Starting phenix.real_space_refine on Sun Jun 15 05:32:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c5b_45213/06_2025/9c5b_45213.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c5b_45213/06_2025/9c5b_45213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c5b_45213/06_2025/9c5b_45213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c5b_45213/06_2025/9c5b_45213.map" model { file = "/net/cci-nas-00/data/ceres_data/9c5b_45213/06_2025/9c5b_45213.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c5b_45213/06_2025/9c5b_45213.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 88 5.16 5 C 10770 2.51 5 N 2876 2.21 5 O 3132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16874 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1330 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 3, 'TRANS': 161} Chain: "C" Number of atoms: 1447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1447 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 3, 'TRANS': 176} Chain: "D" Number of atoms: 4770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4770 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 20, 'TRANS': 584} Chain: "M" Number of atoms: 3309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3309 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 391} Chain: "S" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1219 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain: "Y" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 62 Classifications: {'peptide': 8} Modifications used: {'COO': 1} Link IDs: {'TRANS': 7} Chain: "B" Number of atoms: 4671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4671 Classifications: {'peptide': 587} Link IDs: {'PTRANS': 25, 'TRANS': 561} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.17, per 1000 atoms: 0.60 Number of scatterers: 16874 At special positions: 0 Unit cell: (128.018, 142.83, 154.468, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 P 6 15.00 Mg 2 11.99 O 3132 8.00 N 2876 7.00 C 10770 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.02 Conformation dependent library (CDL) restraints added in 2.0 seconds 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4038 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 10 sheets defined 63.4% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 29 through 40 Processing helix chain 'A' and resid 71 through 82 Proline residue: A 76 - end of helix removed outlier: 3.645A pdb=" N ARG A 79 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 112 Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 135 through 144 Processing helix chain 'A' and resid 145 through 148 removed outlier: 3.557A pdb=" N LEU A 148 " --> pdb=" O LEU A 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 145 through 148' Processing helix chain 'A' and resid 165 through 178 Processing helix chain 'C' and resid 4 through 14 removed outlier: 3.755A pdb=" N PHE C 13 " --> pdb=" O PHE C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 39 Processing helix chain 'C' and resid 74 through 82 Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 135 through 144 Processing helix chain 'C' and resid 145 through 148 Processing helix chain 'C' and resid 165 through 177 Processing helix chain 'D' and resid 2 through 14 Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 47 Processing helix chain 'D' and resid 51 through 68 Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'D' and resid 75 through 84 Processing helix chain 'D' and resid 87 through 102 removed outlier: 4.556A pdb=" N ILE D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 112 Processing helix chain 'D' and resid 112 through 122 Processing helix chain 'D' and resid 124 through 138 removed outlier: 3.704A pdb=" N CYS D 137 " --> pdb=" O THR D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 155 removed outlier: 4.488A pdb=" N ASN D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP D 150 " --> pdb=" O ASP D 146 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR D 153 " --> pdb=" O ASN D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 177 removed outlier: 3.685A pdb=" N LYS D 172 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 192 removed outlier: 3.644A pdb=" N LEU D 181 " --> pdb=" O TYR D 177 " (cutoff:3.500A) Proline residue: D 183 - end of helix Proline residue: D 186 - end of helix Processing helix chain 'D' and resid 196 through 214 Processing helix chain 'D' and resid 215 through 218 Processing helix chain 'D' and resid 221 through 232 Processing helix chain 'D' and resid 234 through 249 Processing helix chain 'D' and resid 252 through 270 removed outlier: 3.630A pdb=" N GLY D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLU D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Proline residue: D 262 - end of helix Processing helix chain 'D' and resid 272 through 292 removed outlier: 3.509A pdb=" N GLU D 278 " --> pdb=" O SER D 274 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER D 292 " --> pdb=" O ILE D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 314 Processing helix chain 'D' and resid 316 through 332 Processing helix chain 'D' and resid 334 through 339 Processing helix chain 'D' and resid 341 through 349 removed outlier: 3.695A pdb=" N LEU D 349 " --> pdb=" O ILE D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 368 Processing helix chain 'D' and resid 372 through 387 Processing helix chain 'D' and resid 389 through 410 removed outlier: 6.709A pdb=" N SER D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASN D 408 " --> pdb=" O CYS D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 426 Processing helix chain 'D' and resid 433 through 448 Processing helix chain 'D' and resid 451 through 465 Processing helix chain 'D' and resid 465 through 470 Processing helix chain 'D' and resid 479 through 492 removed outlier: 3.614A pdb=" N TYR D 483 " --> pdb=" O CYS D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 496 Processing helix chain 'D' and resid 498 through 507 Processing helix chain 'D' and resid 508 through 514 Processing helix chain 'D' and resid 515 through 541 Processing helix chain 'D' and resid 542 through 555 Processing helix chain 'D' and resid 556 through 561 removed outlier: 3.537A pdb=" N PHE D 560 " --> pdb=" O ARG D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 588 Processing helix chain 'D' and resid 592 through 602 removed outlier: 3.806A pdb=" N LEU D 599 " --> pdb=" O GLU D 595 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE D 600 " --> pdb=" O VAL D 596 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY D 602 " --> pdb=" O ALA D 598 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 27 No H-bonds generated for 'chain 'M' and resid 25 through 27' Processing helix chain 'M' and resid 28 through 39 removed outlier: 4.023A pdb=" N PHE M 32 " --> pdb=" O VAL M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 45 Processing helix chain 'M' and resid 75 through 95 Processing helix chain 'M' and resid 98 through 105 Processing helix chain 'M' and resid 105 through 116 Processing helix chain 'M' and resid 126 through 134 removed outlier: 3.669A pdb=" N GLU M 132 " --> pdb=" O ASN M 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 138 through 149 Processing helix chain 'M' and resid 158 through 163 Processing helix chain 'M' and resid 224 through 228 Processing helix chain 'M' and resid 238 through 245 Processing helix chain 'S' and resid 24 through 41 removed outlier: 3.801A pdb=" N LYS S 41 " --> pdb=" O HIS S 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 102 Processing helix chain 'S' and resid 105 through 112 Processing helix chain 'S' and resid 112 through 123 Processing helix chain 'S' and resid 133 through 151 Processing helix chain 'B' and resid 39 through 53 Processing helix chain 'B' and resid 55 through 72 Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 79 through 84 Processing helix chain 'B' and resid 85 through 89 removed outlier: 4.342A pdb=" N ALA B 88 " --> pdb=" O LYS B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 106 Processing helix chain 'B' and resid 109 through 114 removed outlier: 3.715A pdb=" N LEU B 114 " --> pdb=" O GLN B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 124 Processing helix chain 'B' and resid 128 through 142 Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 147 through 160 Processing helix chain 'B' and resid 163 through 181 Processing helix chain 'B' and resid 184 through 196 Processing helix chain 'B' and resid 200 through 215 removed outlier: 4.349A pdb=" N GLY B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N SER B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 224 removed outlier: 4.273A pdb=" N HIS B 223 " --> pdb=" O ASP B 220 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LYS B 224 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 233 Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 237 through 256 removed outlier: 4.282A pdb=" N THR B 254 " --> pdb=" O ARG B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 305 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 312 through 326 Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 334 through 343 removed outlier: 4.015A pdb=" N SER B 338 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 362 removed outlier: 3.656A pdb=" N ILE B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 376 removed outlier: 3.868A pdb=" N GLU B 369 " --> pdb=" O GLY B 366 " (cutoff:3.500A) Proline residue: B 370 - end of helix removed outlier: 5.601A pdb=" N LYS B 373 " --> pdb=" O PRO B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 397 Processing helix chain 'B' and resid 401 through 414 removed outlier: 3.756A pdb=" N LYS B 414 " --> pdb=" O GLN B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 435 Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 450 through 452 No H-bonds generated for 'chain 'B' and resid 450 through 452' Processing helix chain 'B' and resid 454 through 472 Processing helix chain 'B' and resid 476 through 487 Processing helix chain 'B' and resid 492 through 506 Processing helix chain 'B' and resid 513 through 525 Processing helix chain 'B' and resid 526 through 528 No H-bonds generated for 'chain 'B' and resid 526 through 528' Processing helix chain 'B' and resid 529 through 565 removed outlier: 7.343A pdb=" N LYS B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLN B 550 " --> pdb=" O THR B 546 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU B 553 " --> pdb=" O LYS B 549 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 582 Processing helix chain 'B' and resid 590 through 592 No H-bonds generated for 'chain 'B' and resid 590 through 592' Processing helix chain 'B' and resid 593 through 599 Processing helix chain 'B' and resid 609 through 615 removed outlier: 3.991A pdb=" N ASP B 615 " --> pdb=" O LYS B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 627 removed outlier: 3.512A pdb=" N THR B 625 " --> pdb=" O THR B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 650 Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 58 removed outlier: 3.806A pdb=" N VAL A 68 " --> pdb=" O MET A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 51 through 58 removed outlier: 5.173A pdb=" N GLY C 24 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARG C 19 " --> pdb=" O GLY C 87 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE C 89 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU C 21 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL C 91 " --> pdb=" O LEU C 21 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL C 23 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N ASP C 93 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU C 121 " --> pdb=" O TYR C 154 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLN C 156 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL C 123 " --> pdb=" O GLN C 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 14 through 19 removed outlier: 6.499A pdb=" N LEU M 7 " --> pdb=" O PHE M 15 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU M 17 " --> pdb=" O LEU M 5 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU M 5 " --> pdb=" O GLU M 17 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 117 through 118 Processing sheet with id=AA5, first strand: chain 'M' and resid 229 through 233 removed outlier: 5.089A pdb=" N ASP M 230 " --> pdb=" O ARG M 263 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG M 263 " --> pdb=" O ASP M 230 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ASN M 256 " --> pdb=" O ILE M 210 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE M 210 " --> pdb=" O ASN M 256 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ARG M 258 " --> pdb=" O ALA M 208 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA M 208 " --> pdb=" O ARG M 258 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE M 202 " --> pdb=" O VAL M 264 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE M 190 " --> pdb=" O VAL M 198 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA M 200 " --> pdb=" O ASP M 188 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASP M 188 " --> pdb=" O ALA M 200 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE M 202 " --> pdb=" O GLU M 186 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU M 186 " --> pdb=" O ILE M 202 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLY M 204 " --> pdb=" O VAL M 184 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL M 184 " --> pdb=" O GLY M 204 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE M 206 " --> pdb=" O ASP M 182 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASP M 182 " --> pdb=" O ILE M 206 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA M 208 " --> pdb=" O TYR M 180 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR M 180 " --> pdb=" O ALA M 208 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ILE M 210 " --> pdb=" O GLU M 178 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLU M 178 " --> pdb=" O ILE M 210 " (cutoff:3.500A) removed outlier: 11.065A pdb=" N ALA M 179 " --> pdb=" O VAL M 405 " (cutoff:3.500A) removed outlier: 11.780A pdb=" N TYR M 407 " --> pdb=" O ALA M 179 " (cutoff:3.500A) removed outlier: 11.123A pdb=" N PHE M 181 " --> pdb=" O TYR M 407 " (cutoff:3.500A) removed outlier: 11.398A pdb=" N THR M 409 " --> pdb=" O PHE M 181 " (cutoff:3.500A) removed outlier: 10.777A pdb=" N VAL M 183 " --> pdb=" O THR M 409 " (cutoff:3.500A) removed outlier: 10.960A pdb=" N ALA M 411 " --> pdb=" O VAL M 183 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N GLU M 185 " --> pdb=" O ALA M 411 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N LYS M 413 " --> pdb=" O GLU M 185 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE M 187 " --> pdb=" O LYS M 413 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLN M 415 " --> pdb=" O ILE M 187 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ALA M 189 " --> pdb=" O GLN M 415 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ARG M 417 " --> pdb=" O ALA M 189 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE M 191 " --> pdb=" O ARG M 417 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N PHE M 377 " --> pdb=" O ALA M 411 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LYS M 413 " --> pdb=" O ILE M 375 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE M 375 " --> pdb=" O LYS M 413 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLN M 415 " --> pdb=" O LEU M 373 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU M 373 " --> pdb=" O GLN M 415 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ARG M 417 " --> pdb=" O PRO M 371 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N SER M 372 " --> pdb=" O HIS M 313 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N HIS M 313 " --> pdb=" O SER M 372 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS M 378 " --> pdb=" O GLY M 307 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N GLY M 307 " --> pdb=" O LYS M 378 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ILE M 308 " --> pdb=" O VAL M 343 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 229 through 233 removed outlier: 5.089A pdb=" N ASP M 230 " --> pdb=" O ARG M 263 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG M 263 " --> pdb=" O ASP M 230 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ASN M 256 " --> pdb=" O ILE M 210 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE M 210 " --> pdb=" O ASN M 256 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ARG M 258 " --> pdb=" O ALA M 208 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA M 208 " --> pdb=" O ARG M 258 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE M 202 " --> pdb=" O VAL M 264 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE M 190 " --> pdb=" O VAL M 198 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA M 200 " --> pdb=" O ASP M 188 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASP M 188 " --> pdb=" O ALA M 200 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE M 202 " --> pdb=" O GLU M 186 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU M 186 " --> pdb=" O ILE M 202 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLY M 204 " --> pdb=" O VAL M 184 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL M 184 " --> pdb=" O GLY M 204 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE M 206 " --> pdb=" O ASP M 182 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASP M 182 " --> pdb=" O ILE M 206 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA M 208 " --> pdb=" O TYR M 180 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR M 180 " --> pdb=" O ALA M 208 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ILE M 210 " --> pdb=" O GLU M 178 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLU M 178 " --> pdb=" O ILE M 210 " (cutoff:3.500A) removed outlier: 11.065A pdb=" N ALA M 179 " --> pdb=" O VAL M 405 " (cutoff:3.500A) removed outlier: 11.780A pdb=" N TYR M 407 " --> pdb=" O ALA M 179 " (cutoff:3.500A) removed outlier: 11.123A pdb=" N PHE M 181 " --> pdb=" O TYR M 407 " (cutoff:3.500A) removed outlier: 11.398A pdb=" N THR M 409 " --> pdb=" O PHE M 181 " (cutoff:3.500A) removed outlier: 10.777A pdb=" N VAL M 183 " --> pdb=" O THR M 409 " (cutoff:3.500A) removed outlier: 10.960A pdb=" N ALA M 411 " --> pdb=" O VAL M 183 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N GLU M 185 " --> pdb=" O ALA M 411 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N LYS M 413 " --> pdb=" O GLU M 185 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE M 187 " --> pdb=" O LYS M 413 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLN M 415 " --> pdb=" O ILE M 187 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ALA M 189 " --> pdb=" O GLN M 415 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ARG M 417 " --> pdb=" O ALA M 189 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE M 191 " --> pdb=" O ARG M 417 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 248 through 250 Processing sheet with id=AA8, first strand: chain 'M' and resid 274 through 281 removed outlier: 6.898A pdb=" N SER M 353 " --> pdb=" O PRO M 325 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LYS M 355 " --> pdb=" O LEU M 323 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N LEU M 323 " --> pdb=" O LYS M 355 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU M 357 " --> pdb=" O MET M 321 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N MET M 321 " --> pdb=" O LEU M 357 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN M 359 " --> pdb=" O LEU M 319 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 14 through 19 removed outlier: 6.167A pdb=" N ILE S 7 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER S 17 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE S 5 " --> pdb=" O SER S 17 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N PHE S 19 " --> pdb=" O LYS S 3 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LYS S 3 " --> pdb=" O PHE S 19 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 124 through 125 1004 hydrogen bonds defined for protein. 2835 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.35 Time building geometry restraints manager: 4.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3852 1.32 - 1.45: 3874 1.45 - 1.57: 9294 1.57 - 1.69: 10 1.69 - 1.81: 147 Bond restraints: 17177 Sorted by residual: bond pdb=" CA ILE C 89 " pdb=" C ILE C 89 " ideal model delta sigma weight residual 1.522 1.474 0.048 1.21e-02 6.83e+03 1.59e+01 bond pdb=" CA ILE S 86 " pdb=" C ILE S 86 " ideal model delta sigma weight residual 1.524 1.480 0.044 1.22e-02 6.72e+03 1.30e+01 bond pdb=" CA LEU D 373 " pdb=" C LEU D 373 " ideal model delta sigma weight residual 1.524 1.481 0.043 1.24e-02 6.50e+03 1.22e+01 bond pdb=" CA ILE D 162 " pdb=" C ILE D 162 " ideal model delta sigma weight residual 1.524 1.476 0.047 1.39e-02 5.18e+03 1.16e+01 bond pdb=" CA ASP C 67 " pdb=" C ASP C 67 " ideal model delta sigma weight residual 1.526 1.487 0.039 1.20e-02 6.94e+03 1.04e+01 ... (remaining 17172 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 20649 1.98 - 3.96: 2214 3.96 - 5.94: 287 5.94 - 7.92: 66 7.92 - 9.90: 37 Bond angle restraints: 23253 Sorted by residual: angle pdb=" C LYS M 135 " pdb=" N PRO M 136 " pdb=" CA PRO M 136 " ideal model delta sigma weight residual 119.66 126.73 -7.07 7.30e-01 1.88e+00 9.39e+01 angle pdb=" C ASN M 224 " pdb=" N PRO M 225 " pdb=" CA PRO M 225 " ideal model delta sigma weight residual 119.56 129.17 -9.61 1.02e+00 9.61e-01 8.88e+01 angle pdb=" C ASN D 214 " pdb=" N PRO D 215 " pdb=" CA PRO D 215 " ideal model delta sigma weight residual 119.56 129.10 -9.54 1.02e+00 9.61e-01 8.74e+01 angle pdb=" C SER B 609 " pdb=" N PRO B 610 " pdb=" CA PRO B 610 " ideal model delta sigma weight residual 119.56 128.94 -9.38 1.02e+00 9.61e-01 8.45e+01 angle pdb=" C ILE M 165 " pdb=" N PRO M 166 " pdb=" CA PRO M 166 " ideal model delta sigma weight residual 119.56 128.84 -9.28 1.02e+00 9.61e-01 8.28e+01 ... (remaining 23248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 10376 35.80 - 71.60: 119 71.60 - 107.40: 15 107.40 - 143.20: 4 143.20 - 179.00: 4 Dihedral angle restraints: 10518 sinusoidal: 4307 harmonic: 6211 Sorted by residual: dihedral pdb=" O3B GTP A 202 " pdb=" O3A GTP A 202 " pdb=" PB GTP A 202 " pdb=" PA GTP A 202 " ideal model delta sinusoidal sigma weight residual -68.92 110.08 -179.00 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O3B GTP C 202 " pdb=" O3A GTP C 202 " pdb=" PB GTP C 202 " pdb=" PA GTP C 202 " ideal model delta sinusoidal sigma weight residual -68.92 110.08 -179.00 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C8 GTP C 202 " pdb=" C1' GTP C 202 " pdb=" N9 GTP C 202 " pdb=" O4' GTP C 202 " ideal model delta sinusoidal sigma weight residual 104.59 -70.89 175.48 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 10515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1675 0.059 - 0.118: 841 0.118 - 0.177: 168 0.177 - 0.237: 20 0.237 - 0.296: 1 Chirality restraints: 2705 Sorted by residual: chirality pdb=" CA TYR C 35 " pdb=" N TYR C 35 " pdb=" C TYR C 35 " pdb=" CB TYR C 35 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA ILE C 46 " pdb=" N ILE C 46 " pdb=" C ILE C 46 " pdb=" CB ILE C 46 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA MET D 459 " pdb=" N MET D 459 " pdb=" C MET D 459 " pdb=" CB MET D 459 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 2702 not shown) Planarity restraints: 2931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR M 110 " -0.064 2.00e-02 2.50e+03 3.62e-02 2.62e+01 pdb=" CG TYR M 110 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR M 110 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR M 110 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR M 110 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR M 110 " 0.025 2.00e-02 2.50e+03 pdb=" CZ TYR M 110 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR M 110 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 639 " -0.045 2.00e-02 2.50e+03 2.41e-02 1.46e+01 pdb=" CG TRP B 639 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TRP B 639 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 639 " 0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP B 639 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP B 639 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 639 " 0.036 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 639 " -0.027 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 639 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP B 639 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 341 " 0.040 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP M 341 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP M 341 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP M 341 " -0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP M 341 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP M 341 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP M 341 " -0.028 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 341 " 0.019 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 341 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP M 341 " 0.027 2.00e-02 2.50e+03 ... (remaining 2928 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 58 2.53 - 3.12: 15004 3.12 - 3.72: 26819 3.72 - 4.31: 40425 4.31 - 4.90: 62295 Nonbonded interactions: 144601 Sorted by model distance: nonbonded pdb="MG MG C 201 " pdb=" O2G GTP C 202 " model vdw 1.940 2.170 nonbonded pdb="MG MG A 201 " pdb=" O2G GTP A 202 " model vdw 1.940 2.170 nonbonded pdb=" OG1 THR C 48 " pdb="MG MG C 201 " model vdw 1.960 2.170 nonbonded pdb=" OG1 THR C 31 " pdb="MG MG C 201 " model vdw 2.055 2.170 nonbonded pdb=" OG1 THR A 31 " pdb="MG MG A 201 " model vdw 2.077 2.170 ... (remaining 144596 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 17 through 181 or resid 201 through 202)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.520 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: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 37.690 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 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 : 0.013 0.055 17177 Z= 0.824 Angle : 1.359 9.905 23253 Z= 0.959 Chirality : 0.067 0.296 2705 Planarity : 0.006 0.037 2931 Dihedral : 12.252 179.004 6480 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.10 % Favored : 97.71 % Rotamer: Outliers : 0.11 % Allowed : 0.32 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.18), residues: 2098 helix: 0.06 (0.14), residues: 1111 sheet: -0.01 (0.33), residues: 240 loop : 1.23 (0.26), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.006 TRP B 639 HIS 0.010 0.002 HIS M 3 PHE 0.024 0.004 PHE B 80 TYR 0.064 0.006 TYR M 110 ARG 0.008 0.001 ARG B 227 Details of bonding type rmsd hydrogen bonds : bond 0.17228 ( 996) hydrogen bonds : angle 7.31368 ( 2835) covalent geometry : bond 0.01280 (17177) covalent geometry : angle 1.35934 (23253) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 634 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8348 (tttt) cc_final: 0.8023 (mttt) REVERT: A 41 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7079 (mm-30) REVERT: A 84 ASN cc_start: 0.6426 (m-40) cc_final: 0.6219 (m-40) REVERT: C 22 MET cc_start: 0.7979 (ttp) cc_final: 0.6970 (tmm) REVERT: C 86 GLN cc_start: 0.7139 (mt0) cc_final: 0.6116 (mt0) REVERT: C 110 MET cc_start: 0.8134 (mtm) cc_final: 0.7849 (ttm) REVERT: C 143 LEU cc_start: 0.7670 (mt) cc_final: 0.7421 (mm) REVERT: C 173 LEU cc_start: 0.8091 (mt) cc_final: 0.7830 (mt) REVERT: D 1 MET cc_start: 0.4789 (ttp) cc_final: 0.4551 (ttp) REVERT: D 66 GLN cc_start: 0.7264 (tp40) cc_final: 0.6993 (tp40) REVERT: D 67 MET cc_start: 0.7768 (ttp) cc_final: 0.6508 (tmm) REVERT: D 110 MET cc_start: 0.6335 (mmm) cc_final: 0.5945 (mmm) REVERT: D 117 ARG cc_start: 0.8110 (mtp-110) cc_final: 0.7901 (ttm-80) REVERT: D 118 LYS cc_start: 0.8707 (tttt) cc_final: 0.8360 (tptm) REVERT: D 126 TYR cc_start: 0.7925 (m-80) cc_final: 0.7664 (m-80) REVERT: D 128 THR cc_start: 0.7586 (m) cc_final: 0.7132 (p) REVERT: D 146 ASP cc_start: 0.7939 (m-30) cc_final: 0.7674 (p0) REVERT: D 155 MET cc_start: 0.7937 (mtm) cc_final: 0.7662 (mtm) REVERT: D 157 HIS cc_start: 0.7635 (t-90) cc_final: 0.7099 (t-90) REVERT: D 169 ILE cc_start: 0.6505 (tt) cc_final: 0.6021 (pt) REVERT: D 189 LYS cc_start: 0.7575 (mtmt) cc_final: 0.7335 (mttt) REVERT: D 200 GLN cc_start: 0.6976 (tt0) cc_final: 0.6684 (mt0) REVERT: D 201 SER cc_start: 0.8136 (m) cc_final: 0.7857 (p) REVERT: D 221 LEU cc_start: 0.7865 (mp) cc_final: 0.6488 (tp) REVERT: D 223 PRO cc_start: 0.7494 (Cg_exo) cc_final: 0.6820 (Cg_endo) REVERT: D 225 PHE cc_start: 0.6101 (m-80) cc_final: 0.5398 (m-80) REVERT: D 239 ILE cc_start: 0.8446 (mt) cc_final: 0.8198 (mt) REVERT: D 240 LYS cc_start: 0.8419 (mmtt) cc_final: 0.7895 (mmtp) REVERT: D 265 ASN cc_start: 0.8207 (m-40) cc_final: 0.7858 (m-40) REVERT: D 268 HIS cc_start: 0.8800 (m-70) cc_final: 0.8598 (m-70) REVERT: D 275 LEU cc_start: 0.8767 (tp) cc_final: 0.8518 (tp) REVERT: D 302 GLN cc_start: 0.8764 (tt0) cc_final: 0.8489 (tt0) REVERT: D 307 LYS cc_start: 0.8019 (mmtt) cc_final: 0.7726 (mmtt) REVERT: D 314 ASP cc_start: 0.5087 (t0) cc_final: 0.4663 (t0) REVERT: D 327 MET cc_start: 0.7803 (tpp) cc_final: 0.7326 (tpp) REVERT: D 339 GLN cc_start: 0.7928 (pt0) cc_final: 0.7395 (pp30) REVERT: D 354 GLU cc_start: 0.8393 (pm20) cc_final: 0.7688 (pm20) REVERT: D 362 ASP cc_start: 0.8723 (m-30) cc_final: 0.8051 (m-30) REVERT: D 367 MET cc_start: 0.7187 (mtm) cc_final: 0.6758 (mtm) REVERT: D 374 MET cc_start: 0.8060 (mtt) cc_final: 0.6912 (mtt) REVERT: D 378 LYS cc_start: 0.8780 (mttt) cc_final: 0.8407 (mttt) REVERT: D 380 LEU cc_start: 0.8172 (mt) cc_final: 0.7853 (mt) REVERT: D 393 ARG cc_start: 0.7926 (mtt180) cc_final: 0.7521 (ptp-110) REVERT: D 400 ILE cc_start: 0.8994 (mt) cc_final: 0.8716 (mm) REVERT: D 403 ILE cc_start: 0.8276 (mt) cc_final: 0.8066 (mt) REVERT: D 406 GLN cc_start: 0.7856 (pt0) cc_final: 0.7508 (pt0) REVERT: D 419 ILE cc_start: 0.8670 (mt) cc_final: 0.8398 (pt) REVERT: D 429 GLU cc_start: 0.8457 (tt0) cc_final: 0.7877 (tm-30) REVERT: D 433 HIS cc_start: 0.7438 (m90) cc_final: 0.7228 (m90) REVERT: D 440 GLN cc_start: 0.7468 (mm-40) cc_final: 0.6912 (tp40) REVERT: D 488 ILE cc_start: 0.8029 (mm) cc_final: 0.7739 (mt) REVERT: D 530 TYR cc_start: 0.7783 (m-80) cc_final: 0.7454 (m-80) REVERT: D 534 LEU cc_start: 0.7974 (mt) cc_final: 0.7660 (tp) REVERT: D 559 GLN cc_start: 0.7116 (tt0) cc_final: 0.6863 (tt0) REVERT: D 573 SER cc_start: 0.8466 (m) cc_final: 0.8210 (p) REVERT: M 6 PHE cc_start: 0.7505 (m-80) cc_final: 0.7039 (m-80) REVERT: M 15 PHE cc_start: 0.6110 (m-80) cc_final: 0.5550 (m-80) REVERT: M 16 LEU cc_start: 0.7210 (tp) cc_final: 0.6994 (tp) REVERT: M 62 ASP cc_start: 0.7911 (m-30) cc_final: 0.7047 (m-30) REVERT: M 67 VAL cc_start: 0.7528 (t) cc_final: 0.7180 (m) REVERT: M 111 GLU cc_start: 0.8136 (tp30) cc_final: 0.7901 (tp30) REVERT: M 156 THR cc_start: 0.8102 (m) cc_final: 0.7629 (p) REVERT: M 157 LEU cc_start: 0.8116 (tp) cc_final: 0.7290 (pt) REVERT: M 196 SER cc_start: 0.6927 (m) cc_final: 0.6581 (p) REVERT: M 201 GLU cc_start: 0.7855 (pt0) cc_final: 0.7565 (pt0) REVERT: M 203 GLN cc_start: 0.7447 (tp40) cc_final: 0.6951 (tm-30) REVERT: M 210 ILE cc_start: 0.6957 (mm) cc_final: 0.6551 (mt) REVERT: M 227 LEU cc_start: 0.7251 (mt) cc_final: 0.6905 (mt) REVERT: M 228 LEU cc_start: 0.8309 (mt) cc_final: 0.8062 (mt) REVERT: M 229 ASP cc_start: 0.6953 (t0) cc_final: 0.6670 (t0) REVERT: M 250 PHE cc_start: 0.7030 (p90) cc_final: 0.6411 (p90) REVERT: M 298 LYS cc_start: 0.7625 (tttt) cc_final: 0.7393 (ttmm) REVERT: M 300 ASN cc_start: 0.6967 (p0) cc_final: 0.6692 (p0) REVERT: M 303 LYS cc_start: 0.7003 (mmtt) cc_final: 0.6555 (mmmt) REVERT: M 332 PHE cc_start: 0.5418 (t80) cc_final: 0.4545 (t80) REVERT: M 333 ASP cc_start: 0.5346 (t0) cc_final: 0.5073 (t0) REVERT: M 345 LYS cc_start: 0.6417 (pttt) cc_final: 0.6007 (pttp) REVERT: M 359 ASN cc_start: 0.6923 (m-40) cc_final: 0.6596 (m-40) REVERT: M 380 GLN cc_start: 0.7261 (mt0) cc_final: 0.6764 (mt0) REVERT: M 397 GLU cc_start: 0.6587 (mm-30) cc_final: 0.6316 (mp0) REVERT: M 409 THR cc_start: 0.6869 (m) cc_final: 0.6580 (p) REVERT: M 410 LYS cc_start: 0.7576 (mttt) cc_final: 0.7301 (mttt) REVERT: S 6 LEU cc_start: 0.7763 (mt) cc_final: 0.7538 (mt) REVERT: S 7 ILE cc_start: 0.7528 (mt) cc_final: 0.7278 (mt) REVERT: S 8 PHE cc_start: 0.7140 (p90) cc_final: 0.6886 (p90) REVERT: S 17 SER cc_start: 0.7778 (t) cc_final: 0.7066 (p) REVERT: S 18 LYS cc_start: 0.7545 (tttp) cc_final: 0.6915 (tttp) REVERT: S 77 VAL cc_start: 0.6796 (m) cc_final: 0.6531 (p) REVERT: S 117 HIS cc_start: 0.8814 (m-70) cc_final: 0.8413 (m-70) REVERT: S 122 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7625 (mm-30) REVERT: S 123 MET cc_start: 0.8072 (tpt) cc_final: 0.7607 (tpt) REVERT: S 125 MET cc_start: 0.8432 (ttt) cc_final: 0.7919 (ttm) REVERT: S 128 MET cc_start: 0.7028 (mtp) cc_final: 0.6560 (mtp) REVERT: B 41 LEU cc_start: 0.7736 (tp) cc_final: 0.7215 (pp) REVERT: B 45 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7242 (mm-30) REVERT: B 63 MET cc_start: 0.6337 (mmm) cc_final: 0.5671 (mmm) REVERT: B 90 LYS cc_start: 0.7998 (mmtt) cc_final: 0.7649 (mtmm) REVERT: B 96 LYS cc_start: 0.7769 (mmmt) cc_final: 0.7413 (tttp) REVERT: B 97 LEU cc_start: 0.7433 (mt) cc_final: 0.7086 (mt) REVERT: B 151 MET cc_start: 0.7715 (mtm) cc_final: 0.7420 (mtt) REVERT: B 152 MET cc_start: 0.6872 (tmm) cc_final: 0.6620 (tmm) REVERT: B 169 ASN cc_start: 0.8251 (m-40) cc_final: 0.7976 (t0) REVERT: B 187 MET cc_start: 0.8459 (mtp) cc_final: 0.8174 (mtp) REVERT: B 241 GLN cc_start: 0.7360 (mt0) cc_final: 0.6994 (mt0) REVERT: B 255 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7397 (mm-40) REVERT: B 307 LEU cc_start: 0.8553 (mt) cc_final: 0.8181 (tp) REVERT: B 335 ILE cc_start: 0.8368 (pt) cc_final: 0.7914 (pt) REVERT: B 342 LEU cc_start: 0.8433 (mt) cc_final: 0.8209 (mm) REVERT: B 346 ASN cc_start: 0.6218 (t0) cc_final: 0.5928 (t0) REVERT: B 372 LEU cc_start: 0.7693 (tp) cc_final: 0.7462 (tp) REVERT: B 389 LYS cc_start: 0.8018 (mttt) cc_final: 0.7745 (mmtp) REVERT: B 390 LEU cc_start: 0.8116 (tp) cc_final: 0.7868 (tt) REVERT: B 391 GLU cc_start: 0.7827 (tp30) cc_final: 0.7413 (tp30) REVERT: B 440 ASP cc_start: 0.7783 (m-30) cc_final: 0.7476 (p0) REVERT: B 442 CYS cc_start: 0.8001 (m) cc_final: 0.7726 (m) REVERT: B 447 VAL cc_start: 0.8000 (t) cc_final: 0.7756 (t) REVERT: B 468 LEU cc_start: 0.8052 (mt) cc_final: 0.7714 (tt) REVERT: B 472 GLN cc_start: 0.7694 (tp40) cc_final: 0.7363 (tp40) REVERT: B 481 LYS cc_start: 0.8837 (mttt) cc_final: 0.8363 (mttp) REVERT: B 483 MET cc_start: 0.8410 (mmt) cc_final: 0.8024 (mmm) REVERT: B 486 LEU cc_start: 0.7984 (mt) cc_final: 0.7643 (mt) REVERT: B 521 MET cc_start: 0.6627 (mmp) cc_final: 0.6231 (mmm) REVERT: B 539 LEU cc_start: 0.8320 (tp) cc_final: 0.8066 (tp) REVERT: B 569 ASP cc_start: 0.7608 (t70) cc_final: 0.7404 (t70) REVERT: B 577 ILE cc_start: 0.8190 (mt) cc_final: 0.7894 (tp) REVERT: B 578 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7652 (ttp80) outliers start: 2 outliers final: 2 residues processed: 635 average time/residue: 0.3115 time to fit residues: 286.9237 Evaluate side-chains 546 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 544 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 0.5980 chunk 157 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 163 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 chunk 188 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN M 177 ASN M 278 HIS M 322 ASN M 359 ASN M 374 ASN ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.148131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.128394 restraints weight = 36286.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.132321 restraints weight = 21889.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.135048 restraints weight = 14339.444| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17177 Z= 0.199 Angle : 0.649 12.298 23253 Z= 0.352 Chirality : 0.045 0.166 2705 Planarity : 0.004 0.036 2931 Dihedral : 10.522 172.018 2299 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.19), residues: 2098 helix: 1.01 (0.15), residues: 1135 sheet: -0.12 (0.33), residues: 235 loop : 1.41 (0.26), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 74 HIS 0.022 0.002 HIS B 223 PHE 0.027 0.002 PHE D 245 TYR 0.028 0.002 TYR M 180 ARG 0.014 0.001 ARG B 649 Details of bonding type rmsd hydrogen bonds : bond 0.05994 ( 996) hydrogen bonds : angle 5.49172 ( 2835) covalent geometry : bond 0.00387 (17177) covalent geometry : angle 0.64909 (23253) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 587 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8203 (tttt) cc_final: 0.7810 (tttt) REVERT: A 61 ILE cc_start: 0.8421 (mm) cc_final: 0.8184 (mm) REVERT: A 84 ASN cc_start: 0.6970 (m-40) cc_final: 0.6404 (m-40) REVERT: C 81 TYR cc_start: 0.7867 (m-80) cc_final: 0.7566 (m-80) REVERT: C 86 GLN cc_start: 0.7367 (mt0) cc_final: 0.6710 (mt0) REVERT: C 110 MET cc_start: 0.7957 (mtm) cc_final: 0.7707 (mtp) REVERT: C 120 VAL cc_start: 0.7791 (t) cc_final: 0.7527 (t) REVERT: C 138 GLU cc_start: 0.7324 (tt0) cc_final: 0.6554 (tt0) REVERT: C 173 LEU cc_start: 0.7940 (mt) cc_final: 0.7716 (mt) REVERT: C 176 GLN cc_start: 0.6807 (mm-40) cc_final: 0.6419 (mm-40) REVERT: D 1 MET cc_start: 0.4094 (ttp) cc_final: 0.3800 (ttp) REVERT: D 59 VAL cc_start: 0.8093 (t) cc_final: 0.7863 (t) REVERT: D 66 GLN cc_start: 0.7690 (tp40) cc_final: 0.7485 (tp40) REVERT: D 67 MET cc_start: 0.7559 (ttp) cc_final: 0.6597 (tmm) REVERT: D 74 TRP cc_start: 0.8412 (p-90) cc_final: 0.8145 (p-90) REVERT: D 120 LEU cc_start: 0.7598 (mt) cc_final: 0.7344 (mt) REVERT: D 126 TYR cc_start: 0.8223 (m-80) cc_final: 0.7923 (m-80) REVERT: D 128 THR cc_start: 0.7546 (m) cc_final: 0.7188 (p) REVERT: D 132 LEU cc_start: 0.7773 (mt) cc_final: 0.7565 (mt) REVERT: D 151 ILE cc_start: 0.7424 (mt) cc_final: 0.7095 (tp) REVERT: D 155 MET cc_start: 0.8047 (mtm) cc_final: 0.7742 (mtm) REVERT: D 157 HIS cc_start: 0.8220 (t-90) cc_final: 0.7951 (t-90) REVERT: D 177 TYR cc_start: 0.7453 (t80) cc_final: 0.6780 (t80) REVERT: D 179 GLU cc_start: 0.8319 (mp0) cc_final: 0.6928 (mp0) REVERT: D 201 SER cc_start: 0.7815 (m) cc_final: 0.7439 (p) REVERT: D 221 LEU cc_start: 0.8050 (mp) cc_final: 0.7001 (mp) REVERT: D 240 LYS cc_start: 0.8321 (mmtt) cc_final: 0.8004 (mmtt) REVERT: D 252 GLU cc_start: 0.6658 (tp30) cc_final: 0.6421 (tp30) REVERT: D 257 LYS cc_start: 0.8143 (tttt) cc_final: 0.7644 (tttm) REVERT: D 273 MET cc_start: 0.8084 (pmm) cc_final: 0.7811 (pmm) REVERT: D 302 GLN cc_start: 0.8754 (tt0) cc_final: 0.8428 (tt0) REVERT: D 307 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7569 (mmtt) REVERT: D 309 ARG cc_start: 0.7921 (ttp-110) cc_final: 0.7163 (ttp-110) REVERT: D 324 LEU cc_start: 0.8480 (mt) cc_final: 0.8095 (mt) REVERT: D 327 MET cc_start: 0.7248 (tpp) cc_final: 0.6470 (tpp) REVERT: D 329 LYS cc_start: 0.9043 (mttt) cc_final: 0.8752 (mttt) REVERT: D 339 GLN cc_start: 0.8216 (pt0) cc_final: 0.7624 (pm20) REVERT: D 362 ASP cc_start: 0.8496 (m-30) cc_final: 0.8296 (m-30) REVERT: D 367 MET cc_start: 0.6987 (mtm) cc_final: 0.6439 (mtm) REVERT: D 374 MET cc_start: 0.7435 (mtt) cc_final: 0.5841 (mtt) REVERT: D 376 ILE cc_start: 0.8197 (mt) cc_final: 0.7861 (mt) REVERT: D 378 LYS cc_start: 0.8820 (mttt) cc_final: 0.8252 (mtmm) REVERT: D 393 ARG cc_start: 0.7757 (mtt180) cc_final: 0.7556 (ttm-80) REVERT: D 394 ASP cc_start: 0.8498 (m-30) cc_final: 0.7879 (m-30) REVERT: D 396 LEU cc_start: 0.8610 (mt) cc_final: 0.8256 (mt) REVERT: D 398 THR cc_start: 0.8097 (p) cc_final: 0.7657 (t) REVERT: D 400 ILE cc_start: 0.8896 (mt) cc_final: 0.8584 (mt) REVERT: D 403 ILE cc_start: 0.8212 (mt) cc_final: 0.7942 (mt) REVERT: D 422 LEU cc_start: 0.9096 (tp) cc_final: 0.8831 (tp) REVERT: D 488 ILE cc_start: 0.7565 (mm) cc_final: 0.7293 (mm) REVERT: D 514 LEU cc_start: 0.6955 (mt) cc_final: 0.6656 (mt) REVERT: D 534 LEU cc_start: 0.8238 (mt) cc_final: 0.7631 (tp) REVERT: D 536 GLN cc_start: 0.8142 (tm-30) cc_final: 0.7902 (tm-30) REVERT: D 559 GLN cc_start: 0.7825 (tt0) cc_final: 0.7610 (tt0) REVERT: D 571 ARG cc_start: 0.8497 (mtt-85) cc_final: 0.8095 (mtt-85) REVERT: D 573 SER cc_start: 0.8133 (m) cc_final: 0.7814 (p) REVERT: M 25 SER cc_start: 0.7849 (t) cc_final: 0.7528 (p) REVERT: M 62 ASP cc_start: 0.8291 (m-30) cc_final: 0.7676 (m-30) REVERT: M 67 VAL cc_start: 0.7956 (t) cc_final: 0.7619 (m) REVERT: M 111 GLU cc_start: 0.8190 (tp30) cc_final: 0.7650 (tp30) REVERT: M 156 THR cc_start: 0.8069 (m) cc_final: 0.7861 (p) REVERT: M 157 LEU cc_start: 0.8388 (tp) cc_final: 0.7579 (pt) REVERT: M 177 ASN cc_start: 0.6771 (m-40) cc_final: 0.6087 (m-40) REVERT: M 196 SER cc_start: 0.6740 (m) cc_final: 0.6355 (p) REVERT: M 201 GLU cc_start: 0.8056 (pt0) cc_final: 0.7223 (pm20) REVERT: M 210 ILE cc_start: 0.7735 (mm) cc_final: 0.7307 (mp) REVERT: M 212 LEU cc_start: 0.7474 (mt) cc_final: 0.6897 (mt) REVERT: M 239 PHE cc_start: 0.8024 (t80) cc_final: 0.7604 (t80) REVERT: M 256 ASN cc_start: 0.7873 (t0) cc_final: 0.7529 (t0) REVERT: M 263 ARG cc_start: 0.6740 (mtp180) cc_final: 0.6112 (mtp180) REVERT: M 303 LYS cc_start: 0.8205 (mmtt) cc_final: 0.7347 (mmtt) REVERT: M 316 LYS cc_start: 0.7912 (mmtm) cc_final: 0.7609 (mmtm) REVERT: M 329 SER cc_start: 0.7414 (t) cc_final: 0.6986 (p) REVERT: M 352 PRO cc_start: 0.8350 (Cg_endo) cc_final: 0.8006 (Cg_exo) REVERT: M 376 GLN cc_start: 0.5998 (mm-40) cc_final: 0.5688 (mp10) REVERT: M 380 GLN cc_start: 0.7599 (mt0) cc_final: 0.7348 (mt0) REVERT: M 399 TYR cc_start: 0.7867 (p90) cc_final: 0.6476 (p90) REVERT: M 409 THR cc_start: 0.7910 (m) cc_final: 0.7523 (p) REVERT: M 410 LYS cc_start: 0.8160 (mttt) cc_final: 0.7829 (mttt) REVERT: S 7 ILE cc_start: 0.8293 (mt) cc_final: 0.8079 (mt) REVERT: S 8 PHE cc_start: 0.7150 (p90) cc_final: 0.6932 (p90) REVERT: S 17 SER cc_start: 0.7812 (t) cc_final: 0.7237 (p) REVERT: S 18 LYS cc_start: 0.8303 (tttp) cc_final: 0.7578 (tttp) REVERT: S 29 GLN cc_start: 0.8475 (mt0) cc_final: 0.8171 (mm-40) REVERT: S 77 VAL cc_start: 0.7359 (m) cc_final: 0.7063 (p) REVERT: S 82 SER cc_start: 0.6967 (t) cc_final: 0.6533 (t) REVERT: S 89 LEU cc_start: 0.7606 (mt) cc_final: 0.7084 (mt) REVERT: S 116 VAL cc_start: 0.7769 (t) cc_final: 0.7466 (t) REVERT: S 117 HIS cc_start: 0.8364 (m-70) cc_final: 0.7977 (m-70) REVERT: S 123 MET cc_start: 0.7321 (tpt) cc_final: 0.6770 (tpt) REVERT: S 125 MET cc_start: 0.8352 (ttt) cc_final: 0.7896 (ttm) REVERT: S 128 MET cc_start: 0.7547 (mtp) cc_final: 0.6697 (mtp) REVERT: B 41 LEU cc_start: 0.7823 (tp) cc_final: 0.7488 (pp) REVERT: B 45 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7141 (mm-30) REVERT: B 63 MET cc_start: 0.6674 (mmm) cc_final: 0.5781 (mmm) REVERT: B 69 MET cc_start: 0.7540 (mtm) cc_final: 0.7249 (mtm) REVERT: B 75 ASN cc_start: 0.8191 (m110) cc_final: 0.7477 (m-40) REVERT: B 78 GLU cc_start: 0.7698 (pm20) cc_final: 0.7482 (pm20) REVERT: B 97 LEU cc_start: 0.7574 (mt) cc_final: 0.7185 (mt) REVERT: B 98 VAL cc_start: 0.8061 (t) cc_final: 0.7844 (p) REVERT: B 151 MET cc_start: 0.7998 (mtm) cc_final: 0.7717 (mtt) REVERT: B 152 MET cc_start: 0.6883 (tmm) cc_final: 0.6623 (tmm) REVERT: B 153 LEU cc_start: 0.7943 (mt) cc_final: 0.7382 (mp) REVERT: B 187 MET cc_start: 0.8185 (mtp) cc_final: 0.7467 (mtp) REVERT: B 213 GLU cc_start: 0.7483 (mm-30) cc_final: 0.6971 (tp30) REVERT: B 241 GLN cc_start: 0.7666 (mt0) cc_final: 0.7056 (mt0) REVERT: B 293 MET cc_start: 0.6583 (ttm) cc_final: 0.5933 (ttm) REVERT: B 307 LEU cc_start: 0.8742 (mt) cc_final: 0.8314 (tp) REVERT: B 323 TYR cc_start: 0.7674 (m-10) cc_final: 0.7450 (m-80) REVERT: B 360 MET cc_start: 0.7882 (mtp) cc_final: 0.7482 (mtm) REVERT: B 368 PHE cc_start: 0.7506 (m-80) cc_final: 0.7238 (m-80) REVERT: B 386 LYS cc_start: 0.8082 (mttt) cc_final: 0.7619 (mttt) REVERT: B 389 LYS cc_start: 0.8446 (mttt) cc_final: 0.8207 (mmmm) REVERT: B 390 LEU cc_start: 0.8162 (tp) cc_final: 0.7917 (tt) REVERT: B 391 GLU cc_start: 0.7742 (tp30) cc_final: 0.7323 (tp30) REVERT: B 426 GLN cc_start: 0.8484 (mt0) cc_final: 0.7829 (mm-40) REVERT: B 437 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7498 (pp20) REVERT: B 440 ASP cc_start: 0.8024 (m-30) cc_final: 0.7745 (m-30) REVERT: B 462 VAL cc_start: 0.8675 (t) cc_final: 0.8424 (t) REVERT: B 481 LYS cc_start: 0.8912 (mttt) cc_final: 0.8472 (tptt) REVERT: B 486 LEU cc_start: 0.8279 (mt) cc_final: 0.7803 (mt) REVERT: B 521 MET cc_start: 0.6789 (mmp) cc_final: 0.6320 (mmm) REVERT: B 539 LEU cc_start: 0.8480 (tp) cc_final: 0.8248 (tp) REVERT: B 543 LEU cc_start: 0.7537 (mt) cc_final: 0.7316 (mt) REVERT: B 545 LEU cc_start: 0.8713 (mt) cc_final: 0.8489 (mt) REVERT: B 577 ILE cc_start: 0.8592 (mt) cc_final: 0.7891 (tp) REVERT: B 578 ARG cc_start: 0.7870 (ttp80) cc_final: 0.7653 (ttp80) REVERT: B 635 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7306 (mp0) REVERT: B 645 ASP cc_start: 0.7154 (p0) cc_final: 0.6880 (p0) REVERT: B 647 SER cc_start: 0.7402 (t) cc_final: 0.7080 (m) outliers start: 0 outliers final: 0 residues processed: 587 average time/residue: 0.3469 time to fit residues: 296.3246 Evaluate side-chains 528 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 21 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 193 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 173 optimal weight: 0.5980 chunk 36 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 150 HIS D 78 ASN D 214 ASN D 268 HIS M 359 ASN M 370 ASN ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.146475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.126140 restraints weight = 36080.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.130022 restraints weight = 21888.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.132701 restraints weight = 14402.201| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 17177 Z= 0.193 Angle : 0.618 12.853 23253 Z= 0.329 Chirality : 0.044 0.162 2705 Planarity : 0.004 0.038 2931 Dihedral : 10.023 171.847 2299 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.05 % Allowed : 1.44 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.19), residues: 2098 helix: 1.10 (0.15), residues: 1149 sheet: -0.09 (0.34), residues: 226 loop : 1.06 (0.26), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 236 HIS 0.015 0.001 HIS B 223 PHE 0.027 0.002 PHE M 15 TYR 0.020 0.002 TYR B 105 ARG 0.005 0.001 ARG C 75 Details of bonding type rmsd hydrogen bonds : bond 0.05363 ( 996) hydrogen bonds : angle 5.23313 ( 2835) covalent geometry : bond 0.00394 (17177) covalent geometry : angle 0.61750 (23253) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 561 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8337 (tttt) cc_final: 0.7867 (tttt) REVERT: A 61 ILE cc_start: 0.8570 (mm) cc_final: 0.8339 (mm) REVERT: A 84 ASN cc_start: 0.7139 (m-40) cc_final: 0.6511 (m-40) REVERT: C 81 TYR cc_start: 0.7850 (m-80) cc_final: 0.7595 (m-80) REVERT: C 86 GLN cc_start: 0.7258 (mt0) cc_final: 0.6393 (mt0) REVERT: C 110 MET cc_start: 0.8021 (mtm) cc_final: 0.7656 (mtp) REVERT: C 138 GLU cc_start: 0.7388 (tt0) cc_final: 0.6764 (tt0) REVERT: C 173 LEU cc_start: 0.8116 (mt) cc_final: 0.7853 (mt) REVERT: C 175 ASN cc_start: 0.7861 (m-40) cc_final: 0.7193 (t0) REVERT: C 176 GLN cc_start: 0.7029 (mm-40) cc_final: 0.6334 (mm-40) REVERT: D 1 MET cc_start: 0.4074 (ttp) cc_final: 0.3736 (ttp) REVERT: D 66 GLN cc_start: 0.7693 (tp40) cc_final: 0.7454 (tp40) REVERT: D 74 TRP cc_start: 0.8457 (p-90) cc_final: 0.8238 (p-90) REVERT: D 126 TYR cc_start: 0.8113 (m-80) cc_final: 0.7835 (m-80) REVERT: D 128 THR cc_start: 0.7623 (m) cc_final: 0.7263 (p) REVERT: D 132 LEU cc_start: 0.7756 (mt) cc_final: 0.7381 (mt) REVERT: D 155 MET cc_start: 0.8067 (mtm) cc_final: 0.7764 (mtm) REVERT: D 157 HIS cc_start: 0.8230 (t-90) cc_final: 0.7999 (t70) REVERT: D 179 GLU cc_start: 0.8234 (mp0) cc_final: 0.7420 (mp0) REVERT: D 189 LYS cc_start: 0.7846 (mtmt) cc_final: 0.7477 (mtmm) REVERT: D 200 GLN cc_start: 0.7073 (mm110) cc_final: 0.6834 (mm-40) REVERT: D 221 LEU cc_start: 0.7910 (mp) cc_final: 0.7178 (mp) REVERT: D 257 LYS cc_start: 0.8179 (tttt) cc_final: 0.7710 (tttm) REVERT: D 265 ASN cc_start: 0.8035 (m-40) cc_final: 0.7808 (m-40) REVERT: D 268 HIS cc_start: 0.8672 (m90) cc_final: 0.8396 (m90) REVERT: D 273 MET cc_start: 0.8170 (pmm) cc_final: 0.7921 (pmm) REVERT: D 307 LYS cc_start: 0.8206 (mmtt) cc_final: 0.7697 (mmtt) REVERT: D 320 LYS cc_start: 0.7987 (mtpt) cc_final: 0.7290 (mtpt) REVERT: D 324 LEU cc_start: 0.8574 (mt) cc_final: 0.8273 (mt) REVERT: D 327 MET cc_start: 0.7279 (tpp) cc_final: 0.6440 (tpp) REVERT: D 329 LYS cc_start: 0.8960 (mttt) cc_final: 0.8674 (mttt) REVERT: D 362 ASP cc_start: 0.8643 (m-30) cc_final: 0.8374 (m-30) REVERT: D 367 MET cc_start: 0.7012 (mtm) cc_final: 0.6437 (mtm) REVERT: D 378 LYS cc_start: 0.8837 (mttt) cc_final: 0.8400 (mttt) REVERT: D 393 ARG cc_start: 0.7797 (mtt180) cc_final: 0.7522 (ttm-80) REVERT: D 394 ASP cc_start: 0.8287 (m-30) cc_final: 0.7869 (m-30) REVERT: D 396 LEU cc_start: 0.8613 (mt) cc_final: 0.8361 (mt) REVERT: D 403 ILE cc_start: 0.8358 (mt) cc_final: 0.7852 (mm) REVERT: D 415 PHE cc_start: 0.6719 (m-80) cc_final: 0.6449 (m-80) REVERT: D 422 LEU cc_start: 0.9139 (tp) cc_final: 0.8724 (mt) REVERT: D 499 PRO cc_start: 0.7888 (Cg_endo) cc_final: 0.7666 (Cg_exo) REVERT: D 503 LEU cc_start: 0.8265 (mt) cc_final: 0.8004 (mm) REVERT: D 514 LEU cc_start: 0.6825 (mt) cc_final: 0.6533 (mt) REVERT: D 521 VAL cc_start: 0.8474 (p) cc_final: 0.7880 (t) REVERT: D 530 TYR cc_start: 0.7495 (m-80) cc_final: 0.7045 (m-80) REVERT: D 534 LEU cc_start: 0.8193 (mt) cc_final: 0.7594 (tp) REVERT: D 553 MET cc_start: 0.7370 (mtm) cc_final: 0.6920 (mtm) REVERT: D 571 ARG cc_start: 0.8505 (mtt-85) cc_final: 0.8159 (mtt-85) REVERT: M 34 GLU cc_start: 0.7198 (tt0) cc_final: 0.6917 (tt0) REVERT: M 60 TYR cc_start: 0.7439 (t80) cc_final: 0.7073 (t80) REVERT: M 62 ASP cc_start: 0.8285 (m-30) cc_final: 0.8022 (m-30) REVERT: M 67 VAL cc_start: 0.8008 (t) cc_final: 0.7711 (m) REVERT: M 111 GLU cc_start: 0.8056 (tp30) cc_final: 0.7633 (tp30) REVERT: M 156 THR cc_start: 0.8037 (m) cc_final: 0.7807 (p) REVERT: M 157 LEU cc_start: 0.8427 (tp) cc_final: 0.8191 (tp) REVERT: M 178 GLU cc_start: 0.6416 (pt0) cc_final: 0.6143 (pt0) REVERT: M 196 SER cc_start: 0.6827 (m) cc_final: 0.6543 (p) REVERT: M 201 GLU cc_start: 0.8147 (pt0) cc_final: 0.7452 (pm20) REVERT: M 230 ASP cc_start: 0.7383 (t0) cc_final: 0.7051 (t0) REVERT: M 239 PHE cc_start: 0.8042 (t80) cc_final: 0.7606 (t80) REVERT: M 250 PHE cc_start: 0.7834 (p90) cc_final: 0.7544 (p90) REVERT: M 256 ASN cc_start: 0.7821 (t0) cc_final: 0.7422 (t0) REVERT: M 333 ASP cc_start: 0.7716 (t0) cc_final: 0.7462 (t0) REVERT: M 376 GLN cc_start: 0.6072 (mm-40) cc_final: 0.5797 (mp10) REVERT: M 380 GLN cc_start: 0.7844 (mt0) cc_final: 0.7464 (mt0) REVERT: M 381 GLN cc_start: 0.7919 (tm-30) cc_final: 0.7497 (tm-30) REVERT: M 394 MET cc_start: 0.7197 (tmm) cc_final: 0.6803 (tmm) REVERT: M 397 GLU cc_start: 0.6290 (mp0) cc_final: 0.5935 (mp0) REVERT: M 409 THR cc_start: 0.7977 (m) cc_final: 0.7485 (p) REVERT: M 410 LYS cc_start: 0.8155 (mttt) cc_final: 0.7875 (mttt) REVERT: S 8 PHE cc_start: 0.7120 (p90) cc_final: 0.6845 (p90) REVERT: S 17 SER cc_start: 0.7917 (t) cc_final: 0.7622 (p) REVERT: S 18 LYS cc_start: 0.8211 (tttp) cc_final: 0.7407 (tttp) REVERT: S 29 GLN cc_start: 0.8533 (mt0) cc_final: 0.8203 (mm-40) REVERT: S 77 VAL cc_start: 0.7477 (m) cc_final: 0.7181 (p) REVERT: S 86 ILE cc_start: 0.8116 (mm) cc_final: 0.7838 (mm) REVERT: S 116 VAL cc_start: 0.7679 (t) cc_final: 0.7422 (t) REVERT: S 117 HIS cc_start: 0.8427 (m-70) cc_final: 0.8070 (m-70) REVERT: S 123 MET cc_start: 0.7462 (tpt) cc_final: 0.6871 (tpt) REVERT: S 125 MET cc_start: 0.8372 (ttt) cc_final: 0.7874 (ttm) REVERT: S 128 MET cc_start: 0.7615 (mtp) cc_final: 0.6968 (mtp) REVERT: B 41 LEU cc_start: 0.7975 (tp) cc_final: 0.7455 (pp) REVERT: B 45 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7168 (mm-30) REVERT: B 75 ASN cc_start: 0.8237 (m110) cc_final: 0.7983 (m-40) REVERT: B 151 MET cc_start: 0.7975 (mtm) cc_final: 0.7764 (mtt) REVERT: B 152 MET cc_start: 0.6954 (tmm) cc_final: 0.6634 (tmm) REVERT: B 153 LEU cc_start: 0.7996 (mt) cc_final: 0.7654 (mt) REVERT: B 156 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7943 (mttm) REVERT: B 187 MET cc_start: 0.8015 (mtp) cc_final: 0.7662 (mtp) REVERT: B 192 ILE cc_start: 0.7882 (mm) cc_final: 0.7672 (mt) REVERT: B 213 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7122 (tp30) REVERT: B 218 ARG cc_start: 0.7507 (mmm-85) cc_final: 0.6926 (tpt170) REVERT: B 220 ASP cc_start: 0.5981 (p0) cc_final: 0.4951 (p0) REVERT: B 239 TRP cc_start: 0.7844 (m100) cc_final: 0.7552 (m100) REVERT: B 297 HIS cc_start: 0.7851 (t-90) cc_final: 0.7650 (t-90) REVERT: B 307 LEU cc_start: 0.8763 (mt) cc_final: 0.8330 (tp) REVERT: B 322 LEU cc_start: 0.8098 (tp) cc_final: 0.7741 (tp) REVERT: B 323 TYR cc_start: 0.7657 (m-10) cc_final: 0.7406 (m-80) REVERT: B 375 PHE cc_start: 0.7663 (m-80) cc_final: 0.7153 (m-80) REVERT: B 376 TYR cc_start: 0.8627 (m-80) cc_final: 0.8178 (m-80) REVERT: B 386 LYS cc_start: 0.8198 (mttt) cc_final: 0.7755 (mttt) REVERT: B 389 LYS cc_start: 0.8567 (mttt) cc_final: 0.8161 (mtpt) REVERT: B 390 LEU cc_start: 0.8262 (tp) cc_final: 0.7958 (tt) REVERT: B 391 GLU cc_start: 0.7686 (tp30) cc_final: 0.7254 (tp30) REVERT: B 412 TYR cc_start: 0.7724 (m-10) cc_final: 0.7513 (m-10) REVERT: B 426 GLN cc_start: 0.8529 (mt0) cc_final: 0.7911 (mm-40) REVERT: B 433 THR cc_start: 0.8293 (t) cc_final: 0.8031 (t) REVERT: B 440 ASP cc_start: 0.7906 (m-30) cc_final: 0.7409 (p0) REVERT: B 447 VAL cc_start: 0.8165 (t) cc_final: 0.7854 (m) REVERT: B 462 VAL cc_start: 0.8629 (t) cc_final: 0.8381 (t) REVERT: B 465 ILE cc_start: 0.8848 (mt) cc_final: 0.8351 (tp) REVERT: B 479 ILE cc_start: 0.8672 (mm) cc_final: 0.8300 (mm) REVERT: B 481 LYS cc_start: 0.8890 (mttt) cc_final: 0.8341 (tptp) REVERT: B 483 MET cc_start: 0.8452 (mmm) cc_final: 0.7525 (mmm) REVERT: B 486 LEU cc_start: 0.8357 (mt) cc_final: 0.7770 (mt) REVERT: B 499 ILE cc_start: 0.8493 (mm) cc_final: 0.7924 (tp) REVERT: B 521 MET cc_start: 0.6816 (mmp) cc_final: 0.6351 (mmm) REVERT: B 539 LEU cc_start: 0.8411 (tp) cc_final: 0.8111 (tt) REVERT: B 556 GLN cc_start: 0.8059 (mt0) cc_final: 0.7827 (mt0) REVERT: B 577 ILE cc_start: 0.8686 (mt) cc_final: 0.7956 (tp) REVERT: B 578 ARG cc_start: 0.7855 (ttp80) cc_final: 0.7587 (ttp80) REVERT: B 635 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7489 (mp0) REVERT: B 647 SER cc_start: 0.7540 (t) cc_final: 0.7210 (m) outliers start: 1 outliers final: 1 residues processed: 562 average time/residue: 0.3495 time to fit residues: 282.3754 Evaluate side-chains 518 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 517 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 37 optimal weight: 7.9990 chunk 89 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 180 optimal weight: 0.0980 chunk 83 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 168 optimal weight: 0.0060 chunk 207 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 201 optimal weight: 2.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 66 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN D 559 GLN ** M 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 370 ASN M 374 ASN S 117 HIS ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 321 GLN B 482 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.149094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.128171 restraints weight = 35998.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.132327 restraints weight = 21490.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.135161 restraints weight = 14057.283| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17177 Z= 0.143 Angle : 0.574 11.060 23253 Z= 0.299 Chirality : 0.043 0.153 2705 Planarity : 0.004 0.042 2931 Dihedral : 9.468 169.754 2299 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.19), residues: 2098 helix: 1.37 (0.15), residues: 1143 sheet: 0.00 (0.35), residues: 221 loop : 0.97 (0.25), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 417 HIS 0.005 0.001 HIS B 297 PHE 0.024 0.002 PHE D 245 TYR 0.032 0.002 TYR B 376 ARG 0.007 0.001 ARG A 79 Details of bonding type rmsd hydrogen bonds : bond 0.04604 ( 996) hydrogen bonds : angle 4.86082 ( 2835) covalent geometry : bond 0.00297 (17177) covalent geometry : angle 0.57421 (23253) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 551 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8331 (tttt) cc_final: 0.7843 (tttt) REVERT: A 41 GLU cc_start: 0.5482 (mm-30) cc_final: 0.5165 (mm-30) REVERT: A 61 ILE cc_start: 0.8540 (mm) cc_final: 0.8309 (mm) REVERT: A 84 ASN cc_start: 0.6942 (m-40) cc_final: 0.6408 (m-40) REVERT: C 16 LYS cc_start: 0.5545 (mmtt) cc_final: 0.5325 (mmtt) REVERT: C 81 TYR cc_start: 0.7782 (m-80) cc_final: 0.7554 (m-80) REVERT: C 104 ARG cc_start: 0.8526 (ttp80) cc_final: 0.8173 (ttm-80) REVERT: C 110 MET cc_start: 0.8058 (mtm) cc_final: 0.7714 (mtp) REVERT: C 138 GLU cc_start: 0.7485 (tt0) cc_final: 0.6717 (tt0) REVERT: C 149 ARG cc_start: 0.6926 (ttm-80) cc_final: 0.6377 (mtp85) REVERT: C 173 LEU cc_start: 0.8149 (mt) cc_final: 0.7880 (mt) REVERT: C 175 ASN cc_start: 0.7738 (m-40) cc_final: 0.7270 (t0) REVERT: C 176 GLN cc_start: 0.6703 (mm-40) cc_final: 0.6220 (mm-40) REVERT: D 1 MET cc_start: 0.4016 (ttp) cc_final: 0.3677 (ttp) REVERT: D 20 ASP cc_start: 0.7088 (t0) cc_final: 0.6656 (t0) REVERT: D 74 TRP cc_start: 0.8446 (p-90) cc_final: 0.8224 (p-90) REVERT: D 126 TYR cc_start: 0.8115 (m-80) cc_final: 0.7810 (m-80) REVERT: D 128 THR cc_start: 0.7521 (m) cc_final: 0.7166 (p) REVERT: D 132 LEU cc_start: 0.7783 (mt) cc_final: 0.7439 (mt) REVERT: D 154 LEU cc_start: 0.8380 (mt) cc_final: 0.8156 (mp) REVERT: D 155 MET cc_start: 0.7943 (mtm) cc_final: 0.7684 (mtm) REVERT: D 157 HIS cc_start: 0.8295 (t-90) cc_final: 0.8024 (t70) REVERT: D 221 LEU cc_start: 0.7840 (mp) cc_final: 0.7040 (mp) REVERT: D 240 LYS cc_start: 0.8176 (mmtp) cc_final: 0.7868 (mmtt) REVERT: D 257 LYS cc_start: 0.8181 (tttt) cc_final: 0.7706 (tttm) REVERT: D 265 ASN cc_start: 0.8056 (m-40) cc_final: 0.7836 (m-40) REVERT: D 307 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7768 (mmtt) REVERT: D 320 LYS cc_start: 0.7964 (mtpt) cc_final: 0.7254 (mtmm) REVERT: D 324 LEU cc_start: 0.8550 (mt) cc_final: 0.8262 (mt) REVERT: D 327 MET cc_start: 0.7238 (tpp) cc_final: 0.6521 (tpp) REVERT: D 329 LYS cc_start: 0.8938 (mttt) cc_final: 0.8688 (mttt) REVERT: D 362 ASP cc_start: 0.8623 (m-30) cc_final: 0.8314 (m-30) REVERT: D 367 MET cc_start: 0.7073 (mtm) cc_final: 0.6384 (mtm) REVERT: D 374 MET cc_start: 0.7482 (mtt) cc_final: 0.5700 (mtt) REVERT: D 377 VAL cc_start: 0.8809 (t) cc_final: 0.8502 (p) REVERT: D 378 LYS cc_start: 0.8886 (mttt) cc_final: 0.8371 (mttt) REVERT: D 393 ARG cc_start: 0.7710 (mtt180) cc_final: 0.7505 (ttm-80) REVERT: D 394 ASP cc_start: 0.8133 (m-30) cc_final: 0.7757 (m-30) REVERT: D 396 LEU cc_start: 0.8604 (mt) cc_final: 0.8352 (mt) REVERT: D 399 LYS cc_start: 0.8133 (mmmt) cc_final: 0.7650 (mmmt) REVERT: D 403 ILE cc_start: 0.8361 (mt) cc_final: 0.8071 (pt) REVERT: D 406 GLN cc_start: 0.7628 (mt0) cc_final: 0.7313 (mt0) REVERT: D 422 LEU cc_start: 0.9008 (tp) cc_final: 0.8756 (tp) REVERT: D 521 VAL cc_start: 0.8359 (p) cc_final: 0.7567 (t) REVERT: D 530 TYR cc_start: 0.7549 (m-80) cc_final: 0.7202 (m-80) REVERT: D 532 SER cc_start: 0.7654 (m) cc_final: 0.7280 (p) REVERT: D 534 LEU cc_start: 0.8114 (mt) cc_final: 0.7507 (tp) REVERT: D 553 MET cc_start: 0.7325 (mtm) cc_final: 0.6891 (mtm) REVERT: D 571 ARG cc_start: 0.8440 (mtt-85) cc_final: 0.8180 (mtt-85) REVERT: M 17 GLU cc_start: 0.7612 (tt0) cc_final: 0.7389 (tt0) REVERT: M 62 ASP cc_start: 0.8371 (m-30) cc_final: 0.8037 (m-30) REVERT: M 63 LYS cc_start: 0.8585 (mttt) cc_final: 0.7995 (mttt) REVERT: M 67 VAL cc_start: 0.8003 (t) cc_final: 0.7644 (m) REVERT: M 111 GLU cc_start: 0.8017 (tp30) cc_final: 0.7556 (tp30) REVERT: M 176 ASN cc_start: 0.6534 (m-40) cc_final: 0.5652 (m-40) REVERT: M 196 SER cc_start: 0.6837 (m) cc_final: 0.6400 (p) REVERT: M 198 VAL cc_start: 0.7777 (t) cc_final: 0.7404 (t) REVERT: M 201 GLU cc_start: 0.8187 (pt0) cc_final: 0.7411 (pm20) REVERT: M 228 LEU cc_start: 0.8607 (mt) cc_final: 0.8342 (tp) REVERT: M 230 ASP cc_start: 0.7364 (t0) cc_final: 0.6922 (t0) REVERT: M 239 PHE cc_start: 0.8112 (t80) cc_final: 0.7805 (t80) REVERT: M 250 PHE cc_start: 0.7803 (p90) cc_final: 0.6856 (p90) REVERT: M 256 ASN cc_start: 0.7748 (t0) cc_final: 0.7395 (t0) REVERT: M 333 ASP cc_start: 0.7772 (t0) cc_final: 0.7423 (t0) REVERT: M 376 GLN cc_start: 0.5980 (mm-40) cc_final: 0.5736 (mp10) REVERT: M 380 GLN cc_start: 0.7785 (mt0) cc_final: 0.7336 (mt0) REVERT: M 381 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7436 (tm-30) REVERT: M 394 MET cc_start: 0.7087 (tmm) cc_final: 0.6860 (tmm) REVERT: M 409 THR cc_start: 0.7948 (m) cc_final: 0.7423 (p) REVERT: M 410 LYS cc_start: 0.8165 (mttt) cc_final: 0.7891 (mttt) REVERT: S 17 SER cc_start: 0.8083 (t) cc_final: 0.7664 (p) REVERT: S 18 LYS cc_start: 0.8243 (tttp) cc_final: 0.7487 (tttp) REVERT: S 29 GLN cc_start: 0.8550 (mt0) cc_final: 0.8258 (mm-40) REVERT: S 77 VAL cc_start: 0.7440 (m) cc_final: 0.7120 (p) REVERT: S 82 SER cc_start: 0.7513 (t) cc_final: 0.7034 (t) REVERT: S 86 ILE cc_start: 0.8020 (mm) cc_final: 0.7718 (mm) REVERT: S 117 HIS cc_start: 0.8371 (m90) cc_final: 0.8116 (m90) REVERT: S 123 MET cc_start: 0.7480 (tpt) cc_final: 0.6913 (tpt) REVERT: S 125 MET cc_start: 0.8419 (ttt) cc_final: 0.7919 (ttm) REVERT: S 128 MET cc_start: 0.7568 (mtp) cc_final: 0.6970 (mtp) REVERT: B 41 LEU cc_start: 0.7923 (tp) cc_final: 0.7439 (pp) REVERT: B 45 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7225 (mm-30) REVERT: B 63 MET cc_start: 0.6731 (mmm) cc_final: 0.5646 (mmm) REVERT: B 75 ASN cc_start: 0.8174 (m110) cc_final: 0.7534 (m110) REVERT: B 78 GLU cc_start: 0.8040 (pm20) cc_final: 0.7807 (pm20) REVERT: B 96 LYS cc_start: 0.7780 (mmmt) cc_final: 0.7565 (tttp) REVERT: B 97 LEU cc_start: 0.7761 (mt) cc_final: 0.7447 (mt) REVERT: B 151 MET cc_start: 0.7982 (mtm) cc_final: 0.7775 (mtt) REVERT: B 152 MET cc_start: 0.7007 (tmm) cc_final: 0.6750 (tmm) REVERT: B 153 LEU cc_start: 0.7985 (mt) cc_final: 0.7225 (mp) REVERT: B 156 LYS cc_start: 0.8224 (mtpt) cc_final: 0.7939 (mttm) REVERT: B 169 ASN cc_start: 0.8449 (m-40) cc_final: 0.8048 (t0) REVERT: B 187 MET cc_start: 0.7950 (mtp) cc_final: 0.7569 (mtp) REVERT: B 213 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7307 (tp30) REVERT: B 239 TRP cc_start: 0.7584 (m100) cc_final: 0.7145 (m100) REVERT: B 241 GLN cc_start: 0.7725 (mt0) cc_final: 0.6877 (mt0) REVERT: B 293 MET cc_start: 0.6851 (ttt) cc_final: 0.6547 (ttt) REVERT: B 307 LEU cc_start: 0.8564 (mt) cc_final: 0.8189 (tp) REVERT: B 311 ARG cc_start: 0.8073 (ptt90) cc_final: 0.7772 (ptt90) REVERT: B 322 LEU cc_start: 0.7963 (tp) cc_final: 0.7677 (tp) REVERT: B 323 TYR cc_start: 0.7609 (m-10) cc_final: 0.7317 (m-80) REVERT: B 331 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7352 (mm-30) REVERT: B 345 SER cc_start: 0.8292 (t) cc_final: 0.8003 (t) REVERT: B 365 LYS cc_start: 0.7810 (mttt) cc_final: 0.7292 (mtpp) REVERT: B 375 PHE cc_start: 0.7630 (m-80) cc_final: 0.7077 (m-80) REVERT: B 376 TYR cc_start: 0.8520 (m-80) cc_final: 0.8135 (m-80) REVERT: B 386 LYS cc_start: 0.8118 (mttt) cc_final: 0.7642 (mttt) REVERT: B 389 LYS cc_start: 0.8400 (mttt) cc_final: 0.7985 (mttt) REVERT: B 390 LEU cc_start: 0.8116 (tp) cc_final: 0.7734 (tt) REVERT: B 391 GLU cc_start: 0.7521 (tp30) cc_final: 0.7024 (tp30) REVERT: B 399 GLU cc_start: 0.8097 (pm20) cc_final: 0.7215 (pp20) REVERT: B 426 GLN cc_start: 0.8563 (mt0) cc_final: 0.7934 (mm-40) REVERT: B 433 THR cc_start: 0.8077 (t) cc_final: 0.7836 (t) REVERT: B 437 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7489 (pp20) REVERT: B 440 ASP cc_start: 0.7901 (m-30) cc_final: 0.7362 (p0) REVERT: B 443 LEU cc_start: 0.8100 (tt) cc_final: 0.7817 (tt) REVERT: B 462 VAL cc_start: 0.8576 (t) cc_final: 0.8337 (t) REVERT: B 465 ILE cc_start: 0.8705 (mt) cc_final: 0.8384 (mt) REVERT: B 481 LYS cc_start: 0.8909 (mttt) cc_final: 0.8318 (mttt) REVERT: B 483 MET cc_start: 0.8539 (mmm) cc_final: 0.7734 (mmm) REVERT: B 486 LEU cc_start: 0.8277 (mt) cc_final: 0.7754 (mt) REVERT: B 498 SER cc_start: 0.8600 (m) cc_final: 0.8204 (p) REVERT: B 499 ILE cc_start: 0.8447 (mm) cc_final: 0.7735 (tp) REVERT: B 521 MET cc_start: 0.6778 (mmp) cc_final: 0.6380 (mmm) REVERT: B 539 LEU cc_start: 0.8337 (tp) cc_final: 0.8071 (tp) REVERT: B 556 GLN cc_start: 0.8085 (mt0) cc_final: 0.7839 (mt0) REVERT: B 577 ILE cc_start: 0.8722 (mt) cc_final: 0.7974 (tp) REVERT: B 578 ARG cc_start: 0.7801 (ttp80) cc_final: 0.7448 (ttp80) outliers start: 0 outliers final: 0 residues processed: 551 average time/residue: 0.3121 time to fit residues: 249.7011 Evaluate side-chains 512 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 512 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 22 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 chunk 27 optimal weight: 0.0070 chunk 113 optimal weight: 0.0070 chunk 180 optimal weight: 0.3980 chunk 204 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN D 268 HIS M 54 HIS M 71 GLN ** M 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 177 ASN M 374 ASN ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.148949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.127723 restraints weight = 36106.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.131907 restraints weight = 21557.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.134818 restraints weight = 14117.639| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17177 Z= 0.133 Angle : 0.546 9.672 23253 Z= 0.287 Chirality : 0.042 0.151 2705 Planarity : 0.004 0.047 2931 Dihedral : 9.048 167.231 2299 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.19), residues: 2098 helix: 1.47 (0.15), residues: 1153 sheet: 0.06 (0.35), residues: 236 loop : 0.83 (0.25), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 417 HIS 0.007 0.001 HIS B 223 PHE 0.021 0.002 PHE B 211 TYR 0.022 0.002 TYR M 174 ARG 0.007 0.000 ARG D 212 Details of bonding type rmsd hydrogen bonds : bond 0.04350 ( 996) hydrogen bonds : angle 4.71054 ( 2835) covalent geometry : bond 0.00276 (17177) covalent geometry : angle 0.54581 (23253) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 556 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8333 (tttt) cc_final: 0.7826 (tttt) REVERT: A 41 GLU cc_start: 0.5367 (mm-30) cc_final: 0.5053 (mm-30) REVERT: A 61 ILE cc_start: 0.8539 (mm) cc_final: 0.8310 (mm) REVERT: A 84 ASN cc_start: 0.6932 (m-40) cc_final: 0.6407 (m-40) REVERT: C 81 TYR cc_start: 0.7751 (m-80) cc_final: 0.7529 (m-80) REVERT: C 86 GLN cc_start: 0.7136 (mt0) cc_final: 0.6490 (mt0) REVERT: C 110 MET cc_start: 0.8102 (mtm) cc_final: 0.7793 (mtp) REVERT: C 149 ARG cc_start: 0.6874 (ttm-80) cc_final: 0.6417 (mtp85) REVERT: C 173 LEU cc_start: 0.8297 (mt) cc_final: 0.8053 (mt) REVERT: C 175 ASN cc_start: 0.7815 (m-40) cc_final: 0.7359 (t0) REVERT: C 176 GLN cc_start: 0.6927 (mm-40) cc_final: 0.6461 (mm-40) REVERT: D 1 MET cc_start: 0.4025 (ttp) cc_final: 0.3680 (ttp) REVERT: D 20 ASP cc_start: 0.7094 (t0) cc_final: 0.6765 (t0) REVERT: D 91 LYS cc_start: 0.7265 (mtmt) cc_final: 0.6958 (mtmt) REVERT: D 117 ARG cc_start: 0.8123 (ttm-80) cc_final: 0.7887 (mtm-85) REVERT: D 126 TYR cc_start: 0.8083 (m-80) cc_final: 0.7772 (m-80) REVERT: D 128 THR cc_start: 0.7430 (m) cc_final: 0.7105 (p) REVERT: D 132 LEU cc_start: 0.7785 (mt) cc_final: 0.7468 (mt) REVERT: D 154 LEU cc_start: 0.8252 (mt) cc_final: 0.7964 (mp) REVERT: D 155 MET cc_start: 0.7898 (mtm) cc_final: 0.7687 (mtm) REVERT: D 157 HIS cc_start: 0.8284 (t-90) cc_final: 0.8036 (t70) REVERT: D 176 LYS cc_start: 0.8129 (mmpt) cc_final: 0.7642 (mmtm) REVERT: D 189 LYS cc_start: 0.7980 (mtmt) cc_final: 0.7688 (mtmt) REVERT: D 221 LEU cc_start: 0.7852 (mp) cc_final: 0.7086 (mp) REVERT: D 257 LYS cc_start: 0.8133 (tttt) cc_final: 0.7622 (tttm) REVERT: D 307 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7813 (mmtt) REVERT: D 320 LYS cc_start: 0.7987 (mtpt) cc_final: 0.7293 (mtmm) REVERT: D 324 LEU cc_start: 0.8590 (mt) cc_final: 0.8314 (mt) REVERT: D 327 MET cc_start: 0.7216 (tpp) cc_final: 0.6524 (tpp) REVERT: D 329 LYS cc_start: 0.8918 (mttt) cc_final: 0.8651 (mttt) REVERT: D 336 LYS cc_start: 0.8104 (ptpp) cc_final: 0.7688 (ptpp) REVERT: D 362 ASP cc_start: 0.8671 (m-30) cc_final: 0.8388 (m-30) REVERT: D 367 MET cc_start: 0.7101 (mtm) cc_final: 0.6532 (mtm) REVERT: D 374 MET cc_start: 0.7492 (mtt) cc_final: 0.6181 (mtt) REVERT: D 377 VAL cc_start: 0.8780 (t) cc_final: 0.8572 (p) REVERT: D 378 LYS cc_start: 0.8825 (mttt) cc_final: 0.8329 (mttt) REVERT: D 393 ARG cc_start: 0.7822 (mtt180) cc_final: 0.7417 (ttm-80) REVERT: D 394 ASP cc_start: 0.8139 (m-30) cc_final: 0.7789 (m-30) REVERT: D 399 LYS cc_start: 0.8122 (mmmt) cc_final: 0.7675 (mmmt) REVERT: D 403 ILE cc_start: 0.8359 (mt) cc_final: 0.8133 (pt) REVERT: D 406 GLN cc_start: 0.7630 (mt0) cc_final: 0.7384 (mt0) REVERT: D 422 LEU cc_start: 0.8991 (tp) cc_final: 0.8704 (mt) REVERT: D 479 CYS cc_start: 0.8566 (m) cc_final: 0.8040 (p) REVERT: D 530 TYR cc_start: 0.7496 (m-80) cc_final: 0.7146 (m-80) REVERT: D 532 SER cc_start: 0.7702 (m) cc_final: 0.7495 (p) REVERT: D 534 LEU cc_start: 0.8123 (mt) cc_final: 0.7440 (tt) REVERT: D 535 GLN cc_start: 0.7982 (pp30) cc_final: 0.7622 (pp30) REVERT: D 553 MET cc_start: 0.7339 (mtm) cc_final: 0.6946 (mtm) REVERT: D 571 ARG cc_start: 0.8477 (mtt-85) cc_final: 0.8164 (mtt-85) REVERT: M 63 LYS cc_start: 0.8467 (mttt) cc_final: 0.7890 (mttt) REVERT: M 67 VAL cc_start: 0.7996 (t) cc_final: 0.7657 (m) REVERT: M 111 GLU cc_start: 0.8075 (tp30) cc_final: 0.7572 (tp30) REVERT: M 157 LEU cc_start: 0.8404 (tp) cc_final: 0.8193 (tp) REVERT: M 176 ASN cc_start: 0.6461 (m-40) cc_final: 0.5529 (m-40) REVERT: M 196 SER cc_start: 0.6677 (m) cc_final: 0.6276 (p) REVERT: M 198 VAL cc_start: 0.7699 (t) cc_final: 0.7491 (t) REVERT: M 201 GLU cc_start: 0.8144 (pt0) cc_final: 0.7727 (pt0) REVERT: M 212 LEU cc_start: 0.7271 (mm) cc_final: 0.6872 (mm) REVERT: M 228 LEU cc_start: 0.8608 (mt) cc_final: 0.8396 (mt) REVERT: M 230 ASP cc_start: 0.7411 (t0) cc_final: 0.6937 (t0) REVERT: M 239 PHE cc_start: 0.8027 (t80) cc_final: 0.7758 (t80) REVERT: M 250 PHE cc_start: 0.7846 (p90) cc_final: 0.6736 (p90) REVERT: M 256 ASN cc_start: 0.7737 (t0) cc_final: 0.7350 (t0) REVERT: M 332 PHE cc_start: 0.5997 (t80) cc_final: 0.5614 (t80) REVERT: M 333 ASP cc_start: 0.7856 (t0) cc_final: 0.7383 (t0) REVERT: M 376 GLN cc_start: 0.5905 (mm-40) cc_final: 0.5639 (mp10) REVERT: M 380 GLN cc_start: 0.7692 (mt0) cc_final: 0.7235 (mt0) REVERT: M 381 GLN cc_start: 0.7808 (tm-30) cc_final: 0.7337 (tm-30) REVERT: M 399 TYR cc_start: 0.7793 (p90) cc_final: 0.7402 (p90) REVERT: M 406 LYS cc_start: 0.8111 (mtpt) cc_final: 0.7676 (mtmt) REVERT: M 409 THR cc_start: 0.7947 (m) cc_final: 0.7451 (p) REVERT: M 410 LYS cc_start: 0.8184 (mttt) cc_final: 0.7968 (mttt) REVERT: S 17 SER cc_start: 0.8098 (t) cc_final: 0.7643 (p) REVERT: S 18 LYS cc_start: 0.8277 (tttp) cc_final: 0.7498 (tttp) REVERT: S 29 GLN cc_start: 0.8629 (mt0) cc_final: 0.8346 (mm-40) REVERT: S 77 VAL cc_start: 0.7371 (m) cc_final: 0.7106 (p) REVERT: S 82 SER cc_start: 0.7422 (t) cc_final: 0.6900 (t) REVERT: S 86 ILE cc_start: 0.7990 (mm) cc_final: 0.7658 (mm) REVERT: S 97 LEU cc_start: 0.7927 (mt) cc_final: 0.7369 (mt) REVERT: S 117 HIS cc_start: 0.8342 (m90) cc_final: 0.8080 (m90) REVERT: S 123 MET cc_start: 0.7435 (tpt) cc_final: 0.6800 (tpt) REVERT: S 125 MET cc_start: 0.8381 (ttt) cc_final: 0.8016 (ttt) REVERT: S 128 MET cc_start: 0.7545 (mtp) cc_final: 0.6855 (mtp) REVERT: B 41 LEU cc_start: 0.7957 (tp) cc_final: 0.7333 (pp) REVERT: B 45 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7191 (mm-30) REVERT: B 75 ASN cc_start: 0.8087 (m110) cc_final: 0.7866 (m110) REVERT: B 96 LYS cc_start: 0.7804 (mmmt) cc_final: 0.7451 (tptt) REVERT: B 129 GLN cc_start: 0.8500 (pm20) cc_final: 0.8058 (pt0) REVERT: B 151 MET cc_start: 0.7969 (mtm) cc_final: 0.7663 (mtt) REVERT: B 152 MET cc_start: 0.7000 (tmm) cc_final: 0.6702 (tmm) REVERT: B 153 LEU cc_start: 0.8031 (mt) cc_final: 0.7191 (mp) REVERT: B 156 LYS cc_start: 0.8209 (mtpt) cc_final: 0.7696 (mtpp) REVERT: B 169 ASN cc_start: 0.8468 (m-40) cc_final: 0.8142 (t0) REVERT: B 187 MET cc_start: 0.7947 (mtp) cc_final: 0.7599 (mtp) REVERT: B 197 LYS cc_start: 0.8590 (mtmm) cc_final: 0.8377 (mtmm) REVERT: B 199 LYS cc_start: 0.8484 (ptmm) cc_final: 0.8220 (ptmm) REVERT: B 213 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7261 (tp30) REVERT: B 239 TRP cc_start: 0.7518 (m100) cc_final: 0.6971 (m100) REVERT: B 241 GLN cc_start: 0.7952 (mt0) cc_final: 0.7128 (mt0) REVERT: B 297 HIS cc_start: 0.7681 (t70) cc_final: 0.6722 (t-170) REVERT: B 307 LEU cc_start: 0.8593 (mt) cc_final: 0.8165 (tp) REVERT: B 322 LEU cc_start: 0.7954 (tp) cc_final: 0.7738 (tp) REVERT: B 323 TYR cc_start: 0.7682 (m-10) cc_final: 0.7414 (m-80) REVERT: B 330 SER cc_start: 0.7805 (t) cc_final: 0.7362 (t) REVERT: B 331 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7036 (mm-30) REVERT: B 365 LYS cc_start: 0.8075 (mttt) cc_final: 0.7469 (mtpp) REVERT: B 375 PHE cc_start: 0.7732 (m-80) cc_final: 0.7233 (m-80) REVERT: B 386 LYS cc_start: 0.8069 (mttt) cc_final: 0.7609 (mttt) REVERT: B 389 LYS cc_start: 0.8393 (mttt) cc_final: 0.8040 (mtpt) REVERT: B 390 LEU cc_start: 0.8137 (tp) cc_final: 0.7755 (tt) REVERT: B 391 GLU cc_start: 0.7538 (tp30) cc_final: 0.6997 (tp30) REVERT: B 399 GLU cc_start: 0.8060 (pm20) cc_final: 0.7345 (pp20) REVERT: B 426 GLN cc_start: 0.8600 (mt0) cc_final: 0.7992 (mm-40) REVERT: B 433 THR cc_start: 0.7937 (t) cc_final: 0.7705 (t) REVERT: B 437 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7417 (tp30) REVERT: B 440 ASP cc_start: 0.7751 (m-30) cc_final: 0.7269 (p0) REVERT: B 462 VAL cc_start: 0.8645 (t) cc_final: 0.8418 (t) REVERT: B 465 ILE cc_start: 0.8678 (mt) cc_final: 0.8240 (tp) REVERT: B 481 LYS cc_start: 0.8871 (mttt) cc_final: 0.8253 (mttt) REVERT: B 483 MET cc_start: 0.8596 (mmm) cc_final: 0.7836 (mmm) REVERT: B 486 LEU cc_start: 0.8245 (mt) cc_final: 0.7774 (mt) REVERT: B 498 SER cc_start: 0.8592 (m) cc_final: 0.8182 (p) REVERT: B 499 ILE cc_start: 0.8481 (mm) cc_final: 0.7811 (tp) REVERT: B 509 ARG cc_start: 0.7990 (mtt180) cc_final: 0.7767 (mtt-85) REVERT: B 521 MET cc_start: 0.6790 (mmp) cc_final: 0.6367 (mmm) REVERT: B 545 LEU cc_start: 0.8779 (mt) cc_final: 0.8521 (mt) REVERT: B 556 GLN cc_start: 0.8057 (mt0) cc_final: 0.7810 (mt0) REVERT: B 558 ILE cc_start: 0.8408 (mt) cc_final: 0.8203 (pt) REVERT: B 577 ILE cc_start: 0.8842 (mt) cc_final: 0.8131 (tp) REVERT: B 635 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7380 (mp0) outliers start: 0 outliers final: 0 residues processed: 556 average time/residue: 0.3291 time to fit residues: 261.1473 Evaluate side-chains 524 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 524 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 69 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 78 ASN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN D 265 ASN ** M 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** 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 = 0.3962 r_free = 0.3962 target = 0.147002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.125504 restraints weight = 36056.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.129707 restraints weight = 21718.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.132653 restraints weight = 14211.493| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17177 Z= 0.182 Angle : 0.595 12.207 23253 Z= 0.317 Chirality : 0.044 0.191 2705 Planarity : 0.004 0.052 2931 Dihedral : 8.942 171.978 2299 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.19), residues: 2098 helix: 1.36 (0.15), residues: 1159 sheet: 0.06 (0.35), residues: 239 loop : 0.56 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 74 HIS 0.006 0.001 HIS S 117 PHE 0.019 0.002 PHE M 78 TYR 0.021 0.002 TYR M 174 ARG 0.008 0.001 ARG D 187 Details of bonding type rmsd hydrogen bonds : bond 0.04854 ( 996) hydrogen bonds : angle 4.86668 ( 2835) covalent geometry : bond 0.00369 (17177) covalent geometry : angle 0.59495 (23253) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 549 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.5695 (mm-30) cc_final: 0.5319 (mm-30) REVERT: A 61 ILE cc_start: 0.8602 (mm) cc_final: 0.8385 (mm) REVERT: A 84 ASN cc_start: 0.6983 (m-40) cc_final: 0.6422 (m-40) REVERT: A 110 MET cc_start: 0.7799 (ttm) cc_final: 0.7548 (ttm) REVERT: C 81 TYR cc_start: 0.7812 (m-80) cc_final: 0.7592 (m-80) REVERT: C 86 GLN cc_start: 0.7030 (mt0) cc_final: 0.6212 (mt0) REVERT: C 88 LEU cc_start: 0.8287 (tt) cc_final: 0.8050 (tt) REVERT: C 104 ARG cc_start: 0.8585 (ttp80) cc_final: 0.8207 (ttm-80) REVERT: C 110 MET cc_start: 0.8177 (mtm) cc_final: 0.7881 (mtp) REVERT: C 149 ARG cc_start: 0.6955 (ttm-80) cc_final: 0.6737 (mmm160) REVERT: C 173 LEU cc_start: 0.8413 (mt) cc_final: 0.8162 (mt) REVERT: C 175 ASN cc_start: 0.7949 (m-40) cc_final: 0.7565 (t0) REVERT: C 176 GLN cc_start: 0.7052 (mm-40) cc_final: 0.6606 (mm-40) REVERT: C 178 ARG cc_start: 0.7527 (ttt180) cc_final: 0.7313 (tmt170) REVERT: D 1 MET cc_start: 0.3977 (ttp) cc_final: 0.3616 (ttp) REVERT: D 20 ASP cc_start: 0.7157 (t0) cc_final: 0.6855 (t0) REVERT: D 110 MET cc_start: 0.6792 (mmt) cc_final: 0.6434 (mmt) REVERT: D 118 LYS cc_start: 0.8362 (tttt) cc_final: 0.8127 (mtpt) REVERT: D 126 TYR cc_start: 0.8094 (m-80) cc_final: 0.7799 (m-80) REVERT: D 128 THR cc_start: 0.7395 (m) cc_final: 0.7036 (p) REVERT: D 132 LEU cc_start: 0.7816 (mt) cc_final: 0.7449 (mt) REVERT: D 154 LEU cc_start: 0.8342 (mt) cc_final: 0.8086 (mp) REVERT: D 155 MET cc_start: 0.8014 (mtm) cc_final: 0.7804 (mtm) REVERT: D 176 LYS cc_start: 0.8289 (mmpt) cc_final: 0.7549 (mmtm) REVERT: D 189 LYS cc_start: 0.8165 (mtmt) cc_final: 0.7920 (mtmt) REVERT: D 221 LEU cc_start: 0.7643 (mp) cc_final: 0.7091 (mp) REVERT: D 236 TRP cc_start: 0.7912 (t-100) cc_final: 0.7347 (t-100) REVERT: D 240 LYS cc_start: 0.8025 (mmmm) cc_final: 0.7716 (mtpt) REVERT: D 257 LYS cc_start: 0.8182 (tttt) cc_final: 0.7643 (tttm) REVERT: D 307 LYS cc_start: 0.8213 (mmtt) cc_final: 0.7851 (mmtt) REVERT: D 320 LYS cc_start: 0.8074 (mtpt) cc_final: 0.7364 (mtpt) REVERT: D 324 LEU cc_start: 0.8561 (mt) cc_final: 0.8252 (mt) REVERT: D 327 MET cc_start: 0.7398 (tpp) cc_final: 0.6833 (tpp) REVERT: D 329 LYS cc_start: 0.8936 (mttt) cc_final: 0.8676 (mttt) REVERT: D 336 LYS cc_start: 0.8191 (ptpp) cc_final: 0.7807 (ptpp) REVERT: D 349 LEU cc_start: 0.7521 (tp) cc_final: 0.7135 (tp) REVERT: D 362 ASP cc_start: 0.8659 (m-30) cc_final: 0.8315 (m-30) REVERT: D 367 MET cc_start: 0.7164 (mtm) cc_final: 0.6540 (mtm) REVERT: D 374 MET cc_start: 0.7475 (mtt) cc_final: 0.6256 (mtt) REVERT: D 377 VAL cc_start: 0.8831 (t) cc_final: 0.8579 (p) REVERT: D 378 LYS cc_start: 0.8880 (mttt) cc_final: 0.8342 (mttt) REVERT: D 392 TYR cc_start: 0.7584 (t80) cc_final: 0.7282 (t80) REVERT: D 393 ARG cc_start: 0.7871 (mtt180) cc_final: 0.7487 (ptp-110) REVERT: D 394 ASP cc_start: 0.8085 (m-30) cc_final: 0.7787 (m-30) REVERT: D 399 LYS cc_start: 0.7968 (mmmt) cc_final: 0.7548 (mmmt) REVERT: D 403 ILE cc_start: 0.8474 (mt) cc_final: 0.8211 (pt) REVERT: D 406 GLN cc_start: 0.7640 (mt0) cc_final: 0.7406 (mt0) REVERT: D 422 LEU cc_start: 0.8997 (tp) cc_final: 0.8661 (mt) REVERT: D 432 ARG cc_start: 0.6870 (mmm-85) cc_final: 0.6480 (mmm-85) REVERT: D 521 VAL cc_start: 0.8376 (p) cc_final: 0.7878 (t) REVERT: D 530 TYR cc_start: 0.7512 (m-80) cc_final: 0.7123 (m-80) REVERT: D 532 SER cc_start: 0.7763 (m) cc_final: 0.7553 (p) REVERT: D 534 LEU cc_start: 0.8175 (mt) cc_final: 0.7537 (tt) REVERT: D 535 GLN cc_start: 0.8042 (pp30) cc_final: 0.7707 (pp30) REVERT: D 547 GLN cc_start: 0.7327 (mm-40) cc_final: 0.6585 (tp40) REVERT: D 553 MET cc_start: 0.7517 (mtm) cc_final: 0.7013 (mtm) REVERT: D 571 ARG cc_start: 0.8535 (mtt-85) cc_final: 0.8153 (mtt-85) REVERT: M 43 GLU cc_start: 0.8534 (mm-30) cc_final: 0.7903 (mm-30) REVERT: M 59 ILE cc_start: 0.8186 (mp) cc_final: 0.7928 (tt) REVERT: M 63 LYS cc_start: 0.8540 (mttt) cc_final: 0.8044 (mttt) REVERT: M 67 VAL cc_start: 0.8081 (t) cc_final: 0.7701 (m) REVERT: M 111 GLU cc_start: 0.8127 (tp30) cc_final: 0.6955 (tp30) REVERT: M 176 ASN cc_start: 0.6449 (m-40) cc_final: 0.5637 (m-40) REVERT: M 196 SER cc_start: 0.6497 (m) cc_final: 0.6082 (p) REVERT: M 230 ASP cc_start: 0.7561 (t0) cc_final: 0.7116 (t0) REVERT: M 233 PHE cc_start: 0.7874 (m-80) cc_final: 0.7450 (m-80) REVERT: M 239 PHE cc_start: 0.7993 (t80) cc_final: 0.7694 (t80) REVERT: M 250 PHE cc_start: 0.7910 (p90) cc_final: 0.6733 (p90) REVERT: M 256 ASN cc_start: 0.7736 (t0) cc_final: 0.7407 (t0) REVERT: M 333 ASP cc_start: 0.8027 (t0) cc_final: 0.7615 (t0) REVERT: M 366 LYS cc_start: 0.8000 (pttt) cc_final: 0.7789 (ptmt) REVERT: M 376 GLN cc_start: 0.6016 (mm-40) cc_final: 0.5772 (mp10) REVERT: M 380 GLN cc_start: 0.7721 (mt0) cc_final: 0.7238 (mt0) REVERT: M 381 GLN cc_start: 0.7828 (tm-30) cc_final: 0.7261 (tm-30) REVERT: M 406 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7743 (mtmt) REVERT: M 409 THR cc_start: 0.7921 (m) cc_final: 0.7451 (p) REVERT: M 410 LYS cc_start: 0.8191 (mttt) cc_final: 0.7989 (mttt) REVERT: S 17 SER cc_start: 0.8254 (t) cc_final: 0.7874 (p) REVERT: S 18 LYS cc_start: 0.8238 (tttp) cc_final: 0.7407 (tttp) REVERT: S 29 GLN cc_start: 0.8656 (mt0) cc_final: 0.8339 (mm-40) REVERT: S 77 VAL cc_start: 0.7316 (m) cc_final: 0.7015 (p) REVERT: S 82 SER cc_start: 0.7383 (t) cc_final: 0.6917 (t) REVERT: S 86 ILE cc_start: 0.7914 (mm) cc_final: 0.7632 (mm) REVERT: S 89 LEU cc_start: 0.7525 (mt) cc_final: 0.6647 (mt) REVERT: S 97 LEU cc_start: 0.7974 (mt) cc_final: 0.7386 (mt) REVERT: S 123 MET cc_start: 0.7472 (tpt) cc_final: 0.6918 (tpt) REVERT: S 125 MET cc_start: 0.8359 (ttt) cc_final: 0.8158 (ttt) REVERT: B 75 ASN cc_start: 0.8038 (m110) cc_final: 0.7438 (m110) REVERT: B 78 GLU cc_start: 0.8221 (pm20) cc_final: 0.7961 (pm20) REVERT: B 89 SER cc_start: 0.8632 (m) cc_final: 0.8416 (t) REVERT: B 96 LYS cc_start: 0.7851 (mmmt) cc_final: 0.7441 (tptm) REVERT: B 129 GLN cc_start: 0.8503 (pm20) cc_final: 0.8207 (pt0) REVERT: B 151 MET cc_start: 0.7946 (mtm) cc_final: 0.7647 (mtt) REVERT: B 152 MET cc_start: 0.7052 (tmm) cc_final: 0.6779 (tmm) REVERT: B 153 LEU cc_start: 0.7996 (mt) cc_final: 0.7185 (mp) REVERT: B 156 LYS cc_start: 0.8064 (mtpt) cc_final: 0.7619 (mtpp) REVERT: B 169 ASN cc_start: 0.8501 (m-40) cc_final: 0.8146 (t0) REVERT: B 185 LYS cc_start: 0.7870 (mtpt) cc_final: 0.7477 (mmmt) REVERT: B 187 MET cc_start: 0.7940 (mtp) cc_final: 0.7625 (mtp) REVERT: B 193 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7430 (tp30) REVERT: B 197 LYS cc_start: 0.8694 (mttp) cc_final: 0.8083 (mtmm) REVERT: B 199 LYS cc_start: 0.8392 (ptmm) cc_final: 0.8026 (ttpp) REVERT: B 208 VAL cc_start: 0.8423 (p) cc_final: 0.8189 (t) REVERT: B 213 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7479 (tp30) REVERT: B 239 TRP cc_start: 0.7687 (m100) cc_final: 0.7160 (m100) REVERT: B 241 GLN cc_start: 0.7943 (mt0) cc_final: 0.7154 (mt0) REVERT: B 307 LEU cc_start: 0.8686 (mt) cc_final: 0.8351 (tp) REVERT: B 323 TYR cc_start: 0.7643 (m-10) cc_final: 0.7433 (m-80) REVERT: B 331 GLU cc_start: 0.7410 (mm-30) cc_final: 0.7090 (mm-30) REVERT: B 342 LEU cc_start: 0.8603 (mm) cc_final: 0.8318 (mt) REVERT: B 365 LYS cc_start: 0.8243 (mttt) cc_final: 0.7575 (mtpp) REVERT: B 371 TYR cc_start: 0.7722 (m-80) cc_final: 0.7440 (m-80) REVERT: B 375 PHE cc_start: 0.7745 (m-80) cc_final: 0.7279 (m-80) REVERT: B 386 LYS cc_start: 0.8159 (mttt) cc_final: 0.7698 (mttt) REVERT: B 389 LYS cc_start: 0.8513 (mttt) cc_final: 0.8173 (mtpt) REVERT: B 390 LEU cc_start: 0.8143 (tp) cc_final: 0.7713 (tt) REVERT: B 391 GLU cc_start: 0.7547 (tp30) cc_final: 0.7077 (tp30) REVERT: B 399 GLU cc_start: 0.8027 (pm20) cc_final: 0.7615 (pp20) REVERT: B 426 GLN cc_start: 0.8579 (mt0) cc_final: 0.7939 (mm-40) REVERT: B 428 ILE cc_start: 0.7486 (mt) cc_final: 0.7085 (pt) REVERT: B 433 THR cc_start: 0.8039 (t) cc_final: 0.7811 (t) REVERT: B 437 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7499 (tp30) REVERT: B 462 VAL cc_start: 0.8636 (t) cc_final: 0.8407 (t) REVERT: B 465 ILE cc_start: 0.8705 (mt) cc_final: 0.8330 (tp) REVERT: B 481 LYS cc_start: 0.8830 (mttt) cc_final: 0.8281 (mttt) REVERT: B 483 MET cc_start: 0.8602 (mmm) cc_final: 0.7803 (mmm) REVERT: B 486 LEU cc_start: 0.8350 (mt) cc_final: 0.7661 (mt) REVERT: B 498 SER cc_start: 0.8602 (m) cc_final: 0.8140 (p) REVERT: B 499 ILE cc_start: 0.8542 (mm) cc_final: 0.7895 (tp) REVERT: B 521 MET cc_start: 0.7014 (mmp) cc_final: 0.6610 (mmm) REVERT: B 556 GLN cc_start: 0.8073 (mt0) cc_final: 0.7831 (mt0) outliers start: 0 outliers final: 0 residues processed: 549 average time/residue: 0.3164 time to fit residues: 248.8085 Evaluate side-chains 534 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 534 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 126 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 171 optimal weight: 0.7980 chunk 188 optimal weight: 0.0570 chunk 5 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 194 optimal weight: 0.6980 chunk 163 optimal weight: 0.8980 chunk 206 optimal weight: 2.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 78 ASN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN ** D 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 562 GLN ** M 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 GLN ** B 169 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 = 0.3962 r_free = 0.3962 target = 0.147239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.125788 restraints weight = 35636.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.129971 restraints weight = 21453.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.132827 restraints weight = 14073.962| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 17177 Z= 0.172 Angle : 0.599 11.885 23253 Z= 0.316 Chirality : 0.045 0.439 2705 Planarity : 0.004 0.052 2931 Dihedral : 8.815 174.894 2299 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.19), residues: 2098 helix: 1.40 (0.15), residues: 1150 sheet: 0.12 (0.35), residues: 240 loop : 0.46 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 74 HIS 0.015 0.001 HIS D 268 PHE 0.019 0.002 PHE B 211 TYR 0.031 0.002 TYR D 95 ARG 0.009 0.001 ARG D 212 Details of bonding type rmsd hydrogen bonds : bond 0.04717 ( 996) hydrogen bonds : angle 4.85883 ( 2835) covalent geometry : bond 0.00357 (17177) covalent geometry : angle 0.59903 (23253) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 545 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.5704 (mm-30) cc_final: 0.5368 (mm-30) REVERT: A 61 ILE cc_start: 0.8648 (mm) cc_final: 0.8428 (mm) REVERT: A 84 ASN cc_start: 0.6985 (m-40) cc_final: 0.6405 (m-40) REVERT: A 88 LEU cc_start: 0.7560 (mm) cc_final: 0.7083 (mm) REVERT: A 102 GLU cc_start: 0.8427 (tt0) cc_final: 0.7737 (tm-30) REVERT: A 110 MET cc_start: 0.7816 (ttm) cc_final: 0.7588 (ttm) REVERT: C 22 MET cc_start: 0.7532 (ttm) cc_final: 0.7094 (ttm) REVERT: C 86 GLN cc_start: 0.7093 (mt0) cc_final: 0.6376 (mt0) REVERT: C 104 ARG cc_start: 0.8551 (ttp80) cc_final: 0.8096 (ttm-80) REVERT: C 110 MET cc_start: 0.8234 (mtm) cc_final: 0.7967 (mtp) REVERT: C 149 ARG cc_start: 0.7027 (ttm-80) cc_final: 0.6632 (mtp85) REVERT: C 173 LEU cc_start: 0.8454 (mt) cc_final: 0.8182 (mt) REVERT: C 175 ASN cc_start: 0.8060 (m-40) cc_final: 0.7594 (t0) REVERT: C 176 GLN cc_start: 0.7061 (mm-40) cc_final: 0.6597 (mm-40) REVERT: D 1 MET cc_start: 0.4032 (ttp) cc_final: 0.3661 (ttp) REVERT: D 20 ASP cc_start: 0.7167 (t0) cc_final: 0.6878 (t0) REVERT: D 83 MET cc_start: 0.7930 (mtt) cc_final: 0.7362 (mtt) REVERT: D 110 MET cc_start: 0.6761 (mmt) cc_final: 0.6403 (mmt) REVERT: D 112 THR cc_start: 0.7991 (p) cc_final: 0.7169 (t) REVERT: D 116 ILE cc_start: 0.8376 (mm) cc_final: 0.7970 (mm) REVERT: D 118 LYS cc_start: 0.8348 (tttt) cc_final: 0.8116 (mtpt) REVERT: D 126 TYR cc_start: 0.8082 (m-80) cc_final: 0.7707 (m-80) REVERT: D 128 THR cc_start: 0.7371 (m) cc_final: 0.7062 (p) REVERT: D 132 LEU cc_start: 0.7809 (mt) cc_final: 0.7363 (mt) REVERT: D 154 LEU cc_start: 0.8276 (mt) cc_final: 0.8022 (mp) REVERT: D 176 LYS cc_start: 0.8390 (mmpt) cc_final: 0.7710 (mmtm) REVERT: D 179 GLU cc_start: 0.8153 (mp0) cc_final: 0.6516 (mp0) REVERT: D 189 LYS cc_start: 0.8144 (mtmt) cc_final: 0.7907 (mtmt) REVERT: D 221 LEU cc_start: 0.7840 (mp) cc_final: 0.7094 (mp) REVERT: D 236 TRP cc_start: 0.7782 (t-100) cc_final: 0.7559 (t-100) REVERT: D 257 LYS cc_start: 0.8098 (tttt) cc_final: 0.7450 (tmtt) REVERT: D 275 LEU cc_start: 0.8049 (tp) cc_final: 0.7760 (tp) REVERT: D 307 LYS cc_start: 0.8225 (mmtt) cc_final: 0.7847 (mmtt) REVERT: D 320 LYS cc_start: 0.8072 (mtpt) cc_final: 0.7348 (mtpt) REVERT: D 324 LEU cc_start: 0.8607 (mt) cc_final: 0.8262 (mt) REVERT: D 327 MET cc_start: 0.7380 (tpp) cc_final: 0.6853 (tpp) REVERT: D 329 LYS cc_start: 0.8934 (mttt) cc_final: 0.8662 (mttt) REVERT: D 346 LEU cc_start: 0.8678 (mt) cc_final: 0.8441 (mt) REVERT: D 349 LEU cc_start: 0.7651 (tp) cc_final: 0.7291 (tp) REVERT: D 354 GLU cc_start: 0.8069 (pm20) cc_final: 0.7630 (pm20) REVERT: D 362 ASP cc_start: 0.8684 (m-30) cc_final: 0.8340 (m-30) REVERT: D 367 MET cc_start: 0.7192 (mtm) cc_final: 0.6603 (mtm) REVERT: D 374 MET cc_start: 0.7474 (mtt) cc_final: 0.6486 (mtt) REVERT: D 377 VAL cc_start: 0.8853 (t) cc_final: 0.8536 (p) REVERT: D 378 LYS cc_start: 0.8895 (mttt) cc_final: 0.8327 (mttt) REVERT: D 393 ARG cc_start: 0.7897 (mtt180) cc_final: 0.7471 (ttm-80) REVERT: D 394 ASP cc_start: 0.8241 (m-30) cc_final: 0.7950 (m-30) REVERT: D 399 LYS cc_start: 0.8073 (mmmt) cc_final: 0.7631 (mmmt) REVERT: D 400 ILE cc_start: 0.8971 (tt) cc_final: 0.8602 (tt) REVERT: D 406 GLN cc_start: 0.7666 (mt0) cc_final: 0.7449 (mt0) REVERT: D 422 LEU cc_start: 0.8981 (tp) cc_final: 0.8608 (mt) REVERT: D 432 ARG cc_start: 0.6822 (mmm-85) cc_final: 0.6620 (mmm-85) REVERT: D 521 VAL cc_start: 0.8245 (p) cc_final: 0.7864 (p) REVERT: D 524 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7893 (tm-30) REVERT: D 530 TYR cc_start: 0.7396 (m-80) cc_final: 0.7000 (m-80) REVERT: D 532 SER cc_start: 0.7750 (m) cc_final: 0.7529 (p) REVERT: D 534 LEU cc_start: 0.8173 (mt) cc_final: 0.7550 (tt) REVERT: D 535 GLN cc_start: 0.8065 (pp30) cc_final: 0.7726 (pp30) REVERT: D 553 MET cc_start: 0.7484 (mtm) cc_final: 0.6838 (mtm) REVERT: D 571 ARG cc_start: 0.8495 (mtt-85) cc_final: 0.8265 (mtt-85) REVERT: M 43 GLU cc_start: 0.8460 (mm-30) cc_final: 0.7837 (mm-30) REVERT: M 59 ILE cc_start: 0.8186 (mp) cc_final: 0.7893 (tt) REVERT: M 63 LYS cc_start: 0.8431 (mttt) cc_final: 0.7915 (mttt) REVERT: M 67 VAL cc_start: 0.8113 (t) cc_final: 0.7707 (m) REVERT: M 85 ARG cc_start: 0.8517 (tpp80) cc_final: 0.7999 (tpp80) REVERT: M 111 GLU cc_start: 0.8118 (tp30) cc_final: 0.6783 (tp30) REVERT: M 114 GLU cc_start: 0.7622 (tp30) cc_final: 0.7375 (tp30) REVERT: M 176 ASN cc_start: 0.6439 (m-40) cc_final: 0.5748 (m110) REVERT: M 201 GLU cc_start: 0.8149 (pt0) cc_final: 0.7659 (pt0) REVERT: M 230 ASP cc_start: 0.7543 (t0) cc_final: 0.6973 (t0) REVERT: M 250 PHE cc_start: 0.7840 (p90) cc_final: 0.6688 (p90) REVERT: M 256 ASN cc_start: 0.7681 (t0) cc_final: 0.7352 (t0) REVERT: M 333 ASP cc_start: 0.8074 (t0) cc_final: 0.7593 (t0) REVERT: M 376 GLN cc_start: 0.6006 (mm-40) cc_final: 0.5710 (mp10) REVERT: M 380 GLN cc_start: 0.7702 (mt0) cc_final: 0.7152 (mt0) REVERT: M 381 GLN cc_start: 0.7859 (tm-30) cc_final: 0.7253 (tm-30) REVERT: M 394 MET cc_start: 0.6953 (tmm) cc_final: 0.6707 (tmm) REVERT: M 406 LYS cc_start: 0.8180 (mtpt) cc_final: 0.7802 (ttmt) REVERT: M 409 THR cc_start: 0.7880 (m) cc_final: 0.7408 (p) REVERT: M 410 LYS cc_start: 0.8127 (mttt) cc_final: 0.7926 (mttt) REVERT: S 17 SER cc_start: 0.8197 (t) cc_final: 0.7923 (p) REVERT: S 18 LYS cc_start: 0.8136 (tttp) cc_final: 0.7318 (tttp) REVERT: S 29 GLN cc_start: 0.8598 (mt0) cc_final: 0.8066 (mm-40) REVERT: S 86 ILE cc_start: 0.7882 (mm) cc_final: 0.7583 (mm) REVERT: S 89 LEU cc_start: 0.7539 (mt) cc_final: 0.6644 (mt) REVERT: S 97 LEU cc_start: 0.7967 (mt) cc_final: 0.7409 (mt) REVERT: S 123 MET cc_start: 0.7474 (tpt) cc_final: 0.6946 (tpt) REVERT: S 125 MET cc_start: 0.8175 (ttt) cc_final: 0.7870 (ttt) REVERT: S 128 MET cc_start: 0.7442 (mtp) cc_final: 0.6751 (mtp) REVERT: B 75 ASN cc_start: 0.7968 (m110) cc_final: 0.7462 (m110) REVERT: B 78 GLU cc_start: 0.8146 (pm20) cc_final: 0.7939 (pm20) REVERT: B 89 SER cc_start: 0.8601 (m) cc_final: 0.8383 (t) REVERT: B 96 LYS cc_start: 0.7937 (mmmt) cc_final: 0.7471 (tptm) REVERT: B 129 GLN cc_start: 0.8492 (pm20) cc_final: 0.8253 (pt0) REVERT: B 151 MET cc_start: 0.7943 (mtm) cc_final: 0.7620 (mtt) REVERT: B 152 MET cc_start: 0.7077 (tmm) cc_final: 0.6837 (tmm) REVERT: B 156 LYS cc_start: 0.8075 (mtpt) cc_final: 0.7743 (mtpp) REVERT: B 185 LYS cc_start: 0.7869 (mtpt) cc_final: 0.7482 (mmmt) REVERT: B 187 MET cc_start: 0.7943 (mtp) cc_final: 0.7582 (mtp) REVERT: B 193 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7356 (tp30) REVERT: B 197 LYS cc_start: 0.8728 (mttp) cc_final: 0.8033 (mtmm) REVERT: B 199 LYS cc_start: 0.8448 (ptmm) cc_final: 0.8102 (ttpp) REVERT: B 208 VAL cc_start: 0.8514 (p) cc_final: 0.8269 (t) REVERT: B 213 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7352 (tp30) REVERT: B 239 TRP cc_start: 0.7745 (m100) cc_final: 0.7353 (m100) REVERT: B 241 GLN cc_start: 0.7921 (mt0) cc_final: 0.7109 (mt0) REVERT: B 297 HIS cc_start: 0.7748 (t70) cc_final: 0.6766 (t-170) REVERT: B 307 LEU cc_start: 0.8682 (mt) cc_final: 0.8274 (tp) REVERT: B 323 TYR cc_start: 0.7719 (m-10) cc_final: 0.7502 (m-80) REVERT: B 331 GLU cc_start: 0.7301 (mm-30) cc_final: 0.6805 (mm-30) REVERT: B 371 TYR cc_start: 0.7759 (m-80) cc_final: 0.7416 (m-80) REVERT: B 378 ARG cc_start: 0.7765 (mtt90) cc_final: 0.7473 (mtm180) REVERT: B 386 LYS cc_start: 0.8171 (mttt) cc_final: 0.7410 (mttt) REVERT: B 389 LYS cc_start: 0.8527 (mttt) cc_final: 0.8106 (mtpp) REVERT: B 390 LEU cc_start: 0.8056 (tp) cc_final: 0.7724 (tt) REVERT: B 399 GLU cc_start: 0.8137 (pm20) cc_final: 0.7800 (pp20) REVERT: B 426 GLN cc_start: 0.8540 (mt0) cc_final: 0.7885 (mm-40) REVERT: B 428 ILE cc_start: 0.7463 (mt) cc_final: 0.7242 (pt) REVERT: B 433 THR cc_start: 0.7967 (t) cc_final: 0.7731 (t) REVERT: B 465 ILE cc_start: 0.8666 (mt) cc_final: 0.8152 (mm) REVERT: B 481 LYS cc_start: 0.8801 (mttt) cc_final: 0.8167 (mttt) REVERT: B 483 MET cc_start: 0.8611 (mmm) cc_final: 0.7633 (mmm) REVERT: B 486 LEU cc_start: 0.8292 (mt) cc_final: 0.7814 (mt) REVERT: B 498 SER cc_start: 0.8608 (m) cc_final: 0.8151 (p) REVERT: B 499 ILE cc_start: 0.8477 (mm) cc_final: 0.7803 (tp) REVERT: B 521 MET cc_start: 0.6958 (mmp) cc_final: 0.6507 (mmm) REVERT: B 545 LEU cc_start: 0.8683 (mt) cc_final: 0.8414 (mt) REVERT: B 556 GLN cc_start: 0.8044 (mt0) cc_final: 0.7802 (mt0) REVERT: B 577 ILE cc_start: 0.8956 (mm) cc_final: 0.8239 (tp) outliers start: 0 outliers final: 0 residues processed: 545 average time/residue: 0.3839 time to fit residues: 304.4321 Evaluate side-chains 531 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 531 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 102 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 154 optimal weight: 0.5980 chunk 182 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 90 optimal weight: 0.0070 chunk 157 optimal weight: 0.3980 chunk 184 optimal weight: 0.3980 chunk 173 optimal weight: 0.0770 chunk 73 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN ** M 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 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 = 0.3992 r_free = 0.3992 target = 0.149266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.127671 restraints weight = 35389.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.131895 restraints weight = 21533.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.134807 restraints weight = 14140.184| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17177 Z= 0.123 Angle : 0.573 8.954 23253 Z= 0.297 Chirality : 0.043 0.176 2705 Planarity : 0.004 0.052 2931 Dihedral : 8.708 176.717 2299 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.19), residues: 2098 helix: 1.45 (0.15), residues: 1151 sheet: 0.22 (0.35), residues: 230 loop : 0.54 (0.25), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 74 HIS 0.016 0.001 HIS D 268 PHE 0.050 0.002 PHE D 245 TYR 0.025 0.002 TYR M 174 ARG 0.008 0.001 ARG B 167 Details of bonding type rmsd hydrogen bonds : bond 0.04166 ( 996) hydrogen bonds : angle 4.66696 ( 2835) covalent geometry : bond 0.00261 (17177) covalent geometry : angle 0.57252 (23253) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 549 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8392 (tttt) cc_final: 0.7877 (tttt) REVERT: A 41 GLU cc_start: 0.5497 (mm-30) cc_final: 0.5186 (mm-30) REVERT: A 61 ILE cc_start: 0.8615 (mm) cc_final: 0.8396 (mm) REVERT: A 84 ASN cc_start: 0.6918 (m-40) cc_final: 0.6336 (m-40) REVERT: A 88 LEU cc_start: 0.7481 (mm) cc_final: 0.6924 (mm) REVERT: C 22 MET cc_start: 0.7569 (ttm) cc_final: 0.7153 (ttm) REVERT: C 86 GLN cc_start: 0.7038 (mt0) cc_final: 0.6214 (mt0) REVERT: C 104 ARG cc_start: 0.8559 (ttp80) cc_final: 0.8112 (ttm-80) REVERT: C 138 GLU cc_start: 0.7067 (tm-30) cc_final: 0.6521 (tt0) REVERT: C 173 LEU cc_start: 0.8410 (mt) cc_final: 0.8157 (mt) REVERT: C 175 ASN cc_start: 0.7988 (m-40) cc_final: 0.7537 (t0) REVERT: C 176 GLN cc_start: 0.6973 (mm-40) cc_final: 0.6591 (mm-40) REVERT: D 1 MET cc_start: 0.4034 (ttp) cc_final: 0.3657 (ttp) REVERT: D 74 TRP cc_start: 0.8353 (p-90) cc_final: 0.8060 (p-90) REVERT: D 83 MET cc_start: 0.7907 (mtt) cc_final: 0.7418 (mtt) REVERT: D 110 MET cc_start: 0.6693 (mmt) cc_final: 0.6350 (mmt) REVERT: D 112 THR cc_start: 0.7801 (p) cc_final: 0.7064 (t) REVERT: D 126 TYR cc_start: 0.8057 (m-80) cc_final: 0.7752 (m-80) REVERT: D 128 THR cc_start: 0.7463 (m) cc_final: 0.7087 (p) REVERT: D 132 LEU cc_start: 0.7676 (mt) cc_final: 0.7285 (mt) REVERT: D 155 MET cc_start: 0.8028 (mtm) cc_final: 0.7697 (mtm) REVERT: D 157 HIS cc_start: 0.8339 (t-90) cc_final: 0.8094 (t70) REVERT: D 176 LYS cc_start: 0.8397 (mmpt) cc_final: 0.7325 (mmtm) REVERT: D 189 LYS cc_start: 0.8043 (mtmt) cc_final: 0.7802 (mttt) REVERT: D 221 LEU cc_start: 0.7583 (mp) cc_final: 0.7084 (mp) REVERT: D 236 TRP cc_start: 0.7755 (t-100) cc_final: 0.7412 (t-100) REVERT: D 257 LYS cc_start: 0.8042 (tttt) cc_final: 0.7493 (tttm) REVERT: D 273 MET cc_start: 0.8162 (pmm) cc_final: 0.7955 (pmm) REVERT: D 275 LEU cc_start: 0.7927 (tp) cc_final: 0.7603 (tp) REVERT: D 302 GLN cc_start: 0.8557 (tt0) cc_final: 0.7655 (tm-30) REVERT: D 307 LYS cc_start: 0.8211 (mmtt) cc_final: 0.7800 (mmtt) REVERT: D 308 LEU cc_start: 0.8247 (mt) cc_final: 0.8031 (mt) REVERT: D 324 LEU cc_start: 0.8537 (mt) cc_final: 0.8235 (mt) REVERT: D 327 MET cc_start: 0.7233 (tpp) cc_final: 0.6701 (tpp) REVERT: D 329 LYS cc_start: 0.8900 (mttt) cc_final: 0.8591 (mttt) REVERT: D 346 LEU cc_start: 0.8592 (mt) cc_final: 0.8344 (mt) REVERT: D 362 ASP cc_start: 0.8620 (m-30) cc_final: 0.8342 (m-30) REVERT: D 367 MET cc_start: 0.7168 (mtm) cc_final: 0.6783 (mtm) REVERT: D 373 LEU cc_start: 0.8493 (tp) cc_final: 0.8234 (pp) REVERT: D 374 MET cc_start: 0.7217 (mtt) cc_final: 0.6129 (mtt) REVERT: D 378 LYS cc_start: 0.8888 (mttt) cc_final: 0.8323 (mttt) REVERT: D 381 MET cc_start: 0.7878 (mtp) cc_final: 0.7528 (mtp) REVERT: D 392 TYR cc_start: 0.7469 (t80) cc_final: 0.7234 (t80) REVERT: D 393 ARG cc_start: 0.7878 (mtt180) cc_final: 0.7430 (ttm-80) REVERT: D 394 ASP cc_start: 0.8127 (m-30) cc_final: 0.7812 (m-30) REVERT: D 399 LYS cc_start: 0.8022 (mmmt) cc_final: 0.7508 (mmmt) REVERT: D 400 ILE cc_start: 0.8897 (tt) cc_final: 0.8453 (tp) REVERT: D 403 ILE cc_start: 0.8503 (pt) cc_final: 0.8070 (pt) REVERT: D 421 ILE cc_start: 0.8402 (mm) cc_final: 0.8175 (mm) REVERT: D 422 LEU cc_start: 0.8915 (tp) cc_final: 0.8594 (mt) REVERT: D 432 ARG cc_start: 0.6846 (mmm-85) cc_final: 0.6438 (mmm-85) REVERT: D 530 TYR cc_start: 0.7374 (m-80) cc_final: 0.6997 (m-80) REVERT: D 532 SER cc_start: 0.7727 (m) cc_final: 0.7519 (p) REVERT: D 534 LEU cc_start: 0.8118 (mt) cc_final: 0.7469 (tt) REVERT: D 535 GLN cc_start: 0.8006 (pp30) cc_final: 0.7668 (pp30) REVERT: D 553 MET cc_start: 0.7512 (mtm) cc_final: 0.6872 (mtm) REVERT: M 43 GLU cc_start: 0.8391 (mm-30) cc_final: 0.7690 (mm-30) REVERT: M 67 VAL cc_start: 0.8035 (t) cc_final: 0.7681 (m) REVERT: M 105 ASN cc_start: 0.7453 (m-40) cc_final: 0.7102 (m-40) REVERT: M 111 GLU cc_start: 0.8085 (tp30) cc_final: 0.7637 (tp30) REVERT: M 167 TRP cc_start: 0.7911 (p90) cc_final: 0.6853 (p90) REVERT: M 176 ASN cc_start: 0.6454 (m-40) cc_final: 0.5717 (m110) REVERT: M 250 PHE cc_start: 0.7883 (p90) cc_final: 0.6668 (p90) REVERT: M 256 ASN cc_start: 0.7668 (t0) cc_final: 0.7402 (t0) REVERT: M 333 ASP cc_start: 0.8118 (t0) cc_final: 0.7699 (t0) REVERT: M 376 GLN cc_start: 0.5984 (mm-40) cc_final: 0.5683 (mp10) REVERT: M 380 GLN cc_start: 0.7582 (mt0) cc_final: 0.7030 (mt0) REVERT: M 381 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7239 (tm-30) REVERT: M 394 MET cc_start: 0.6870 (tmm) cc_final: 0.6630 (tmm) REVERT: M 406 LYS cc_start: 0.8145 (mtpt) cc_final: 0.7779 (ttmt) REVERT: M 409 THR cc_start: 0.7868 (m) cc_final: 0.7430 (p) REVERT: S 17 SER cc_start: 0.8129 (t) cc_final: 0.7831 (p) REVERT: S 18 LYS cc_start: 0.8108 (tttp) cc_final: 0.7279 (tttp) REVERT: S 29 GLN cc_start: 0.8603 (mt0) cc_final: 0.8360 (mt0) REVERT: S 86 ILE cc_start: 0.7854 (mm) cc_final: 0.7650 (mm) REVERT: S 89 LEU cc_start: 0.7534 (mt) cc_final: 0.6559 (mt) REVERT: S 97 LEU cc_start: 0.7970 (mt) cc_final: 0.7372 (mt) REVERT: S 123 MET cc_start: 0.7412 (tpt) cc_final: 0.6842 (tpt) REVERT: S 125 MET cc_start: 0.8228 (ttt) cc_final: 0.7921 (ttt) REVERT: S 128 MET cc_start: 0.7330 (mtp) cc_final: 0.6955 (mtp) REVERT: S 134 MET cc_start: 0.5291 (tmm) cc_final: 0.5069 (tmm) REVERT: B 50 MET cc_start: 0.7489 (ptp) cc_final: 0.7279 (ptp) REVERT: B 75 ASN cc_start: 0.7975 (m110) cc_final: 0.7330 (m110) REVERT: B 78 GLU cc_start: 0.8083 (pm20) cc_final: 0.7760 (pm20) REVERT: B 89 SER cc_start: 0.8518 (m) cc_final: 0.8289 (t) REVERT: B 96 LYS cc_start: 0.7825 (mmmt) cc_final: 0.7485 (tptt) REVERT: B 129 GLN cc_start: 0.8472 (pm20) cc_final: 0.8216 (pt0) REVERT: B 151 MET cc_start: 0.7907 (mtm) cc_final: 0.7618 (mtt) REVERT: B 152 MET cc_start: 0.7055 (tmm) cc_final: 0.6789 (tmm) REVERT: B 153 LEU cc_start: 0.8020 (mt) cc_final: 0.7233 (mp) REVERT: B 156 LYS cc_start: 0.8056 (mtpt) cc_final: 0.7824 (mttm) REVERT: B 185 LYS cc_start: 0.7811 (mtpt) cc_final: 0.7421 (mmmt) REVERT: B 187 MET cc_start: 0.7826 (mtp) cc_final: 0.7470 (mtp) REVERT: B 197 LYS cc_start: 0.8686 (mttp) cc_final: 0.8197 (mtmm) REVERT: B 199 LYS cc_start: 0.8444 (ptmm) cc_final: 0.8198 (ptmm) REVERT: B 213 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7411 (tp30) REVERT: B 239 TRP cc_start: 0.7579 (m100) cc_final: 0.7213 (m100) REVERT: B 297 HIS cc_start: 0.7666 (t70) cc_final: 0.6755 (t-170) REVERT: B 307 LEU cc_start: 0.8629 (mt) cc_final: 0.8285 (tp) REVERT: B 323 TYR cc_start: 0.7642 (m-10) cc_final: 0.7413 (m-80) REVERT: B 331 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6712 (mm-30) REVERT: B 342 LEU cc_start: 0.8464 (mt) cc_final: 0.8245 (mt) REVERT: B 345 SER cc_start: 0.8260 (t) cc_final: 0.8009 (t) REVERT: B 365 LYS cc_start: 0.8208 (mttt) cc_final: 0.7538 (mtpp) REVERT: B 371 TYR cc_start: 0.7775 (m-80) cc_final: 0.7343 (m-80) REVERT: B 376 TYR cc_start: 0.8562 (m-80) cc_final: 0.8228 (m-80) REVERT: B 378 ARG cc_start: 0.7755 (mtt90) cc_final: 0.7368 (mtm180) REVERT: B 386 LYS cc_start: 0.8125 (mttt) cc_final: 0.7337 (mttt) REVERT: B 389 LYS cc_start: 0.8499 (mttt) cc_final: 0.8094 (mtpt) REVERT: B 390 LEU cc_start: 0.8088 (tp) cc_final: 0.7766 (tt) REVERT: B 391 GLU cc_start: 0.7293 (tp30) cc_final: 0.6849 (tp30) REVERT: B 426 GLN cc_start: 0.8523 (mt0) cc_final: 0.7885 (mm-40) REVERT: B 428 ILE cc_start: 0.7461 (mt) cc_final: 0.7054 (pt) REVERT: B 433 THR cc_start: 0.7846 (t) cc_final: 0.7583 (t) REVERT: B 465 ILE cc_start: 0.8646 (mt) cc_final: 0.8221 (tp) REVERT: B 481 LYS cc_start: 0.8763 (mttt) cc_final: 0.8130 (mttt) REVERT: B 483 MET cc_start: 0.8577 (mmm) cc_final: 0.7700 (mmm) REVERT: B 486 LEU cc_start: 0.8321 (mt) cc_final: 0.7814 (mt) REVERT: B 498 SER cc_start: 0.8589 (m) cc_final: 0.8130 (p) REVERT: B 499 ILE cc_start: 0.8491 (mm) cc_final: 0.7797 (tp) REVERT: B 521 MET cc_start: 0.6861 (mmp) cc_final: 0.6454 (mmm) REVERT: B 545 LEU cc_start: 0.8710 (mt) cc_final: 0.8505 (mt) REVERT: B 556 GLN cc_start: 0.8026 (mt0) cc_final: 0.7786 (mt0) outliers start: 0 outliers final: 0 residues processed: 549 average time/residue: 0.3252 time to fit residues: 257.2125 Evaluate side-chains 533 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 533 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 25 optimal weight: 0.0870 chunk 167 optimal weight: 0.7980 chunk 165 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 chunk 107 optimal weight: 0.3980 chunk 113 optimal weight: 0.0980 chunk 18 optimal weight: 0.9990 chunk 145 optimal weight: 0.2980 chunk 40 optimal weight: 0.9980 chunk 171 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN ** M 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 HIS ** 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 = 0.4000 r_free = 0.4000 target = 0.149921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.128380 restraints weight = 35393.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.132637 restraints weight = 21200.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.135582 restraints weight = 13853.942| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17177 Z= 0.122 Angle : 0.566 9.199 23253 Z= 0.293 Chirality : 0.043 0.177 2705 Planarity : 0.004 0.052 2931 Dihedral : 8.595 177.631 2299 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.19), residues: 2098 helix: 1.46 (0.15), residues: 1153 sheet: 0.23 (0.35), residues: 229 loop : 0.56 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 236 HIS 0.015 0.001 HIS D 268 PHE 0.038 0.002 PHE D 245 TYR 0.019 0.002 TYR M 174 ARG 0.010 0.001 ARG A 97 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 996) hydrogen bonds : angle 4.62357 ( 2835) covalent geometry : bond 0.00265 (17177) covalent geometry : angle 0.56623 (23253) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 542 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8386 (tttt) cc_final: 0.7898 (tttt) REVERT: A 41 GLU cc_start: 0.5465 (mm-30) cc_final: 0.5156 (mm-30) REVERT: A 61 ILE cc_start: 0.8622 (mm) cc_final: 0.8396 (mm) REVERT: A 84 ASN cc_start: 0.6966 (m-40) cc_final: 0.6337 (m-40) REVERT: A 102 GLU cc_start: 0.8386 (tt0) cc_final: 0.7622 (tm-30) REVERT: A 134 MET cc_start: 0.4377 (mpp) cc_final: 0.3969 (mpp) REVERT: C 38 LYS cc_start: 0.8443 (tmtt) cc_final: 0.8162 (tmtt) REVERT: C 39 LEU cc_start: 0.8572 (mp) cc_final: 0.7634 (mp) REVERT: C 57 GLU cc_start: 0.6702 (mt-10) cc_final: 0.6470 (mt-10) REVERT: C 86 GLN cc_start: 0.7256 (mt0) cc_final: 0.6555 (mt0) REVERT: C 104 ARG cc_start: 0.8598 (ttp80) cc_final: 0.8133 (ttm-80) REVERT: C 110 MET cc_start: 0.8115 (ttm) cc_final: 0.7848 (ttm) REVERT: C 173 LEU cc_start: 0.8399 (mt) cc_final: 0.8119 (mt) REVERT: C 175 ASN cc_start: 0.7945 (m-40) cc_final: 0.7434 (t0) REVERT: C 176 GLN cc_start: 0.6934 (mm-40) cc_final: 0.6581 (mm-40) REVERT: D 1 MET cc_start: 0.4006 (ttp) cc_final: 0.3649 (ttp) REVERT: D 74 TRP cc_start: 0.8377 (p-90) cc_final: 0.8125 (p-90) REVERT: D 83 MET cc_start: 0.7931 (mtt) cc_final: 0.7433 (mtt) REVERT: D 110 MET cc_start: 0.6624 (mmt) cc_final: 0.6293 (mmt) REVERT: D 112 THR cc_start: 0.7715 (p) cc_final: 0.7246 (m) REVERT: D 116 ILE cc_start: 0.8292 (mm) cc_final: 0.8030 (mm) REVERT: D 117 ARG cc_start: 0.8149 (ttm-80) cc_final: 0.7941 (mtm-85) REVERT: D 126 TYR cc_start: 0.8004 (m-80) cc_final: 0.7721 (m-80) REVERT: D 128 THR cc_start: 0.7413 (m) cc_final: 0.7057 (p) REVERT: D 132 LEU cc_start: 0.7648 (mt) cc_final: 0.7236 (mt) REVERT: D 155 MET cc_start: 0.7979 (mtm) cc_final: 0.7607 (mtm) REVERT: D 176 LYS cc_start: 0.8416 (mmpt) cc_final: 0.7387 (mmtm) REVERT: D 179 GLU cc_start: 0.8009 (mp0) cc_final: 0.6367 (mp0) REVERT: D 221 LEU cc_start: 0.7769 (mp) cc_final: 0.7015 (mp) REVERT: D 236 TRP cc_start: 0.7799 (t-100) cc_final: 0.7313 (t-100) REVERT: D 257 LYS cc_start: 0.8075 (tttt) cc_final: 0.7541 (tttm) REVERT: D 275 LEU cc_start: 0.7923 (tp) cc_final: 0.7603 (tp) REVERT: D 307 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7845 (mmtt) REVERT: D 324 LEU cc_start: 0.8540 (mt) cc_final: 0.8228 (mt) REVERT: D 327 MET cc_start: 0.7182 (tpp) cc_final: 0.6642 (tpp) REVERT: D 329 LYS cc_start: 0.8898 (mttt) cc_final: 0.8571 (mttt) REVERT: D 339 GLN cc_start: 0.8361 (pt0) cc_final: 0.8000 (pp30) REVERT: D 346 LEU cc_start: 0.8605 (mt) cc_final: 0.8380 (mt) REVERT: D 349 LEU cc_start: 0.7748 (tp) cc_final: 0.7247 (tp) REVERT: D 362 ASP cc_start: 0.8622 (m-30) cc_final: 0.8355 (m-30) REVERT: D 367 MET cc_start: 0.7214 (mtm) cc_final: 0.6826 (mtm) REVERT: D 373 LEU cc_start: 0.8664 (tp) cc_final: 0.8287 (pp) REVERT: D 374 MET cc_start: 0.6917 (mtt) cc_final: 0.5716 (mtt) REVERT: D 378 LYS cc_start: 0.8910 (mttt) cc_final: 0.8403 (mttt) REVERT: D 381 MET cc_start: 0.7867 (mtp) cc_final: 0.7519 (mtp) REVERT: D 383 HIS cc_start: 0.7545 (t70) cc_final: 0.6885 (t70) REVERT: D 393 ARG cc_start: 0.7858 (mtt180) cc_final: 0.7428 (ttm-80) REVERT: D 394 ASP cc_start: 0.8170 (m-30) cc_final: 0.7765 (m-30) REVERT: D 399 LYS cc_start: 0.8000 (mmmt) cc_final: 0.7526 (mmmt) REVERT: D 400 ILE cc_start: 0.8871 (tt) cc_final: 0.8480 (tp) REVERT: D 403 ILE cc_start: 0.8538 (pt) cc_final: 0.8090 (pt) REVERT: D 432 ARG cc_start: 0.6702 (mmm-85) cc_final: 0.6488 (mmm-85) REVERT: D 440 GLN cc_start: 0.7546 (mm-40) cc_final: 0.6893 (tp40) REVERT: D 524 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7827 (tm-30) REVERT: D 530 TYR cc_start: 0.7406 (m-80) cc_final: 0.7017 (m-80) REVERT: D 532 SER cc_start: 0.7715 (m) cc_final: 0.7515 (p) REVERT: D 534 LEU cc_start: 0.8242 (mt) cc_final: 0.7605 (tt) REVERT: D 535 GLN cc_start: 0.7991 (pp30) cc_final: 0.7667 (pp30) REVERT: D 536 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7945 (tm-30) REVERT: D 553 MET cc_start: 0.7499 (mtm) cc_final: 0.6853 (mtm) REVERT: M 43 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7670 (mm-30) REVERT: M 59 ILE cc_start: 0.8253 (mp) cc_final: 0.8042 (mp) REVERT: M 67 VAL cc_start: 0.8053 (t) cc_final: 0.7639 (m) REVERT: M 85 ARG cc_start: 0.8341 (tpp80) cc_final: 0.7979 (tpp80) REVERT: M 105 ASN cc_start: 0.7459 (m-40) cc_final: 0.7089 (m-40) REVERT: M 111 GLU cc_start: 0.8121 (tp30) cc_final: 0.7643 (tp30) REVERT: M 167 TRP cc_start: 0.7889 (p90) cc_final: 0.6852 (p90) REVERT: M 176 ASN cc_start: 0.6453 (m-40) cc_final: 0.5651 (m-40) REVERT: M 196 SER cc_start: 0.6798 (m) cc_final: 0.6343 (p) REVERT: M 250 PHE cc_start: 0.7887 (p90) cc_final: 0.6639 (p90) REVERT: M 333 ASP cc_start: 0.8179 (t0) cc_final: 0.7772 (t0) REVERT: M 376 GLN cc_start: 0.6032 (mm-40) cc_final: 0.5781 (mp10) REVERT: M 380 GLN cc_start: 0.7608 (mt0) cc_final: 0.7052 (mt0) REVERT: M 381 GLN cc_start: 0.7835 (tm-30) cc_final: 0.7192 (tm-30) REVERT: M 394 MET cc_start: 0.6903 (tmm) cc_final: 0.6620 (tmm) REVERT: M 406 LYS cc_start: 0.8075 (mtpt) cc_final: 0.7722 (ttmt) REVERT: M 409 THR cc_start: 0.7822 (m) cc_final: 0.7479 (p) REVERT: S 17 SER cc_start: 0.8140 (t) cc_final: 0.7885 (p) REVERT: S 18 LYS cc_start: 0.8129 (tttp) cc_final: 0.7300 (tttp) REVERT: S 29 GLN cc_start: 0.8585 (mt0) cc_final: 0.8363 (mt0) REVERT: S 86 ILE cc_start: 0.7851 (mm) cc_final: 0.7639 (mm) REVERT: S 89 LEU cc_start: 0.7490 (mt) cc_final: 0.6532 (mt) REVERT: S 97 LEU cc_start: 0.7979 (mt) cc_final: 0.7383 (mt) REVERT: S 123 MET cc_start: 0.7450 (tpt) cc_final: 0.6829 (tpt) REVERT: S 125 MET cc_start: 0.8229 (ttt) cc_final: 0.7873 (ttt) REVERT: S 128 MET cc_start: 0.7319 (mtp) cc_final: 0.6791 (mtp) REVERT: B 50 MET cc_start: 0.7515 (ptp) cc_final: 0.7281 (ptp) REVERT: B 75 ASN cc_start: 0.7989 (m110) cc_final: 0.7356 (m110) REVERT: B 78 GLU cc_start: 0.8051 (pm20) cc_final: 0.7784 (pm20) REVERT: B 85 LYS cc_start: 0.7701 (mttt) cc_final: 0.7441 (tppt) REVERT: B 89 SER cc_start: 0.8527 (m) cc_final: 0.8305 (t) REVERT: B 96 LYS cc_start: 0.7803 (mmmt) cc_final: 0.7602 (tptt) REVERT: B 129 GLN cc_start: 0.8475 (pm20) cc_final: 0.7974 (mt0) REVERT: B 151 MET cc_start: 0.7867 (mtm) cc_final: 0.7605 (mtt) REVERT: B 152 MET cc_start: 0.7130 (tmm) cc_final: 0.6863 (tmm) REVERT: B 185 LYS cc_start: 0.7823 (mtpt) cc_final: 0.7570 (mtpt) REVERT: B 187 MET cc_start: 0.7840 (mtp) cc_final: 0.7409 (mtp) REVERT: B 197 LYS cc_start: 0.8647 (mttp) cc_final: 0.8145 (mtmm) REVERT: B 199 LYS cc_start: 0.8432 (ptmm) cc_final: 0.8174 (ptmm) REVERT: B 207 VAL cc_start: 0.8023 (p) cc_final: 0.7734 (m) REVERT: B 213 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7556 (tp30) REVERT: B 241 GLN cc_start: 0.7991 (mt0) cc_final: 0.7184 (mt0) REVERT: B 297 HIS cc_start: 0.7572 (t70) cc_final: 0.6731 (t-170) REVERT: B 307 LEU cc_start: 0.8574 (mt) cc_final: 0.8202 (tp) REVERT: B 323 TYR cc_start: 0.7659 (m-10) cc_final: 0.7369 (m-80) REVERT: B 331 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6855 (mm-30) REVERT: B 342 LEU cc_start: 0.8459 (mt) cc_final: 0.8237 (mt) REVERT: B 345 SER cc_start: 0.8176 (t) cc_final: 0.7942 (t) REVERT: B 365 LYS cc_start: 0.8178 (mttt) cc_final: 0.7537 (mtpp) REVERT: B 371 TYR cc_start: 0.7700 (m-80) cc_final: 0.7346 (m-80) REVERT: B 386 LYS cc_start: 0.8072 (mttt) cc_final: 0.7393 (mttt) REVERT: B 389 LYS cc_start: 0.8439 (mttt) cc_final: 0.8047 (mttm) REVERT: B 390 LEU cc_start: 0.8060 (tp) cc_final: 0.7811 (tt) REVERT: B 391 GLU cc_start: 0.7341 (tp30) cc_final: 0.6658 (tp30) REVERT: B 394 THR cc_start: 0.7977 (m) cc_final: 0.7772 (m) REVERT: B 426 GLN cc_start: 0.8511 (mt0) cc_final: 0.7914 (mm-40) REVERT: B 437 GLU cc_start: 0.7679 (tp30) cc_final: 0.7409 (tp30) REVERT: B 462 VAL cc_start: 0.8542 (t) cc_final: 0.8318 (t) REVERT: B 465 ILE cc_start: 0.8622 (mt) cc_final: 0.8214 (tp) REVERT: B 481 LYS cc_start: 0.8765 (mttt) cc_final: 0.8122 (mttt) REVERT: B 482 HIS cc_start: 0.8588 (t70) cc_final: 0.8297 (t70) REVERT: B 483 MET cc_start: 0.8551 (mmm) cc_final: 0.7669 (mmm) REVERT: B 486 LEU cc_start: 0.8281 (mt) cc_final: 0.7766 (mt) REVERT: B 498 SER cc_start: 0.8571 (m) cc_final: 0.8140 (p) REVERT: B 499 ILE cc_start: 0.8477 (mm) cc_final: 0.7806 (tp) REVERT: B 521 MET cc_start: 0.6843 (mmp) cc_final: 0.6476 (mmm) REVERT: B 556 GLN cc_start: 0.8014 (mt0) cc_final: 0.7761 (mt0) outliers start: 0 outliers final: 0 residues processed: 542 average time/residue: 0.4487 time to fit residues: 354.0453 Evaluate side-chains 530 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 530 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 68 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 94 optimal weight: 0.6980 chunk 183 optimal weight: 0.0270 chunk 137 optimal weight: 0.0060 chunk 170 optimal weight: 0.0870 chunk 190 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 133 optimal weight: 0.2980 chunk 58 optimal weight: 2.9990 overall best weight: 0.1632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 125 GLN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN ** M 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 145 ASN ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 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 = 0.4017 r_free = 0.4017 target = 0.150999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.129516 restraints weight = 35446.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.133820 restraints weight = 21225.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.136791 restraints weight = 13844.139| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.5441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17177 Z= 0.120 Angle : 0.558 7.099 23253 Z= 0.290 Chirality : 0.043 0.246 2705 Planarity : 0.004 0.053 2931 Dihedral : 8.495 176.965 2299 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.19), residues: 2098 helix: 1.44 (0.16), residues: 1155 sheet: 0.29 (0.34), residues: 231 loop : 0.58 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 74 HIS 0.015 0.001 HIS D 268 PHE 0.019 0.001 PHE D 245 TYR 0.031 0.002 TYR C 58 ARG 0.008 0.001 ARG A 97 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 996) hydrogen bonds : angle 4.58528 ( 2835) covalent geometry : bond 0.00260 (17177) covalent geometry : angle 0.55784 (23253) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4196 Ramachandran restraints generated. 2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 540 time to evaluate : 2.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8351 (tttt) cc_final: 0.7861 (tttt) REVERT: A 41 GLU cc_start: 0.5331 (mm-30) cc_final: 0.5042 (mm-30) REVERT: A 61 ILE cc_start: 0.8503 (mm) cc_final: 0.8252 (mm) REVERT: A 84 ASN cc_start: 0.6915 (m-40) cc_final: 0.6312 (m-40) REVERT: A 102 GLU cc_start: 0.8327 (tt0) cc_final: 0.7573 (tm-30) REVERT: A 134 MET cc_start: 0.4391 (mpp) cc_final: 0.3949 (mpp) REVERT: C 38 LYS cc_start: 0.8485 (tmtt) cc_final: 0.8187 (tmtt) REVERT: C 39 LEU cc_start: 0.8591 (mp) cc_final: 0.7680 (mp) REVERT: C 58 TYR cc_start: 0.5870 (t80) cc_final: 0.4897 (t80) REVERT: C 86 GLN cc_start: 0.7161 (mt0) cc_final: 0.6547 (mt0) REVERT: C 104 ARG cc_start: 0.8609 (ttp80) cc_final: 0.8094 (mtp85) REVERT: C 110 MET cc_start: 0.8210 (ttm) cc_final: 0.7842 (ttm) REVERT: C 173 LEU cc_start: 0.8400 (mt) cc_final: 0.8144 (mt) REVERT: C 175 ASN cc_start: 0.7836 (m-40) cc_final: 0.7364 (t0) REVERT: C 176 GLN cc_start: 0.6955 (mm-40) cc_final: 0.6581 (mm-40) REVERT: D 1 MET cc_start: 0.3951 (ttp) cc_final: 0.3557 (ttp) REVERT: D 83 MET cc_start: 0.7870 (mtt) cc_final: 0.7350 (mtt) REVERT: D 110 MET cc_start: 0.6551 (mmt) cc_final: 0.6203 (mmt) REVERT: D 112 THR cc_start: 0.7665 (p) cc_final: 0.7206 (m) REVERT: D 116 ILE cc_start: 0.8291 (mm) cc_final: 0.8002 (mm) REVERT: D 117 ARG cc_start: 0.8114 (ttm-80) cc_final: 0.7904 (mtm-85) REVERT: D 128 THR cc_start: 0.7368 (m) cc_final: 0.6994 (p) REVERT: D 132 LEU cc_start: 0.7609 (mt) cc_final: 0.7265 (mt) REVERT: D 155 MET cc_start: 0.7976 (mtm) cc_final: 0.7527 (mtm) REVERT: D 157 HIS cc_start: 0.8322 (t-90) cc_final: 0.8076 (t70) REVERT: D 176 LYS cc_start: 0.8401 (mmpt) cc_final: 0.7394 (mmtm) REVERT: D 189 LYS cc_start: 0.7836 (mtmm) cc_final: 0.7576 (mtmm) REVERT: D 200 GLN cc_start: 0.6113 (mp10) cc_final: 0.5674 (mm-40) REVERT: D 221 LEU cc_start: 0.7417 (mp) cc_final: 0.6938 (mp) REVERT: D 236 TRP cc_start: 0.7654 (t-100) cc_final: 0.7370 (t-100) REVERT: D 239 ILE cc_start: 0.8576 (pt) cc_final: 0.8374 (pt) REVERT: D 273 MET cc_start: 0.8166 (pmm) cc_final: 0.7955 (pmm) REVERT: D 275 LEU cc_start: 0.7815 (tp) cc_final: 0.7514 (tp) REVERT: D 302 GLN cc_start: 0.8490 (tt0) cc_final: 0.7824 (tm-30) REVERT: D 306 GLN cc_start: 0.7529 (mm-40) cc_final: 0.6912 (mm-40) REVERT: D 307 LYS cc_start: 0.8207 (mmtt) cc_final: 0.7803 (mmtt) REVERT: D 308 LEU cc_start: 0.8319 (mt) cc_final: 0.8102 (mt) REVERT: D 324 LEU cc_start: 0.8564 (mt) cc_final: 0.8238 (mt) REVERT: D 327 MET cc_start: 0.7159 (tpp) cc_final: 0.6607 (tpp) REVERT: D 329 LYS cc_start: 0.8875 (mttt) cc_final: 0.8576 (mttt) REVERT: D 336 LYS cc_start: 0.7942 (ptpp) cc_final: 0.7562 (ptpp) REVERT: D 339 GLN cc_start: 0.8327 (pt0) cc_final: 0.8031 (pp30) REVERT: D 346 LEU cc_start: 0.8608 (mt) cc_final: 0.8405 (mt) REVERT: D 349 LEU cc_start: 0.7712 (tp) cc_final: 0.7161 (tp) REVERT: D 362 ASP cc_start: 0.8609 (m-30) cc_final: 0.8340 (m-30) REVERT: D 367 MET cc_start: 0.7255 (mtm) cc_final: 0.6871 (mtm) REVERT: D 373 LEU cc_start: 0.8648 (tp) cc_final: 0.8299 (pp) REVERT: D 378 LYS cc_start: 0.8782 (mttt) cc_final: 0.8261 (mttt) REVERT: D 383 HIS cc_start: 0.7611 (t70) cc_final: 0.6889 (t70) REVERT: D 392 TYR cc_start: 0.7415 (t80) cc_final: 0.7076 (t80) REVERT: D 393 ARG cc_start: 0.7594 (mtt180) cc_final: 0.7268 (mmm-85) REVERT: D 394 ASP cc_start: 0.8186 (m-30) cc_final: 0.7886 (m-30) REVERT: D 399 LYS cc_start: 0.7976 (mmmt) cc_final: 0.7443 (mmmt) REVERT: D 403 ILE cc_start: 0.8452 (pt) cc_final: 0.7987 (pt) REVERT: D 429 GLU cc_start: 0.7440 (tm-30) cc_final: 0.7048 (tm-30) REVERT: D 432 ARG cc_start: 0.6764 (mmm-85) cc_final: 0.6524 (mmm-85) REVERT: D 440 GLN cc_start: 0.7567 (mm-40) cc_final: 0.6950 (tp40) REVERT: D 479 CYS cc_start: 0.8630 (m) cc_final: 0.8401 (m) REVERT: D 530 TYR cc_start: 0.7385 (m-80) cc_final: 0.7007 (m-80) REVERT: D 534 LEU cc_start: 0.8238 (mt) cc_final: 0.7595 (tt) REVERT: D 535 GLN cc_start: 0.7962 (pp30) cc_final: 0.7643 (pp30) REVERT: D 536 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7966 (tm-30) REVERT: D 553 MET cc_start: 0.7434 (mtm) cc_final: 0.6845 (mtm) REVERT: D 567 GLU cc_start: 0.7732 (tp30) cc_final: 0.7346 (tp30) REVERT: M 43 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7574 (mm-30) REVERT: M 59 ILE cc_start: 0.8194 (mp) cc_final: 0.7837 (mm) REVERT: M 67 VAL cc_start: 0.7998 (t) cc_final: 0.7552 (m) REVERT: M 85 ARG cc_start: 0.8318 (tpp80) cc_final: 0.7892 (tpp80) REVERT: M 88 ASP cc_start: 0.7975 (m-30) cc_final: 0.7729 (m-30) REVERT: M 105 ASN cc_start: 0.7438 (m-40) cc_final: 0.6874 (m-40) REVERT: M 111 GLU cc_start: 0.8086 (tp30) cc_final: 0.7519 (tp30) REVERT: M 114 GLU cc_start: 0.7536 (tp30) cc_final: 0.7335 (tp30) REVERT: M 167 TRP cc_start: 0.7890 (p90) cc_final: 0.6811 (p90) REVERT: M 176 ASN cc_start: 0.6451 (m-40) cc_final: 0.6170 (m-40) REVERT: M 250 PHE cc_start: 0.7810 (p90) cc_final: 0.6606 (p90) REVERT: M 256 ASN cc_start: 0.7754 (m110) cc_final: 0.7550 (m110) REVERT: M 301 MET cc_start: 0.7195 (tpt) cc_final: 0.6521 (tpt) REVERT: M 303 LYS cc_start: 0.8214 (mmtt) cc_final: 0.7847 (mmtt) REVERT: M 333 ASP cc_start: 0.8156 (t0) cc_final: 0.7787 (t0) REVERT: M 376 GLN cc_start: 0.6037 (mm-40) cc_final: 0.5804 (mp10) REVERT: M 380 GLN cc_start: 0.7606 (mt0) cc_final: 0.7046 (mt0) REVERT: M 381 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7347 (tm-30) REVERT: M 394 MET cc_start: 0.6889 (tmm) cc_final: 0.6615 (tmm) REVERT: M 406 LYS cc_start: 0.8062 (mtpt) cc_final: 0.7764 (ttmt) REVERT: M 409 THR cc_start: 0.7742 (m) cc_final: 0.7342 (p) REVERT: S 17 SER cc_start: 0.8134 (t) cc_final: 0.7933 (p) REVERT: S 18 LYS cc_start: 0.8061 (tttp) cc_final: 0.7257 (tttp) REVERT: S 29 GLN cc_start: 0.8555 (mt0) cc_final: 0.8100 (mm-40) REVERT: S 89 LEU cc_start: 0.7382 (mt) cc_final: 0.6399 (mt) REVERT: S 97 LEU cc_start: 0.7958 (mt) cc_final: 0.7400 (mt) REVERT: S 123 MET cc_start: 0.7350 (tpt) cc_final: 0.6754 (tpt) REVERT: S 125 MET cc_start: 0.8199 (ttt) cc_final: 0.7907 (ttt) REVERT: S 128 MET cc_start: 0.7167 (mtp) cc_final: 0.6717 (mtp) REVERT: B 50 MET cc_start: 0.7559 (ptp) cc_final: 0.7272 (ptp) REVERT: B 75 ASN cc_start: 0.7953 (m110) cc_final: 0.7411 (m110) REVERT: B 78 GLU cc_start: 0.8022 (pm20) cc_final: 0.7779 (pm20) REVERT: B 85 LYS cc_start: 0.7738 (mttt) cc_final: 0.7472 (tppt) REVERT: B 89 SER cc_start: 0.8543 (m) cc_final: 0.8287 (t) REVERT: B 96 LYS cc_start: 0.7819 (mmmt) cc_final: 0.7489 (tttt) REVERT: B 129 GLN cc_start: 0.8453 (pm20) cc_final: 0.8006 (mt0) REVERT: B 151 MET cc_start: 0.7874 (mtm) cc_final: 0.7593 (mtt) REVERT: B 152 MET cc_start: 0.7178 (tmm) cc_final: 0.6876 (tmm) REVERT: B 185 LYS cc_start: 0.7813 (mtpt) cc_final: 0.7513 (mtpt) REVERT: B 187 MET cc_start: 0.7883 (mtp) cc_final: 0.7442 (mtp) REVERT: B 197 LYS cc_start: 0.8611 (mttp) cc_final: 0.8095 (mtmm) REVERT: B 199 LYS cc_start: 0.8409 (ptmm) cc_final: 0.8142 (ptmm) REVERT: B 207 VAL cc_start: 0.7990 (p) cc_final: 0.7743 (m) REVERT: B 241 GLN cc_start: 0.7987 (mt0) cc_final: 0.7181 (mt0) REVERT: B 297 HIS cc_start: 0.7520 (t70) cc_final: 0.6712 (t-170) REVERT: B 307 LEU cc_start: 0.8542 (mt) cc_final: 0.8164 (tp) REVERT: B 323 TYR cc_start: 0.7580 (m-10) cc_final: 0.7338 (m-80) REVERT: B 330 SER cc_start: 0.7557 (t) cc_final: 0.7349 (t) REVERT: B 331 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6695 (mm-30) REVERT: B 342 LEU cc_start: 0.8442 (mt) cc_final: 0.8179 (mt) REVERT: B 345 SER cc_start: 0.8108 (t) cc_final: 0.7540 (p) REVERT: B 365 LYS cc_start: 0.8170 (mttt) cc_final: 0.7495 (mtpp) REVERT: B 371 TYR cc_start: 0.7625 (m-80) cc_final: 0.7364 (m-80) REVERT: B 375 PHE cc_start: 0.7548 (m-80) cc_final: 0.7334 (m-10) REVERT: B 386 LYS cc_start: 0.8062 (mttt) cc_final: 0.7339 (mttt) REVERT: B 389 LYS cc_start: 0.8369 (mttt) cc_final: 0.7843 (mtpp) REVERT: B 390 LEU cc_start: 0.8037 (tp) cc_final: 0.7779 (tt) REVERT: B 391 GLU cc_start: 0.7329 (tp30) cc_final: 0.6551 (tp30) REVERT: B 426 GLN cc_start: 0.8525 (mt0) cc_final: 0.7888 (mm-40) REVERT: B 437 GLU cc_start: 0.7687 (tp30) cc_final: 0.7344 (tp30) REVERT: B 465 ILE cc_start: 0.8588 (mt) cc_final: 0.8179 (tp) REVERT: B 481 LYS cc_start: 0.8739 (mttt) cc_final: 0.8140 (mttt) REVERT: B 483 MET cc_start: 0.8523 (mmm) cc_final: 0.7997 (mmm) REVERT: B 486 LEU cc_start: 0.8284 (mt) cc_final: 0.7819 (mt) REVERT: B 498 SER cc_start: 0.8554 (m) cc_final: 0.8115 (p) REVERT: B 499 ILE cc_start: 0.8463 (mm) cc_final: 0.7834 (tp) REVERT: B 521 MET cc_start: 0.6771 (mmp) cc_final: 0.6393 (mmm) REVERT: B 556 GLN cc_start: 0.7932 (mt0) cc_final: 0.7686 (mt0) outliers start: 0 outliers final: 0 residues processed: 540 average time/residue: 0.4097 time to fit residues: 321.5728 Evaluate side-chains 528 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 200 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 127 optimal weight: 0.6980 chunk 118 optimal weight: 0.0050 chunk 111 optimal weight: 0.1980 chunk 117 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN D 406 GLN ** M 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 145 ASN ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS B 482 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.147938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.126510 restraints weight = 34921.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.130698 restraints weight = 21021.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.133576 restraints weight = 13807.444| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.5617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17177 Z= 0.148 Angle : 0.577 7.900 23253 Z= 0.305 Chirality : 0.044 0.257 2705 Planarity : 0.004 0.060 2931 Dihedral : 8.460 178.536 2299 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.19), residues: 2098 helix: 1.36 (0.15), residues: 1148 sheet: 0.24 (0.35), residues: 231 loop : 0.48 (0.25), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 66 HIS 0.013 0.001 HIS D 268 PHE 0.019 0.002 PHE D 245 TYR 0.035 0.002 TYR C 58 ARG 0.009 0.001 ARG A 97 Details of bonding type rmsd hydrogen bonds : bond 0.04351 ( 996) hydrogen bonds : angle 4.72946 ( 2835) covalent geometry : bond 0.00314 (17177) covalent geometry : angle 0.57738 (23253) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7973.82 seconds wall clock time: 144 minutes 16.48 seconds (8656.48 seconds total)