N LYS I 4 " --> pdb=" O LEU I 67 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU I 69 " --> pdb=" O LYS I 4 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LYS I 6 " --> pdb=" O LEU I 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 522 through 525 removed outlier: 5.916A pdb=" N ASP J 522 " --> pdb=" O TRP K 27 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ALA K 29 " --> pdb=" O ASP J 522 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N THR J 524 " --> pdb=" O ALA K 29 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL J 577 " --> pdb=" O LYS K 25 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TRP K 27 " --> pdb=" O HIS J 575 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N HIS J 575 " --> pdb=" O TRP K 27 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ALA K 29 " --> pdb=" O LEU J 573 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N LEU J 573 " --> pdb=" O ALA K 29 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 528 through 529 removed outlier: 6.628A pdb=" N LEU J 528 " --> pdb=" O TRP K 33 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'J' and resid 710 through 711 Processing sheet with id=AA6, first strand: chain 'D' and resid 318 through 320 removed outlier: 7.048A pdb=" N THR B 367 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL A 382 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU C 315 " --> pdb=" O ALA A 415 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL A 417 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU C 317 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE C 351 " --> pdb=" O THR H 126 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE H 128 " --> pdb=" O ILE C 351 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 40 through 43 removed outlier: 5.907A pdb=" N SER F 40 " --> pdb=" O ILE F 81 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL F 83 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ALA F 42 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ASN F 85 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE F 73 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER F 86 " --> pdb=" O ALA F 71 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA F 71 " --> pdb=" O SER F 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AA9, first strand: chain 'F' and resid 123 through 127 removed outlier: 6.611A pdb=" N TRP F 124 " --> pdb=" O LEU F 152 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N LEU F 154 " --> pdb=" O TRP F 124 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR F 126 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL F 167 " --> pdb=" O LEU F 186 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 110 through 112 removed outlier: 6.835A pdb=" N GLN G 142 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 72 through 73 removed outlier: 3.738A pdb=" N GLN K 104 " --> pdb=" O TRP K 72 " (cutoff:3.500A) 1440 hydrogen bonds defined for protein. 4200 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: 4.58 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6910 1.33 - 1.46: 4463 1.46 - 1.58: 13577 1.58 - 1.70: 0 1.70 - 1.82: 235 Bond restraints: 25185 Sorted by residual: bond pdb=" CA ASP B 266 " pdb=" C ASP B 266 " ideal model delta sigma weight residual 1.524 1.487 0.037 1.24e-02 6.50e+03 8.80e+00 bond pdb=" CA SER B 270 " pdb=" C SER B 270 " ideal model delta sigma weight residual 1.524 1.496 0.028 1.26e-02 6.30e+03 5.03e+00 bond pdb=" N LEU D 45 " pdb=" CA LEU D 45 " ideal model delta sigma weight residual 1.459 1.433 0.026 1.21e-02 6.83e+03 4.71e+00 bond pdb=" N ASP B 266 " pdb=" CA ASP B 266 " ideal model delta sigma weight residual 1.459 1.434 0.025 1.17e-02 7.31e+03 4.62e+00 bond pdb=" CA LEU B 72 " pdb=" C LEU B 72 " ideal model delta sigma weight residual 1.524 1.498 0.027 1.28e-02 6.10e+03 4.41e+00 ... (remaining 25180 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 33652 2.65 - 5.30: 271 5.30 - 7.94: 34 7.94 - 10.59: 10 10.59 - 13.24: 1 Bond angle restraints: 33968 Sorted by residual: angle pdb=" CB MET F 181 " pdb=" CG MET F 181 " pdb=" SD MET F 181 " ideal model delta sigma weight residual 112.70 125.94 -13.24 3.00e+00 1.11e-01 1.95e+01 angle pdb=" C THR A 85 " pdb=" N PHE A 86 " pdb=" CA PHE A 86 " ideal model delta sigma weight residual 121.54 128.94 -7.40 1.91e+00 2.74e-01 1.50e+01 angle pdb=" N ILE B 343 " pdb=" CA ILE B 343 " pdb=" C ILE B 343 " ideal model delta sigma weight residual 111.81 108.69 3.12 8.60e-01 1.35e+00 1.32e+01 angle pdb=" N THR A 128 " pdb=" CA THR A 128 " pdb=" C THR A 128 " ideal model delta sigma weight residual 114.56 110.09 4.47 1.27e+00 6.20e-01 1.24e+01 angle pdb=" C CYS K 53 " pdb=" N ILE K 54 " pdb=" CA ILE K 54 " ideal model delta sigma weight residual 121.97 128.24 -6.27 1.80e+00 3.09e-01 1.21e+01 ... (remaining 33963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 12699 17.96 - 35.91: 1972 35.91 - 53.87: 573 53.87 - 71.83: 112 71.83 - 89.78: 38 Dihedral angle restraints: 15394 sinusoidal: 6321 harmonic: 9073 Sorted by residual: dihedral pdb=" CA LEU D 73 " pdb=" C LEU D 73 " pdb=" N PRO D 74 " pdb=" CA PRO D 74 " ideal model delta harmonic sigma weight residual -180.00 -154.04 -25.96 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA GLY F 293 " pdb=" C GLY F 293 " pdb=" N THR F 294 " pdb=" CA THR F 294 " ideal model delta harmonic sigma weight residual 180.00 160.09 19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA ILE D 330 " pdb=" C ILE D 330 " pdb=" N PRO D 331 " pdb=" CA PRO D 331 " ideal model delta harmonic sigma weight residual -180.00 -161.98 -18.02 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 15391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2928 0.043 - 0.086: 702 0.086 - 0.130: 176 0.130 - 0.173: 10 0.173 - 0.216: 2 Chirality restraints: 3818 Sorted by residual: chirality pdb=" CG LEU A 149 " pdb=" CB LEU A 149 " pdb=" CD1 LEU A 149 " pdb=" CD2 LEU A 149 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CG LEU A 75 " pdb=" CB LEU A 75 " pdb=" CD1 LEU A 75 " pdb=" CD2 LEU A 75 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB VAL G 213 " pdb=" CA VAL G 213 " pdb=" CG1 VAL G 213 " pdb=" CG2 VAL G 213 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.07e-01 ... (remaining 3815 not shown) Planarity restraints: 4342 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 92 " 0.036 2.00e-02 2.50e+03 3.44e-02 2.37e+01 pdb=" CG TYR B 92 " -0.081 2.00e-02 2.50e+03 pdb=" CD1 TYR B 92 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR B 92 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 92 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR B 92 " 0.022 2.00e-02 2.50e+03 pdb=" CZ TYR B 92 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 92 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 67 " 0.017 2.00e-02 2.50e+03 1.48e-02 5.50e+00 pdb=" CG TRP B 67 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP B 67 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 67 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 67 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 67 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 67 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 67 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 67 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 67 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN G 190 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" C GLN G 190 " 0.037 2.00e-02 2.50e+03 pdb=" O GLN G 190 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN G 191 " -0.012 2.00e-02 2.50e+03 ... (remaining 4339 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 9 2.55 - 3.14: 19674 3.14 - 3.73: 39230 3.73 - 4.31: 50407 4.31 - 4.90: 84313 Nonbonded interactions: 193633 Sorted by model distance: nonbonded pdb=" OD2 ASP K 97 " pdb="ZN ZN K 203 " model vdw 1.966 2.230 nonbonded pdb=" OD1 ASP K 97 " pdb="ZN ZN K 203 " model vdw 2.000 2.230 nonbonded pdb=" CG ASP K 97 " pdb="ZN ZN K 203 " model vdw 2.168 2.460 nonbonded pdb=" O TYR A 91 " pdb=" CB HIS A 95 " model vdw 2.502 2.752 nonbonded pdb=" O SER H 157 " pdb=" OG1 THR H 158 " model vdw 2.503 3.040 ... (remaining 193628 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.130 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: 0.610 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 26.050 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 25196 Z= 0.157 Angle : 0.609 13.238 33971 Z= 0.324 Chirality : 0.039 0.216 3818 Planarity : 0.004 0.052 4342 Dihedral : 19.009 89.784 9506 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.58 % Favored : 94.12 % Rotamer: Outliers : 2.66 % Allowed : 29.31 % Favored : 68.02 % 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 (0.16), residues: 3044 helix: 1.40 (0.12), residues: 1887 sheet: -0.48 (0.43), residues: 157 loop : -1.98 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 84 TYR 0.081 0.001 TYR B 92 PHE 0.024 0.001 PHE J 656 TRP 0.040 0.001 TRP B 67 HIS 0.009 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00277 (25185) covalent geometry : angle 0.60930 (33968) hydrogen bonds : bond 0.13013 ( 1440) hydrogen bonds : angle 5.85094 ( 4200) metal coordination : bond 0.01197 ( 10) metal coordination : angle 1.63574 ( 3) Misc. bond : bond 0.09647 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 302 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 193 TYR cc_start: 0.6991 (OUTLIER) cc_final: 0.6415 (t80) REVERT: E 194 LYS cc_start: 0.6903 (OUTLIER) cc_final: 0.6228 (mtmm) REVERT: E 213 ASP cc_start: 0.7246 (p0) cc_final: 0.6215 (p0) REVERT: I 14 GLU cc_start: 0.6774 (mm-30) cc_final: 0.6203 (mm-30) REVERT: J 425 THR cc_start: 0.6183 (OUTLIER) cc_final: 0.5822 (p) REVERT: J 475 MET cc_start: 0.7803 (tpp) cc_final: 0.7422 (tpt) REVERT: J 662 HIS cc_start: 0.6256 (OUTLIER) cc_final: 0.5259 (t70) REVERT: J 704 MET cc_start: 0.8327 (mmt) cc_final: 0.7531 (mmt) REVERT: A 183 LYS cc_start: 0.9199 (mmtt) cc_final: 0.8647 (ptmt) REVERT: A 361 HIS cc_start: 0.7648 (m-70) cc_final: 0.7434 (m-70) REVERT: B 61 GLU cc_start: 0.7935 (pp20) cc_final: 0.7579 (tm-30) REVERT: C 109 ASN cc_start: 0.7912 (OUTLIER) cc_final: 0.7458 (m-40) REVERT: C 214 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.6934 (ppp) REVERT: C 237 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7100 (pttm) REVERT: H 128 ILE cc_start: 0.7986 (tp) cc_final: 0.7619 (tt) outliers start: 72 outliers final: 45 residues processed: 353 average time/residue: 0.1772 time to fit residues: 98.4827 Evaluate side-chains 349 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 297 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 193 TYR Chi-restraints excluded: chain E residue 194 LYS Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain J residue 425 THR Chi-restraints excluded: chain J residue 437 MET Chi-restraints excluded: chain J residue 440 PHE Chi-restraints excluded: chain J residue 483 CYS Chi-restraints excluded: chain J residue 525 VAL Chi-restraints excluded: chain J residue 543 LEU Chi-restraints excluded: chain J residue 662 HIS Chi-restraints excluded: chain J residue 717 SER Chi-restraints excluded: chain J residue 727 VAL Chi-restraints excluded: chain J residue 741 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 162 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.0970 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.0040 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 HIS C 369 ASN ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS F 141 GLN H 22 ASN ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.123506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.097025 restraints weight = 61299.801| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.81 r_work: 0.3416 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 25196 Z= 0.154 Angle : 0.555 9.987 33971 Z= 0.285 Chirality : 0.040 0.276 3818 Planarity : 0.003 0.049 4342 Dihedral : 6.093 63.434 3411 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.49 % Favored : 94.22 % Rotamer: Outliers : 4.37 % Allowed : 27.17 % Favored : 68.47 % 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: 0.73 (0.16), residues: 3044 helix: 1.77 (0.12), residues: 1909 sheet: -0.63 (0.43), residues: 162 loop : -2.02 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 84 TYR 0.029 0.001 TYR B 92 PHE 0.017 0.001 PHE J 554 TRP 0.013 0.001 TRP B 67 HIS 0.006 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00337 (25185) covalent geometry : angle 0.55475 (33968) hydrogen bonds : bond 0.04547 ( 1440) hydrogen bonds : angle 4.46783 ( 4200) metal coordination : bond 0.02085 ( 10) metal coordination : angle 2.17791 ( 3) Misc. bond : bond 0.00088 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 299 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 213 ASP cc_start: 0.7441 (p0) cc_final: 0.7186 (p0) REVERT: E 242 TRP cc_start: 0.5950 (t-100) cc_final: 0.4966 (m-10) REVERT: I 14 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6502 (mm-30) REVERT: I 28 GLU cc_start: 0.7281 (pp20) cc_final: 0.7064 (pp20) REVERT: I 29 ARG cc_start: 0.7361 (mmp80) cc_final: 0.7149 (mmp80) REVERT: J 425 THR cc_start: 0.6304 (OUTLIER) cc_final: 0.5875 (p) REVERT: J 494 MET cc_start: 0.8128 (mtm) cc_final: 0.7911 (mtt) REVERT: J 662 HIS cc_start: 0.6535 (OUTLIER) cc_final: 0.5686 (t70) REVERT: J 733 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7595 (tptm) REVERT: A 183 LYS cc_start: 0.9189 (mmtt) cc_final: 0.8659 (ttpt) REVERT: A 201 MET cc_start: 0.5948 (tpt) cc_final: 0.5711 (ptt) REVERT: C 109 ASN cc_start: 0.8042 (OUTLIER) cc_final: 0.7579 (m-40) REVERT: D 328 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8071 (pp) REVERT: H 128 ILE cc_start: 0.7831 (tp) cc_final: 0.7453 (tt) REVERT: H 149 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7944 (tp) outliers start: 118 outliers final: 71 residues processed: 390 average time/residue: 0.1695 time to fit residues: 105.5939 Evaluate side-chains 368 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 291 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain J residue 425 THR Chi-restraints excluded: chain J residue 437 MET Chi-restraints excluded: chain J residue 483 CYS Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 537 THR Chi-restraints excluded: chain J residue 543 LEU Chi-restraints excluded: chain J residue 544 THR Chi-restraints excluded: chain J residue 559 LEU Chi-restraints excluded: chain J residue 575 HIS Chi-restraints excluded: chain J residue 628 LEU Chi-restraints excluded: chain J residue 662 HIS Chi-restraints excluded: chain J residue 727 VAL Chi-restraints excluded: chain J residue 733 LYS Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 50 MET Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 60 GLN Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 84 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 131 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 211 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 210 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS E 182 ASN ** I 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN B 255 HIS ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 HIS ** C 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 GLN ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS F 141 GLN F 202 HIS ** H 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.121167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.094668 restraints weight = 61204.882| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.96 r_work: 0.3364 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 25196 Z= 0.217 Angle : 0.605 10.429 33971 Z= 0.307 Chirality : 0.042 0.219 3818 Planarity : 0.004 0.048 4342 Dihedral : 5.496 79.415 3358 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.98 % Favored : 93.73 % Rotamer: Outliers : 5.85 % Allowed : 26.20 % Favored : 67.95 % 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: 0.63 (0.16), residues: 3044 helix: 1.69 (0.12), residues: 1899 sheet: -0.57 (0.42), residues: 157 loop : -2.05 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 165 TYR 0.047 0.002 TYR B 92 PHE 0.022 0.002 PHE F 87 TRP 0.019 0.002 TRP B 67 HIS 0.006 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00518 (25185) covalent geometry : angle 0.60407 (33968) hydrogen bonds : bond 0.04738 ( 1440) hydrogen bonds : angle 4.37749 ( 4200) metal coordination : bond 0.02265 ( 10) metal coordination : angle 2.58932 ( 3) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 292 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 213 ASP cc_start: 0.7590 (p0) cc_final: 0.6877 (p0) REVERT: J 425 THR cc_start: 0.6540 (OUTLIER) cc_final: 0.6142 (p) REVERT: J 667 ILE cc_start: 0.7905 (mm) cc_final: 0.7624 (mt) REVERT: J 733 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.7705 (tptm) REVERT: J 735 ARG cc_start: 0.7951 (mmm160) cc_final: 0.7460 (mmp-170) REVERT: A 90 MET cc_start: 0.6470 (pmm) cc_final: 0.6256 (pmm) REVERT: A 170 ASP cc_start: 0.8154 (m-30) cc_final: 0.7925 (m-30) REVERT: A 183 LYS cc_start: 0.9175 (mmtt) cc_final: 0.8620 (ttpt) REVERT: A 201 MET cc_start: 0.6039 (tpt) cc_final: 0.5671 (ptm) REVERT: B 67 TRP cc_start: 0.8203 (m100) cc_final: 0.7996 (m100) REVERT: C 109 ASN cc_start: 0.8014 (OUTLIER) cc_final: 0.7583 (m-40) REVERT: C 214 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7150 (ppp) REVERT: D 12 LEU cc_start: 0.7167 (tp) cc_final: 0.6942 (tt) REVERT: F 168 PHE cc_start: 0.7680 (m-10) cc_final: 0.7447 (m-10) REVERT: F 206 MET cc_start: 0.6541 (mtp) cc_final: 0.5935 (mtp) REVERT: H 128 ILE cc_start: 0.7956 (tp) cc_final: 0.7627 (tt) outliers start: 158 outliers final: 107 residues processed: 409 average time/residue: 0.1728 time to fit residues: 112.5089 Evaluate side-chains 393 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 282 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 22 LYS Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain J residue 425 THR Chi-restraints excluded: chain J residue 437 MET Chi-restraints excluded: chain J residue 440 PHE Chi-restraints excluded: chain J residue 462 LEU Chi-restraints excluded: chain J residue 483 CYS Chi-restraints excluded: chain J residue 488 THR Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 525 VAL Chi-restraints excluded: chain J residue 537 THR Chi-restraints excluded: chain J residue 544 THR Chi-restraints excluded: chain J residue 559 LEU Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 601 MET Chi-restraints excluded: chain J residue 628 LEU Chi-restraints excluded: chain J residue 662 HIS Chi-restraints excluded: chain J residue 727 VAL Chi-restraints excluded: chain J residue 733 LYS Chi-restraints excluded: chain J residue 741 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 69 PHE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 183 PHE Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 60 GLN Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 75 CYS Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 93 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 177 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 216 optimal weight: 0.7980 chunk 188 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 229 optimal weight: 0.3980 chunk 29 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 185 optimal weight: 0.8980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS E 159 GLN J 662 HIS ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 GLN ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.121941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.095619 restraints weight = 60943.806| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.83 r_work: 0.3386 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 25196 Z= 0.155 Angle : 0.550 9.915 33971 Z= 0.279 Chirality : 0.040 0.222 3818 Planarity : 0.003 0.049 4342 Dihedral : 5.382 82.113 3353 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.65 % Favored : 94.05 % Rotamer: Outliers : 5.29 % Allowed : 26.76 % Favored : 67.95 % 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: 0.75 (0.16), residues: 3044 helix: 1.83 (0.12), residues: 1893 sheet: -0.77 (0.42), residues: 159 loop : -2.02 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 456 TYR 0.026 0.001 TYR B 92 PHE 0.020 0.001 PHE B 69 TRP 0.010 0.001 TRP F 124 HIS 0.007 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00363 (25185) covalent geometry : angle 0.54930 (33968) hydrogen bonds : bond 0.04134 ( 1440) hydrogen bonds : angle 4.21510 ( 4200) metal coordination : bond 0.01977 ( 10) metal coordination : angle 2.80491 ( 3) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 295 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 194 LYS cc_start: 0.7024 (OUTLIER) cc_final: 0.6354 (mtmm) REVERT: E 213 ASP cc_start: 0.7614 (p0) cc_final: 0.7376 (p0) REVERT: I 14 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6800 (mm-30) REVERT: J 425 THR cc_start: 0.6419 (OUTLIER) cc_final: 0.6003 (p) REVERT: J 733 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7656 (tptm) REVERT: J 735 ARG cc_start: 0.7909 (mmm160) cc_final: 0.7421 (mmp-170) REVERT: A 51 TYR cc_start: 0.4155 (OUTLIER) cc_final: 0.2860 (m-80) REVERT: A 160 SER cc_start: 0.4869 (OUTLIER) cc_final: 0.4433 (p) REVERT: A 183 LYS cc_start: 0.9150 (mmtt) cc_final: 0.8624 (ttpt) REVERT: A 357 TYR cc_start: 0.6215 (OUTLIER) cc_final: 0.5731 (t80) REVERT: B 67 TRP cc_start: 0.8137 (m100) cc_final: 0.7909 (m100) REVERT: B 109 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8372 (tt0) REVERT: C 109 ASN cc_start: 0.7983 (OUTLIER) cc_final: 0.7578 (m-40) REVERT: C 214 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7423 (ppp) REVERT: D 13 MET cc_start: 0.6596 (tmm) cc_final: 0.6357 (tmm) REVERT: F 168 PHE cc_start: 0.7688 (m-80) cc_final: 0.7400 (m-10) REVERT: F 206 MET cc_start: 0.6567 (mtp) cc_final: 0.6103 (mtp) REVERT: G 144 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8319 (mtmt) REVERT: H 128 ILE cc_start: 0.8041 (tp) cc_final: 0.7726 (tt) outliers start: 143 outliers final: 99 residues processed: 400 average time/residue: 0.1623 time to fit residues: 103.5754 Evaluate side-chains 391 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 282 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 194 LYS Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain J residue 425 THR Chi-restraints excluded: chain J residue 440 PHE Chi-restraints excluded: chain J residue 488 THR Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 537 THR Chi-restraints excluded: chain J residue 543 LEU Chi-restraints excluded: chain J residue 544 THR Chi-restraints excluded: chain J residue 559 LEU Chi-restraints excluded: chain J residue 628 LEU Chi-restraints excluded: chain J residue 662 HIS Chi-restraints excluded: chain J residue 733 LYS Chi-restraints excluded: chain J residue 741 ASP Chi-restraints excluded: chain J residue 743 ASP Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 69 PHE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 144 LYS Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 60 GLN Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 75 CYS Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 93 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 181 optimal weight: 7.9990 chunk 295 optimal weight: 6.9990 chunk 199 optimal weight: 4.9990 chunk 179 optimal weight: 0.7980 chunk 69 optimal weight: 30.0000 chunk 258 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 275 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 206 optimal weight: 0.0980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 568 GLN B 84 ASN B 435 ASN ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 ASN ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.122625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.096214 restraints weight = 60715.013| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.78 r_work: 0.3411 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 25196 Z= 0.128 Angle : 0.542 11.379 33971 Z= 0.272 Chirality : 0.039 0.210 3818 Planarity : 0.003 0.049 4342 Dihedral : 5.165 82.542 3348 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.65 % Favored : 94.02 % Rotamer: Outliers : 5.03 % Allowed : 27.13 % Favored : 67.84 % 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: 0.91 (0.16), residues: 3044 helix: 1.97 (0.12), residues: 1887 sheet: -0.59 (0.42), residues: 154 loop : -1.98 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 204 TYR 0.024 0.001 TYR B 92 PHE 0.022 0.001 PHE B 69 TRP 0.010 0.001 TRP K 33 HIS 0.007 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00292 (25185) covalent geometry : angle 0.54123 (33968) hydrogen bonds : bond 0.03840 ( 1440) hydrogen bonds : angle 4.09141 ( 4200) metal coordination : bond 0.01725 ( 10) metal coordination : angle 2.72415 ( 3) Misc. bond : bond 0.00031 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 290 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 194 LYS cc_start: 0.6993 (OUTLIER) cc_final: 0.6313 (mtmm) REVERT: E 213 ASP cc_start: 0.7516 (p0) cc_final: 0.7282 (p0) REVERT: I 14 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6717 (mm-30) REVERT: J 425 THR cc_start: 0.6393 (OUTLIER) cc_final: 0.6086 (p) REVERT: J 479 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8348 (mp) REVERT: J 733 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7641 (tptm) REVERT: J 735 ARG cc_start: 0.7900 (mmm160) cc_final: 0.7459 (mmp-170) REVERT: A 51 TYR cc_start: 0.4219 (OUTLIER) cc_final: 0.2978 (m-80) REVERT: A 86 PHE cc_start: 0.3656 (OUTLIER) cc_final: 0.2207 (p90) REVERT: A 90 MET cc_start: 0.6150 (pmm) cc_final: 0.5699 (pmm) REVERT: A 160 SER cc_start: 0.4637 (OUTLIER) cc_final: 0.4267 (p) REVERT: A 183 LYS cc_start: 0.9143 (mmtt) cc_final: 0.8585 (ptmt) REVERT: A 201 MET cc_start: 0.5920 (ptm) cc_final: 0.5564 (tpt) REVERT: A 357 TYR cc_start: 0.6146 (OUTLIER) cc_final: 0.5657 (t80) REVERT: B 67 TRP cc_start: 0.8085 (m100) cc_final: 0.7824 (m100) REVERT: B 109 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8453 (tt0) REVERT: C 80 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7568 (tp40) REVERT: C 109 ASN cc_start: 0.7931 (OUTLIER) cc_final: 0.7561 (m-40) REVERT: C 214 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7496 (ppp) REVERT: D 13 MET cc_start: 0.6851 (tmm) cc_final: 0.6575 (tmm) REVERT: F 168 PHE cc_start: 0.7706 (m-80) cc_final: 0.7382 (m-10) REVERT: F 206 MET cc_start: 0.6484 (mtp) cc_final: 0.6075 (mtp) REVERT: H 128 ILE cc_start: 0.8146 (tp) cc_final: 0.7836 (tt) REVERT: H 165 ARG cc_start: 0.7613 (ptt-90) cc_final: 0.7101 (ptp90) outliers start: 136 outliers final: 96 residues processed: 388 average time/residue: 0.1752 time to fit residues: 107.4473 Evaluate side-chains 384 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 276 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 194 LYS Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain J residue 425 THR Chi-restraints excluded: chain J residue 440 PHE Chi-restraints excluded: chain J residue 462 LEU Chi-restraints excluded: chain J residue 479 LEU Chi-restraints excluded: chain J residue 488 THR Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 525 VAL Chi-restraints excluded: chain J residue 543 LEU Chi-restraints excluded: chain J residue 559 LEU Chi-restraints excluded: chain J residue 628 LEU Chi-restraints excluded: chain J residue 662 HIS Chi-restraints excluded: chain J residue 733 LYS Chi-restraints excluded: chain J residue 741 ASP Chi-restraints excluded: chain J residue 743 ASP Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 42 CYS Chi-restraints excluded: chain K residue 50 MET Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 60 GLN Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 75 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 159 optimal weight: 0.1980 chunk 69 optimal weight: 6.9990 chunk 268 optimal weight: 2.9990 chunk 73 optimal weight: 30.0000 chunk 10 optimal weight: 0.5980 chunk 291 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 280 optimal weight: 30.0000 chunk 286 optimal weight: 0.9990 chunk 9 optimal weight: 0.0980 chunk 231 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS ** I 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.122681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.096204 restraints weight = 60776.669| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.80 r_work: 0.3396 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 25196 Z= 0.127 Angle : 0.548 13.460 33971 Z= 0.271 Chirality : 0.040 0.335 3818 Planarity : 0.003 0.049 4342 Dihedral : 5.141 83.661 3348 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.78 % Favored : 93.89 % Rotamer: Outliers : 5.03 % Allowed : 27.20 % Favored : 67.76 % 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: 1.00 (0.16), residues: 3044 helix: 2.02 (0.12), residues: 1889 sheet: -0.40 (0.43), residues: 149 loop : -1.94 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 105 TYR 0.023 0.001 TYR B 92 PHE 0.020 0.001 PHE A 86 TRP 0.010 0.001 TRP H 153 HIS 0.008 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00289 (25185) covalent geometry : angle 0.54720 (33968) hydrogen bonds : bond 0.03722 ( 1440) hydrogen bonds : angle 4.03054 ( 4200) metal coordination : bond 0.03027 ( 10) metal coordination : angle 2.75418 ( 3) Misc. bond : bond 0.00032 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 284 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 193 TYR cc_start: 0.6947 (OUTLIER) cc_final: 0.6457 (t80) REVERT: E 194 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6329 (mtmm) REVERT: E 213 ASP cc_start: 0.7513 (p0) cc_final: 0.7297 (p0) REVERT: J 425 THR cc_start: 0.6453 (OUTLIER) cc_final: 0.6035 (p) REVERT: J 733 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7643 (tptm) REVERT: J 735 ARG cc_start: 0.7882 (mmm160) cc_final: 0.7421 (mmp-170) REVERT: A 51 TYR cc_start: 0.4278 (OUTLIER) cc_final: 0.2995 (m-80) REVERT: A 86 PHE cc_start: 0.4052 (OUTLIER) cc_final: 0.2530 (p90) REVERT: A 90 MET cc_start: 0.6514 (pmm) cc_final: 0.6002 (pmm) REVERT: A 183 LYS cc_start: 0.9119 (mmtt) cc_final: 0.8572 (ptmt) REVERT: A 201 MET cc_start: 0.6050 (ptm) cc_final: 0.5692 (tpt) REVERT: A 357 TYR cc_start: 0.5978 (OUTLIER) cc_final: 0.5557 (t80) REVERT: B 67 TRP cc_start: 0.8044 (m100) cc_final: 0.7788 (m100) REVERT: C 109 ASN cc_start: 0.7959 (OUTLIER) cc_final: 0.7586 (m-40) REVERT: D 13 MET cc_start: 0.7006 (tmm) cc_final: 0.6680 (tmm) REVERT: F 168 PHE cc_start: 0.7712 (m-80) cc_final: 0.7390 (m-10) REVERT: F 206 MET cc_start: 0.6505 (mtp) cc_final: 0.6138 (mtp) REVERT: G 144 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8342 (mtmt) REVERT: H 128 ILE cc_start: 0.8096 (tp) cc_final: 0.7803 (tt) REVERT: H 165 ARG cc_start: 0.7677 (ptt-90) cc_final: 0.7187 (ptp90) outliers start: 136 outliers final: 106 residues processed: 387 average time/residue: 0.1648 time to fit residues: 100.5794 Evaluate side-chains 390 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 275 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 193 TYR Chi-restraints excluded: chain E residue 194 LYS Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain J residue 425 THR Chi-restraints excluded: chain J residue 440 PHE Chi-restraints excluded: chain J residue 462 LEU Chi-restraints excluded: chain J residue 488 THR Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 525 VAL Chi-restraints excluded: chain J residue 537 THR Chi-restraints excluded: chain J residue 543 LEU Chi-restraints excluded: chain J residue 559 LEU Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 601 MET Chi-restraints excluded: chain J residue 628 LEU Chi-restraints excluded: chain J residue 662 HIS Chi-restraints excluded: chain J residue 733 LYS Chi-restraints excluded: chain J residue 741 ASP Chi-restraints excluded: chain J residue 743 ASP Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 69 PHE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 144 LYS Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 42 CYS Chi-restraints excluded: chain K residue 50 MET Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 75 CYS Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 93 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 97 optimal weight: 3.9990 chunk 234 optimal weight: 0.8980 chunk 216 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 206 optimal weight: 0.5980 chunk 231 optimal weight: 0.9990 chunk 298 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 163 optimal weight: 8.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS ** I 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.122166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.096046 restraints weight = 60965.232| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.93 r_work: 0.3378 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 25196 Z= 0.146 Angle : 0.563 12.729 33971 Z= 0.279 Chirality : 0.040 0.366 3818 Planarity : 0.003 0.049 4342 Dihedral : 5.172 86.014 3348 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.81 % Favored : 93.92 % Rotamer: Outliers : 5.00 % Allowed : 27.46 % Favored : 67.54 % 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: 0.96 (0.16), residues: 3044 helix: 2.01 (0.12), residues: 1887 sheet: -0.42 (0.43), residues: 149 loop : -1.97 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 105 TYR 0.028 0.001 TYR B 92 PHE 0.021 0.001 PHE A 86 TRP 0.012 0.001 TRP H 153 HIS 0.004 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00341 (25185) covalent geometry : angle 0.56283 (33968) hydrogen bonds : bond 0.03797 ( 1440) hydrogen bonds : angle 4.01086 ( 4200) metal coordination : bond 0.02693 ( 10) metal coordination : angle 2.89137 ( 3) Misc. bond : bond 0.00036 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 277 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 194 LYS cc_start: 0.6981 (OUTLIER) cc_final: 0.6312 (mtmm) REVERT: E 213 ASP cc_start: 0.7583 (p0) cc_final: 0.7382 (p0) REVERT: J 425 THR cc_start: 0.6521 (OUTLIER) cc_final: 0.6112 (p) REVERT: J 733 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7690 (tptm) REVERT: J 735 ARG cc_start: 0.7929 (mmm160) cc_final: 0.7453 (mmp-170) REVERT: A 86 PHE cc_start: 0.4097 (OUTLIER) cc_final: 0.2532 (p90) REVERT: A 90 MET cc_start: 0.6463 (pmm) cc_final: 0.5799 (pmm) REVERT: A 183 LYS cc_start: 0.9111 (mmtt) cc_final: 0.8570 (ptmt) REVERT: A 201 MET cc_start: 0.6105 (ptm) cc_final: 0.5713 (tpt) REVERT: A 357 TYR cc_start: 0.6073 (OUTLIER) cc_final: 0.5582 (t80) REVERT: B 67 TRP cc_start: 0.8090 (m100) cc_final: 0.7792 (m100) REVERT: C 109 ASN cc_start: 0.7973 (OUTLIER) cc_final: 0.7590 (m-40) REVERT: C 126 GLN cc_start: 0.8517 (tp40) cc_final: 0.8253 (tp-100) REVERT: F 168 PHE cc_start: 0.7788 (m-80) cc_final: 0.7429 (m-10) REVERT: G 144 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8334 (mtmt) REVERT: H 128 ILE cc_start: 0.8080 (tp) cc_final: 0.7804 (tt) REVERT: H 165 ARG cc_start: 0.7691 (ptt-90) cc_final: 0.7167 (ptp90) outliers start: 135 outliers final: 110 residues processed: 379 average time/residue: 0.1774 time to fit residues: 105.8131 Evaluate side-chains 393 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 276 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 194 LYS Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain J residue 425 THR Chi-restraints excluded: chain J residue 440 PHE Chi-restraints excluded: chain J residue 462 LEU Chi-restraints excluded: chain J residue 488 THR Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 525 VAL Chi-restraints excluded: chain J residue 537 THR Chi-restraints excluded: chain J residue 543 LEU Chi-restraints excluded: chain J residue 559 LEU Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 601 MET Chi-restraints excluded: chain J residue 628 LEU Chi-restraints excluded: chain J residue 662 HIS Chi-restraints excluded: chain J residue 733 LYS Chi-restraints excluded: chain J residue 741 ASP Chi-restraints excluded: chain J residue 743 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 69 PHE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 144 LYS Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 42 CYS Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 75 CYS Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 93 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 8 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 204 optimal weight: 0.5980 chunk 186 optimal weight: 0.7980 chunk 233 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 268 optimal weight: 5.9990 chunk 281 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 270 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.120850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.094688 restraints weight = 60937.489| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.84 r_work: 0.3345 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 25196 Z= 0.202 Angle : 0.614 12.789 33971 Z= 0.305 Chirality : 0.042 0.371 3818 Planarity : 0.004 0.048 4342 Dihedral : 5.215 87.419 3345 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.21 % Favored : 93.53 % Rotamer: Outliers : 5.48 % Allowed : 26.83 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.16), residues: 3044 helix: 1.85 (0.12), residues: 1891 sheet: -0.55 (0.44), residues: 147 loop : -2.07 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 25 TYR 0.027 0.001 TYR B 92 PHE 0.021 0.002 PHE F 87 TRP 0.024 0.002 TRP H 153 HIS 0.006 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00483 (25185) covalent geometry : angle 0.61358 (33968) hydrogen bonds : bond 0.04281 ( 1440) hydrogen bonds : angle 4.13474 ( 4200) metal coordination : bond 0.03176 ( 10) metal coordination : angle 3.48552 ( 3) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 277 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 425 THR cc_start: 0.6780 (OUTLIER) cc_final: 0.6343 (p) REVERT: J 733 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7771 (tptm) REVERT: A 86 PHE cc_start: 0.4236 (OUTLIER) cc_final: 0.2597 (p90) REVERT: A 90 MET cc_start: 0.6549 (pmm) cc_final: 0.5862 (pmm) REVERT: A 183 LYS cc_start: 0.9126 (mmtt) cc_final: 0.8576 (ptmt) REVERT: A 201 MET cc_start: 0.6140 (ptm) cc_final: 0.5723 (tpt) REVERT: A 357 TYR cc_start: 0.6185 (OUTLIER) cc_final: 0.5711 (t80) REVERT: C 109 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7737 (m-40) REVERT: C 166 MET cc_start: 0.7218 (mmm) cc_final: 0.6997 (mmm) REVERT: G 144 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8342 (mtmt) REVERT: H 128 ILE cc_start: 0.8162 (tp) cc_final: 0.7905 (tt) REVERT: H 165 ARG cc_start: 0.7603 (ptt-90) cc_final: 0.7204 (ptp90) outliers start: 148 outliers final: 118 residues processed: 387 average time/residue: 0.1730 time to fit residues: 106.4118 Evaluate side-chains 395 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 271 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 145 CYS Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 194 LYS Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain J residue 425 THR Chi-restraints excluded: chain J residue 440 PHE Chi-restraints excluded: chain J residue 462 LEU Chi-restraints excluded: chain J residue 488 THR Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 525 VAL Chi-restraints excluded: chain J residue 537 THR Chi-restraints excluded: chain J residue 559 LEU Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 628 LEU Chi-restraints excluded: chain J residue 662 HIS Chi-restraints excluded: chain J residue 727 VAL Chi-restraints excluded: chain J residue 733 LYS Chi-restraints excluded: chain J residue 741 ASP Chi-restraints excluded: chain J residue 743 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 69 PHE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 144 LYS Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 42 CYS Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 75 CYS Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 93 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 80 optimal weight: 30.0000 chunk 133 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 300 optimal weight: 0.6980 chunk 180 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 181 optimal weight: 0.6980 chunk 203 optimal weight: 0.6980 chunk 134 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS ** I 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 568 GLN ** J 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.122342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.095881 restraints weight = 60932.431| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.83 r_work: 0.3401 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 25196 Z= 0.119 Angle : 0.568 13.430 33971 Z= 0.281 Chirality : 0.040 0.362 3818 Planarity : 0.003 0.048 4342 Dihedral : 5.091 89.648 3345 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.12 % Favored : 94.61 % Rotamer: Outliers : 4.00 % Allowed : 28.50 % Favored : 67.51 % 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: 0.94 (0.16), residues: 3044 helix: 1.97 (0.12), residues: 1893 sheet: -0.55 (0.43), residues: 149 loop : -1.95 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 116 TYR 0.029 0.001 TYR B 92 PHE 0.029 0.001 PHE H 118 TRP 0.025 0.001 TRP H 153 HIS 0.008 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00266 (25185) covalent geometry : angle 0.56764 (33968) hydrogen bonds : bond 0.03628 ( 1440) hydrogen bonds : angle 3.96058 ( 4200) metal coordination : bond 0.02577 ( 10) metal coordination : angle 3.35112 ( 3) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 279 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 40 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7717 (mt0) REVERT: J 425 THR cc_start: 0.6453 (OUTLIER) cc_final: 0.6009 (p) REVERT: J 733 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7688 (tptm) REVERT: A 86 PHE cc_start: 0.3974 (OUTLIER) cc_final: 0.2426 (p90) REVERT: A 90 MET cc_start: 0.6083 (pmm) cc_final: 0.5476 (pmm) REVERT: A 183 LYS cc_start: 0.9127 (mmtt) cc_final: 0.8599 (ptmt) REVERT: A 201 MET cc_start: 0.5956 (ptm) cc_final: 0.5633 (tpt) REVERT: A 357 TYR cc_start: 0.6048 (OUTLIER) cc_final: 0.5596 (t80) REVERT: B 33 GLU cc_start: 0.6261 (OUTLIER) cc_final: 0.5847 (mp0) REVERT: B 311 MET cc_start: 0.8795 (mmt) cc_final: 0.8237 (mmt) REVERT: C 109 ASN cc_start: 0.8054 (OUTLIER) cc_final: 0.7778 (m-40) REVERT: C 166 MET cc_start: 0.7160 (mmm) cc_final: 0.6948 (mmt) REVERT: F 168 PHE cc_start: 0.7806 (m-80) cc_final: 0.7456 (m-10) REVERT: F 205 ARG cc_start: 0.8263 (mmt90) cc_final: 0.8048 (mmt180) REVERT: G 144 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8286 (mtmt) REVERT: H 128 ILE cc_start: 0.8278 (tp) cc_final: 0.8023 (tt) REVERT: H 165 ARG cc_start: 0.7478 (ptt-90) cc_final: 0.7154 (ptp90) outliers start: 108 outliers final: 88 residues processed: 356 average time/residue: 0.1743 time to fit residues: 98.0835 Evaluate side-chains 368 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 272 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 194 LYS Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain I residue 22 LYS Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 40 GLN Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain J residue 425 THR Chi-restraints excluded: chain J residue 440 PHE Chi-restraints excluded: chain J residue 462 LEU Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 525 VAL Chi-restraints excluded: chain J residue 537 THR Chi-restraints excluded: chain J residue 559 LEU Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 662 HIS Chi-restraints excluded: chain J residue 733 LYS Chi-restraints excluded: chain J residue 741 ASP Chi-restraints excluded: chain J residue 743 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 69 PHE Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 144 LYS Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 42 CYS Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 75 CYS Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 172 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 238 optimal weight: 0.0010 chunk 53 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 186 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 199 optimal weight: 4.9990 chunk 290 optimal weight: 8.9990 chunk 286 optimal weight: 0.6980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS ** I 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN F 137 HIS ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.122423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.096042 restraints weight = 60992.490| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.81 r_work: 0.3404 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 25196 Z= 0.117 Angle : 0.571 13.340 33971 Z= 0.280 Chirality : 0.039 0.366 3818 Planarity : 0.003 0.048 4342 Dihedral : 4.981 88.950 3345 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.68 % Favored : 94.05 % Rotamer: Outliers : 3.66 % Allowed : 28.76 % Favored : 67.58 % 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: 0.99 (0.16), residues: 3044 helix: 2.03 (0.12), residues: 1889 sheet: -0.46 (0.43), residues: 152 loop : -1.98 (0.20), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 105 TYR 0.028 0.001 TYR B 92 PHE 0.025 0.001 PHE H 118 TRP 0.010 0.001 TRP K 33 HIS 0.009 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00261 (25185) covalent geometry : angle 0.56995 (33968) hydrogen bonds : bond 0.03504 ( 1440) hydrogen bonds : angle 3.91392 ( 4200) metal coordination : bond 0.02350 ( 10) metal coordination : angle 2.99612 ( 3) Misc. bond : bond 0.00003 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 274 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 40 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7752 (mt0) REVERT: J 425 THR cc_start: 0.6527 (OUTLIER) cc_final: 0.6078 (p) REVERT: J 733 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7574 (tptm) REVERT: A 86 PHE cc_start: 0.3817 (OUTLIER) cc_final: 0.2255 (p90) REVERT: A 90 MET cc_start: 0.6063 (pmm) cc_final: 0.5405 (pmm) REVERT: A 183 LYS cc_start: 0.9095 (mmtt) cc_final: 0.8585 (ptmt) REVERT: A 201 MET cc_start: 0.6052 (ptm) cc_final: 0.5672 (tpt) REVERT: A 357 TYR cc_start: 0.6025 (OUTLIER) cc_final: 0.5570 (t80) REVERT: B 311 MET cc_start: 0.8855 (mmt) cc_final: 0.8251 (mmt) REVERT: C 109 ASN cc_start: 0.7914 (OUTLIER) cc_final: 0.7604 (m-40) REVERT: C 166 MET cc_start: 0.7220 (mmm) cc_final: 0.7014 (mmm) REVERT: F 168 PHE cc_start: 0.7870 (m-80) cc_final: 0.7542 (m-10) REVERT: G 144 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8337 (mtmt) REVERT: H 128 ILE cc_start: 0.8263 (tp) cc_final: 0.8013 (tt) outliers start: 99 outliers final: 80 residues processed: 343 average time/residue: 0.1770 time to fit residues: 94.8352 Evaluate side-chains 356 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 269 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 194 LYS Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain I residue 22 LYS Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 40 GLN Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain J residue 425 THR Chi-restraints excluded: chain J residue 440 PHE Chi-restraints excluded: chain J residue 462 LEU Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 525 VAL Chi-restraints excluded: chain J residue 537 THR Chi-restraints excluded: chain J residue 559 LEU Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 662 HIS Chi-restraints excluded: chain J residue 733 LYS Chi-restraints excluded: chain J residue 741 ASP Chi-restraints excluded: chain J residue 743 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 69 PHE Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 144 LYS Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 42 CYS Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 75 CYS Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 281 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 156 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 240 optimal weight: 0.1980 chunk 66 optimal weight: 8.9990 chunk 250 optimal weight: 0.8980 chunk 267 optimal weight: 2.9990 chunk 253 optimal weight: 1.9990 chunk 218 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS ** I 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.122198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.096458 restraints weight = 61002.964| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.87 r_work: 0.3394 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 25196 Z= 0.129 Angle : 0.587 13.171 33971 Z= 0.288 Chirality : 0.040 0.364 3818 Planarity : 0.003 0.047 4342 Dihedral : 4.928 88.950 3345 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.45 % Favored : 94.28 % Rotamer: Outliers : 3.44 % Allowed : 29.09 % Favored : 67.47 % 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: 1.00 (0.16), residues: 3044 helix: 2.04 (0.12), residues: 1892 sheet: -0.45 (0.43), residues: 151 loop : -1.98 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 13 TYR 0.027 0.001 TYR B 92 PHE 0.021 0.001 PHE A 86 TRP 0.040 0.001 TRP H 153 HIS 0.009 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00297 (25185) covalent geometry : angle 0.58635 (33968) hydrogen bonds : bond 0.03543 ( 1440) hydrogen bonds : angle 3.89172 ( 4200) metal coordination : bond 0.02322 ( 10) metal coordination : angle 3.02026 ( 3) Misc. bond : bond 0.00005 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6966.53 seconds wall clock time: 120 minutes 11.37 seconds (7211.37 seconds total)