Starting phenix.real_space_refine on Thu Sep 18 13:07:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c5b_45213/09_2025/9c5b_45213.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c5b_45213/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9c5b_45213/09_2025/9c5b_45213.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c5b_45213/09_2025/9c5b_45213.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c5b_45213/09_2025/9c5b_45213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c5b_45213/09_2025/9c5b_45213.map" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.87, per 1000 atoms: 0.23 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: 1.64 Conformation dependent library (CDL) restraints added in 726.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.62 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: 3.14 Time building geometry restraints manager: 2.12 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 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: 5.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.850 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.130 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG B 227 TYR 0.064 0.006 TYR M 110 PHE 0.024 0.004 PHE B 80 TRP 0.045 0.006 TRP B 639 HIS 0.010 0.002 HIS M 3 Details of bonding type rmsd covalent geometry : bond 0.01280 (17177) covalent geometry : angle 1.35934 (23253) hydrogen bonds : bond 0.17228 ( 996) hydrogen bonds : angle 7.31368 ( 2835) *********************** 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 : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 0.7080 (mm-30) REVERT: A 84 ASN cc_start: 0.6426 (m-40) cc_final: 0.6218 (m-40) REVERT: C 22 MET cc_start: 0.7979 (ttp) cc_final: 0.6971 (tmm) REVERT: C 86 GLN cc_start: 0.7139 (mt0) cc_final: 0.6115 (mt0) REVERT: C 110 MET cc_start: 0.8134 (mtm) cc_final: 0.7848 (ttm) REVERT: C 143 LEU cc_start: 0.7670 (mt) cc_final: 0.7420 (mm) REVERT: C 173 LEU cc_start: 0.8091 (mt) cc_final: 0.7832 (mt) REVERT: D 1 MET cc_start: 0.4789 (ttp) cc_final: 0.4550 (ttp) REVERT: D 66 GLN cc_start: 0.7264 (tp40) cc_final: 0.6994 (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: 0.7131 (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: 0.7101 (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: 0.6685 (mt0) REVERT: D 201 SER cc_start: 0.8136 (m) cc_final: 0.7858 (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: 0.6818 (Cg_endo) REVERT: D 225 PHE cc_start: 0.6101 (m-80) cc_final: 0.5397 (m-80) REVERT: D 239 ILE cc_start: 0.8446 (mt) cc_final: 0.8192 (mt) REVERT: D 240 LYS cc_start: 0.8419 (mmtt) cc_final: 0.7873 (mmtp) REVERT: D 265 ASN cc_start: 0.8207 (m-40) cc_final: 0.7859 (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: 0.8517 (tp) REVERT: D 302 GLN cc_start: 0.8764 (tt0) cc_final: 0.8490 (tt0) REVERT: D 307 LYS cc_start: 0.8019 (mmtt) cc_final: 0.7725 (mmtt) REVERT: D 314 ASP cc_start: 0.5087 (t0) cc_final: 0.4660 (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: 0.7399 (pp30) REVERT: D 354 GLU cc_start: 0.8393 (pm20) cc_final: 0.7694 (pm20) REVERT: D 362 ASP cc_start: 0.8723 (m-30) cc_final: 0.8055 (m-30) REVERT: D 367 MET cc_start: 0.7187 (mtm) cc_final: 0.6757 (mtm) REVERT: D 374 MET cc_start: 0.8060 (mtt) cc_final: 0.6913 (mtt) REVERT: D 378 LYS cc_start: 0.8780 (mttt) cc_final: 0.8406 (mttt) REVERT: D 380 LEU cc_start: 0.8172 (mt) cc_final: 0.7849 (mt) REVERT: D 393 ARG cc_start: 0.7926 (mtt180) cc_final: 0.7523 (ptp-110) REVERT: D 400 ILE cc_start: 0.8994 (mt) cc_final: 0.8714 (mm) REVERT: D 403 ILE cc_start: 0.8276 (mt) cc_final: 0.8070 (mt) REVERT: D 406 GLN cc_start: 0.7856 (pt0) cc_final: 0.7504 (pt0) REVERT: D 419 ILE cc_start: 0.8670 (mt) cc_final: 0.8397 (pt) REVERT: D 429 GLU cc_start: 0.8457 (tt0) cc_final: 0.7879 (tm-30) REVERT: D 433 HIS cc_start: 0.7438 (m90) cc_final: 0.7231 (m90) REVERT: D 440 GLN cc_start: 0.7468 (mm-40) cc_final: 0.6913 (tp40) REVERT: D 488 ILE cc_start: 0.8029 (mm) cc_final: 0.7764 (mt) REVERT: D 530 TYR cc_start: 0.7783 (m-80) cc_final: 0.7456 (m-80) REVERT: D 534 LEU cc_start: 0.7974 (mt) cc_final: 0.7661 (tp) REVERT: D 559 GLN cc_start: 0.7116 (tt0) cc_final: 0.6859 (tt0) REVERT: D 573 SER cc_start: 0.8466 (m) cc_final: 0.8207 (p) REVERT: M 6 PHE cc_start: 0.7505 (m-80) cc_final: 0.7023 (m-80) REVERT: M 15 PHE cc_start: 0.6110 (m-80) cc_final: 0.5547 (m-80) REVERT: M 16 LEU cc_start: 0.7210 (tp) cc_final: 0.6990 (tp) REVERT: M 62 ASP cc_start: 0.7911 (m-30) cc_final: 0.7019 (m-30) REVERT: M 67 VAL cc_start: 0.7528 (t) cc_final: 0.7149 (m) REVERT: M 111 GLU cc_start: 0.8136 (tp30) cc_final: 0.7903 (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: 0.7288 (pt) REVERT: M 196 SER cc_start: 0.6927 (m) cc_final: 0.6585 (p) REVERT: M 201 GLU cc_start: 0.7855 (pt0) cc_final: 0.7568 (pt0) REVERT: M 203 GLN cc_start: 0.7447 (tp40) cc_final: 0.6952 (tm-30) REVERT: M 210 ILE cc_start: 0.6957 (mm) cc_final: 0.6549 (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: 0.8064 (mt) REVERT: M 229 ASP cc_start: 0.6953 (t0) cc_final: 0.6668 (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: 0.7390 (ttmm) REVERT: M 300 ASN cc_start: 0.6967 (p0) cc_final: 0.6685 (p0) REVERT: M 303 LYS cc_start: 0.7003 (mmtt) cc_final: 0.6553 (mmmt) REVERT: M 332 PHE cc_start: 0.5418 (t80) cc_final: 0.4542 (t80) REVERT: M 333 ASP cc_start: 0.5346 (t0) cc_final: 0.5082 (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: 0.6598 (m-40) REVERT: M 380 GLN cc_start: 0.7261 (mt0) cc_final: 0.6768 (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: 0.6575 (p) REVERT: M 410 LYS cc_start: 0.7576 (mttt) cc_final: 0.7302 (mttt) REVERT: S 6 LEU cc_start: 0.7763 (mt) cc_final: 0.7537 (mt) REVERT: S 7 ILE cc_start: 0.7528 (mt) cc_final: 0.7276 (mt) REVERT: S 8 PHE cc_start: 0.7140 (p90) cc_final: 0.6885 (p90) REVERT: S 17 SER cc_start: 0.7778 (t) cc_final: 0.7065 (p) REVERT: S 18 LYS cc_start: 0.7545 (tttp) cc_final: 0.6914 (tttp) REVERT: S 77 VAL cc_start: 0.6796 (m) cc_final: 0.6529 (p) REVERT: S 117 HIS cc_start: 0.8814 (m-70) cc_final: 0.8414 (m-70) REVERT: S 122 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7627 (mm-30) REVERT: S 123 MET cc_start: 0.8072 (tpt) cc_final: 0.7609 (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: 0.6558 (mtp) REVERT: B 41 LEU cc_start: 0.7736 (tp) cc_final: 0.7214 (pp) REVERT: B 45 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7241 (mm-30) REVERT: B 63 MET cc_start: 0.6337 (mmm) cc_final: 0.5669 (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: 0.7414 (tttp) REVERT: B 97 LEU cc_start: 0.7433 (mt) cc_final: 0.7087 (mt) REVERT: B 151 MET cc_start: 0.7715 (mtm) cc_final: 0.7421 (mtt) REVERT: B 152 MET cc_start: 0.6872 (tmm) cc_final: 0.6626 (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: 0.8162 (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: 0.7393 (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: 0.7913 (pt) REVERT: B 342 LEU cc_start: 0.8433 (mt) cc_final: 0.8204 (mm) REVERT: B 346 ASN cc_start: 0.6218 (t0) cc_final: 0.5950 (t0) REVERT: B 372 LEU cc_start: 0.7693 (tp) cc_final: 0.7467 (tp) REVERT: B 389 LYS cc_start: 0.8018 (mttt) cc_final: 0.7747 (mmtp) REVERT: B 390 LEU cc_start: 0.8116 (tp) cc_final: 0.7870 (tt) REVERT: B 391 GLU cc_start: 0.7827 (tp30) cc_final: 0.7416 (tp30) REVERT: B 440 ASP cc_start: 0.7783 (m-30) cc_final: 0.7469 (p0) REVERT: B 442 CYS cc_start: 0.8001 (m) cc_final: 0.7724 (m) REVERT: B 447 VAL cc_start: 0.8000 (t) cc_final: 0.7748 (t) REVERT: B 468 LEU cc_start: 0.8052 (mt) cc_final: 0.7718 (tt) REVERT: B 472 GLN cc_start: 0.7694 (tp40) cc_final: 0.7367 (tp40) REVERT: B 481 LYS cc_start: 0.8837 (mttt) cc_final: 0.8362 (mttp) REVERT: B 483 MET cc_start: 0.8410 (mmt) cc_final: 0.8027 (mmm) REVERT: B 486 LEU cc_start: 0.7984 (mt) cc_final: 0.7644 (mt) REVERT: B 521 MET cc_start: 0.6627 (mmp) cc_final: 0.6235 (mmm) REVERT: B 539 LEU cc_start: 0.8320 (tp) cc_final: 0.8068 (tp) REVERT: B 569 ASP cc_start: 0.7608 (t70) cc_final: 0.7403 (t70) REVERT: B 577 ILE cc_start: 0.8190 (mt) cc_final: 0.7893 (tp) REVERT: B 578 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7653 (ttp80) outliers start: 2 outliers final: 2 residues processed: 635 average time/residue: 0.1521 time to fit residues: 140.7925 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 : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 0.3980 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.0670 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.3980 overall best weight: 0.4318 ------------------------------------------------------------------------------- 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 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.150993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.131317 restraints weight = 36039.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.135458 restraints weight = 21272.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.138270 restraints weight = 13688.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.140223 restraints weight = 9392.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.141495 restraints weight = 6758.514| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17177 Z= 0.163 Angle : 0.628 11.122 23253 Z= 0.336 Chirality : 0.045 0.159 2705 Planarity : 0.004 0.040 2931 Dihedral : 10.489 171.137 2299 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.19), residues: 2098 helix: 0.99 (0.15), residues: 1133 sheet: -0.15 (0.33), residues: 235 loop : 1.38 (0.26), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 357 TYR 0.030 0.002 TYR M 180 PHE 0.028 0.002 PHE D 245 TRP 0.021 0.002 TRP D 74 HIS 0.017 0.002 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00332 (17177) covalent geometry : angle 0.62758 (23253) hydrogen bonds : bond 0.05463 ( 996) hydrogen bonds : angle 5.37006 ( 2835) *********************** 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 579 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 579 time to evaluate : 0.585 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: 0.8159 (tttt) cc_final: 0.7744 (tttt) REVERT: A 84 ASN cc_start: 0.6960 (m-40) cc_final: 0.6393 (m-40) REVERT: C 19 ARG cc_start: 0.7344 (mtp85) cc_final: 0.7061 (mtt90) REVERT: C 59 LYS cc_start: 0.7214 (mmtt) cc_final: 0.7001 (mtmm) REVERT: C 81 TYR cc_start: 0.7818 (m-80) cc_final: 0.7565 (m-80) REVERT: C 86 GLN cc_start: 0.7429 (mt0) cc_final: 0.6760 (mt0) REVERT: C 110 MET cc_start: 0.7964 (mtm) cc_final: 0.7628 (mtp) REVERT: C 120 VAL cc_start: 0.7680 (t) cc_final: 0.7432 (t) REVERT: C 138 GLU cc_start: 0.7316 (tt0) cc_final: 0.6550 (tt0) REVERT: C 173 LEU cc_start: 0.7946 (mt) cc_final: 0.7725 (mt) REVERT: D 1 MET cc_start: 0.4049 (ttp) cc_final: 0.3765 (ttp) REVERT: D 59 VAL cc_start: 0.8072 (t) cc_final: 0.7835 (t) REVERT: D 67 MET cc_start: 0.7510 (ttp) cc_final: 0.6543 (tmm) REVERT: D 74 TRP cc_start: 0.8373 (p-90) cc_final: 0.8094 (p-90) REVERT: D 120 LEU cc_start: 0.7570 (mt) cc_final: 0.7307 (mt) REVERT: D 126 TYR cc_start: 0.8128 (m-80) cc_final: 0.7794 (m-80) REVERT: D 128 THR cc_start: 0.7543 (m) cc_final: 0.7214 (p) REVERT: D 132 LEU cc_start: 0.7794 (mt) cc_final: 0.7382 (mt) REVERT: D 149 ASN cc_start: 0.8421 (m-40) cc_final: 0.8022 (m110) REVERT: D 152 MET cc_start: 0.6899 (mtm) cc_final: 0.6644 (mtm) REVERT: D 155 MET cc_start: 0.7937 (mtm) cc_final: 0.7643 (mtm) REVERT: D 157 HIS cc_start: 0.8210 (t-90) cc_final: 0.7898 (t70) REVERT: D 169 ILE cc_start: 0.7319 (tt) cc_final: 0.6971 (mm) REVERT: D 177 TYR cc_start: 0.7365 (t80) cc_final: 0.6750 (t80) REVERT: D 179 GLU cc_start: 0.8230 (mp0) cc_final: 0.7033 (mp0) REVERT: D 201 SER cc_start: 0.7805 (m) cc_final: 0.7435 (p) REVERT: D 221 LEU cc_start: 0.7986 (mp) cc_final: 0.6983 (mp) REVERT: D 240 LYS cc_start: 0.8303 (mmtt) cc_final: 0.8094 (mmtt) REVERT: D 257 LYS cc_start: 0.8111 (tttt) cc_final: 0.7633 (tttm) REVERT: D 302 GLN cc_start: 0.8721 (tt0) cc_final: 0.8432 (tt0) REVERT: D 307 LYS cc_start: 0.8179 (mmtt) cc_final: 0.7725 (mmtt) REVERT: D 309 ARG cc_start: 0.7866 (ttp-110) cc_final: 0.7067 (ttp-110) REVERT: D 324 LEU cc_start: 0.8476 (mt) cc_final: 0.8129 (mt) REVERT: D 327 MET cc_start: 0.7198 (tpp) cc_final: 0.6392 (tpp) REVERT: D 329 LYS cc_start: 0.9024 (mttt) cc_final: 0.8703 (mttt) REVERT: D 339 GLN cc_start: 0.8149 (pt0) cc_final: 0.7563 (pm20) REVERT: D 367 MET cc_start: 0.6885 (mtm) cc_final: 0.6366 (mtm) REVERT: D 374 MET cc_start: 0.7210 (mtt) cc_final: 0.5942 (mtt) REVERT: D 378 LYS cc_start: 0.8782 (mttt) cc_final: 0.8402 (mttm) REVERT: D 382 THR cc_start: 0.8594 (m) cc_final: 0.8347 (p) REVERT: D 392 TYR cc_start: 0.7175 (t80) cc_final: 0.6783 (t80) REVERT: D 393 ARG cc_start: 0.7730 (mtt180) cc_final: 0.7426 (ttm-80) REVERT: D 394 ASP cc_start: 0.8410 (m-30) cc_final: 0.7732 (m-30) REVERT: D 396 LEU cc_start: 0.8585 (mt) cc_final: 0.7526 (mt) REVERT: D 398 THR cc_start: 0.8083 (p) cc_final: 0.7691 (t) REVERT: D 400 ILE cc_start: 0.8914 (mt) cc_final: 0.8517 (tp) REVERT: D 422 LEU cc_start: 0.9094 (tp) cc_final: 0.8782 (tp) REVERT: D 429 GLU cc_start: 0.8086 (tt0) cc_final: 0.7822 (tm-30) REVERT: D 433 HIS cc_start: 0.7735 (m90) cc_final: 0.7521 (m90) REVERT: D 440 GLN cc_start: 0.7826 (mm-40) cc_final: 0.6998 (tp40) REVERT: D 488 ILE cc_start: 0.7559 (mm) cc_final: 0.7350 (mm) REVERT: D 514 LEU cc_start: 0.6837 (mt) cc_final: 0.6549 (mt) REVERT: D 534 LEU cc_start: 0.8192 (mt) cc_final: 0.7589 (tp) REVERT: D 536 GLN cc_start: 0.8138 (tm-30) cc_final: 0.7874 (tm-30) REVERT: D 559 GLN cc_start: 0.7823 (tt0) cc_final: 0.7602 (tt0) REVERT: D 571 ARG cc_start: 0.8473 (mtt-85) cc_final: 0.8052 (mtt-85) REVERT: D 573 SER cc_start: 0.8029 (m) cc_final: 0.7703 (p) REVERT: M 25 SER cc_start: 0.7809 (t) cc_final: 0.7500 (p) REVERT: M 62 ASP cc_start: 0.8271 (m-30) cc_final: 0.7683 (m-30) REVERT: M 67 VAL cc_start: 0.7877 (t) cc_final: 0.7495 (m) REVERT: M 81 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7935 (mm-30) REVERT: M 105 ASN cc_start: 0.7329 (m-40) cc_final: 0.7123 (m-40) REVERT: M 111 GLU cc_start: 0.8129 (tp30) cc_final: 0.7501 (tp30) REVERT: M 156 THR cc_start: 0.8061 (m) cc_final: 0.7840 (p) REVERT: M 157 LEU cc_start: 0.8343 (tp) cc_final: 0.7549 (pt) REVERT: M 177 ASN cc_start: 0.6637 (m-40) cc_final: 0.5972 (m-40) REVERT: M 196 SER cc_start: 0.6808 (m) cc_final: 0.6390 (p) REVERT: M 198 VAL cc_start: 0.7337 (t) cc_final: 0.7040 (t) REVERT: M 201 GLU cc_start: 0.7993 (pt0) cc_final: 0.7218 (pm20) REVERT: M 210 ILE cc_start: 0.7554 (mm) cc_final: 0.7065 (mp) REVERT: M 212 LEU cc_start: 0.7515 (mt) cc_final: 0.6942 (mt) REVERT: M 239 PHE cc_start: 0.7960 (t80) cc_final: 0.7607 (t80) REVERT: M 250 PHE cc_start: 0.7728 (p90) cc_final: 0.7520 (p90) REVERT: M 256 ASN cc_start: 0.7886 (t0) cc_final: 0.7529 (t0) REVERT: M 263 ARG cc_start: 0.6731 (mtp180) cc_final: 0.6134 (mtp180) REVERT: M 303 LYS cc_start: 0.8069 (mmtt) cc_final: 0.7202 (mmtt) REVERT: M 316 LYS cc_start: 0.7841 (mmtm) cc_final: 0.7541 (mmtm) REVERT: M 329 SER cc_start: 0.7396 (t) cc_final: 0.6913 (p) REVERT: M 352 PRO cc_start: 0.8283 (Cg_endo) cc_final: 0.7960 (Cg_exo) REVERT: M 376 GLN cc_start: 0.5847 (mm-40) cc_final: 0.5588 (mp10) REVERT: M 380 GLN cc_start: 0.7603 (mt0) cc_final: 0.7368 (mt0) REVERT: M 399 TYR cc_start: 0.7857 (p90) cc_final: 0.6550 (p90) REVERT: M 409 THR cc_start: 0.7883 (m) cc_final: 0.7463 (p) REVERT: M 410 LYS cc_start: 0.8127 (mttt) cc_final: 0.7774 (mttt) REVERT: S 7 ILE cc_start: 0.8271 (mt) cc_final: 0.8017 (mt) REVERT: S 8 PHE cc_start: 0.7087 (p90) cc_final: 0.6873 (p90) REVERT: S 17 SER cc_start: 0.7625 (t) cc_final: 0.7077 (p) REVERT: S 18 LYS cc_start: 0.8211 (tttp) cc_final: 0.7501 (tttp) REVERT: S 29 GLN cc_start: 0.8483 (mt0) cc_final: 0.8202 (mm-40) REVERT: S 77 VAL cc_start: 0.7291 (m) cc_final: 0.7006 (p) REVERT: S 86 ILE cc_start: 0.7928 (mm) cc_final: 0.7685 (mm) REVERT: S 116 VAL cc_start: 0.7721 (t) cc_final: 0.7518 (t) REVERT: S 117 HIS cc_start: 0.8391 (m-70) cc_final: 0.8008 (m-70) REVERT: S 123 MET cc_start: 0.7340 (tpt) cc_final: 0.6787 (tpt) REVERT: S 128 MET cc_start: 0.7440 (mtp) cc_final: 0.6584 (mtp) REVERT: B 45 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7096 (mm-30) REVERT: B 63 MET cc_start: 0.6462 (mmm) cc_final: 0.5508 (mmm) REVERT: B 69 MET cc_start: 0.7510 (mtm) cc_final: 0.7194 (mtm) REVERT: B 75 ASN cc_start: 0.8193 (m110) cc_final: 0.7525 (m-40) REVERT: B 78 GLU cc_start: 0.7693 (pm20) cc_final: 0.7443 (pm20) REVERT: B 96 LYS cc_start: 0.7905 (mmmt) cc_final: 0.7567 (tttp) REVERT: B 97 LEU cc_start: 0.7560 (mt) cc_final: 0.7052 (mt) REVERT: B 98 VAL cc_start: 0.8042 (t) cc_final: 0.7792 (p) REVERT: B 151 MET cc_start: 0.7945 (mtm) cc_final: 0.7651 (mtt) REVERT: B 152 MET cc_start: 0.6778 (tmm) cc_final: 0.6528 (tmm) REVERT: B 153 LEU cc_start: 0.7908 (mt) cc_final: 0.7279 (mp) REVERT: B 169 ASN cc_start: 0.8387 (m-40) cc_final: 0.8116 (t0) REVERT: B 187 MET cc_start: 0.8059 (mtp) cc_final: 0.7307 (mtp) REVERT: B 190 GLU cc_start: 0.8231 (mt-10) cc_final: 0.8007 (mt-10) REVERT: B 213 GLU cc_start: 0.7190 (tp30) cc_final: 0.6849 (tp30) REVERT: B 241 GLN cc_start: 0.7709 (mt0) cc_final: 0.7183 (mt0) REVERT: B 249 THR cc_start: 0.7088 (p) cc_final: 0.6887 (p) REVERT: B 307 LEU cc_start: 0.8652 (mt) cc_final: 0.8184 (tp) REVERT: B 323 TYR cc_start: 0.7603 (m-10) cc_final: 0.7360 (m-80) REVERT: B 360 MET cc_start: 0.7854 (mtp) cc_final: 0.7457 (mtm) REVERT: B 368 PHE cc_start: 0.7266 (m-80) cc_final: 0.7023 (m-80) REVERT: B 375 PHE cc_start: 0.7497 (m-80) cc_final: 0.7252 (m-80) REVERT: B 383 THR cc_start: 0.7488 (m) cc_final: 0.7279 (m) REVERT: B 389 LYS cc_start: 0.8347 (mttt) cc_final: 0.8137 (mmtp) REVERT: B 390 LEU cc_start: 0.8125 (tp) cc_final: 0.7907 (tt) REVERT: B 391 GLU cc_start: 0.7721 (tp30) cc_final: 0.7320 (tp30) REVERT: B 426 GLN cc_start: 0.8482 (mt0) cc_final: 0.8130 (mm-40) REVERT: B 440 ASP cc_start: 0.7977 (m-30) cc_final: 0.7474 (p0) REVERT: B 462 VAL cc_start: 0.8650 (t) cc_final: 0.8346 (t) REVERT: B 465 ILE cc_start: 0.8743 (mt) cc_final: 0.8300 (mt) REVERT: B 481 LYS cc_start: 0.8863 (mttt) cc_final: 0.8363 (tptm) REVERT: B 486 LEU cc_start: 0.8230 (mt) cc_final: 0.7771 (mt) REVERT: B 521 MET cc_start: 0.6495 (mmp) cc_final: 0.5947 (mmm) REVERT: B 539 LEU cc_start: 0.8434 (tp) cc_final: 0.8221 (tt) REVERT: B 556 GLN cc_start: 0.7926 (mt0) cc_final: 0.7721 (mt0) REVERT: B 577 ILE cc_start: 0.8554 (mt) cc_final: 0.7875 (tp) REVERT: B 645 ASP cc_start: 0.7196 (p0) cc_final: 0.6889 (p0) REVERT: B 647 SER cc_start: 0.7500 (t) cc_final: 0.7091 (m) outliers start: 0 outliers final: 0 residues processed: 579 average time/residue: 0.1521 time to fit residues: 128.3873 Evaluate side-chains 525 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 525 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 71 optimal weight: 0.5980 chunk 153 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 165 optimal weight: 0.6980 chunk 145 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN D 205 ASN D 214 ASN D 268 HIS ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 359 ASN M 370 ASN ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.146512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.125888 restraints weight = 36251.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.129961 restraints weight = 21769.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.132815 restraints weight = 14227.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.134810 restraints weight = 9888.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.136264 restraints weight = 7209.248| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17177 Z= 0.200 Angle : 0.633 12.715 23253 Z= 0.338 Chirality : 0.045 0.171 2705 Planarity : 0.004 0.041 2931 Dihedral : 9.960 172.164 2299 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.05 % Allowed : 1.65 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.19), residues: 2098 helix: 1.11 (0.15), residues: 1141 sheet: -0.02 (0.34), residues: 223 loop : 1.02 (0.26), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 145 TYR 0.021 0.002 TYR B 105 PHE 0.029 0.002 PHE M 15 TRP 0.016 0.002 TRP M 20 HIS 0.012 0.001 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00402 (17177) covalent geometry : angle 0.63282 (23253) hydrogen bonds : bond 0.05483 ( 996) hydrogen bonds : angle 5.23430 ( 2835) *********************** 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 580 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 579 time to evaluate : 0.788 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: 0.8292 (tttt) cc_final: 0.7820 (tttt) REVERT: A 61 ILE cc_start: 0.8523 (mm) cc_final: 0.8304 (mm) REVERT: A 84 ASN cc_start: 0.7112 (m-40) cc_final: 0.6460 (m-40) REVERT: C 81 TYR cc_start: 0.7889 (m-80) cc_final: 0.7580 (m-80) REVERT: C 106 GLU cc_start: 0.6920 (tp30) cc_final: 0.6688 (tp30) REVERT: C 110 MET cc_start: 0.7946 (mtm) cc_final: 0.7619 (mtp) REVERT: C 120 VAL cc_start: 0.7922 (t) cc_final: 0.7720 (t) REVERT: C 138 GLU cc_start: 0.7400 (tt0) cc_final: 0.6785 (tt0) REVERT: C 173 LEU cc_start: 0.8100 (mt) cc_final: 0.7830 (mt) REVERT: C 175 ASN cc_start: 0.7865 (m-40) cc_final: 0.7163 (t0) REVERT: C 176 GLN cc_start: 0.6929 (mm-40) cc_final: 0.6230 (mm-40) REVERT: D 1 MET cc_start: 0.4031 (ttp) cc_final: 0.3709 (ttp) REVERT: D 59 VAL cc_start: 0.8077 (t) cc_final: 0.7864 (t) REVERT: D 74 TRP cc_start: 0.8489 (p-90) cc_final: 0.8239 (p-90) REVERT: D 126 TYR cc_start: 0.8128 (m-80) cc_final: 0.7786 (m-80) REVERT: D 128 THR cc_start: 0.7594 (m) cc_final: 0.7189 (p) REVERT: D 132 LEU cc_start: 0.7746 (mt) cc_final: 0.7246 (mt) REVERT: D 149 ASN cc_start: 0.8448 (m-40) cc_final: 0.7987 (m-40) REVERT: D 152 MET cc_start: 0.7058 (mtm) cc_final: 0.6725 (mtm) REVERT: D 155 MET cc_start: 0.8038 (mtm) cc_final: 0.7799 (mtm) REVERT: D 157 HIS cc_start: 0.8245 (t-90) cc_final: 0.8007 (t70) REVERT: D 169 ILE cc_start: 0.7319 (tt) cc_final: 0.6988 (mm) REVERT: D 179 GLU cc_start: 0.8305 (mp0) cc_final: 0.8087 (pm20) REVERT: D 189 LYS cc_start: 0.7883 (mtmt) cc_final: 0.7604 (mtmm) REVERT: D 205 ASN cc_start: 0.7064 (t160) cc_final: 0.6827 (t0) REVERT: D 221 LEU cc_start: 0.7917 (mp) cc_final: 0.7191 (mp) REVERT: D 236 TRP cc_start: 0.7899 (t-100) cc_final: 0.7659 (t-100) REVERT: D 240 LYS cc_start: 0.8147 (mmtt) cc_final: 0.7871 (mmmm) REVERT: D 242 ILE cc_start: 0.7814 (mt) cc_final: 0.7558 (tt) REVERT: D 257 LYS cc_start: 0.8202 (tttt) cc_final: 0.7719 (tttm) REVERT: D 265 ASN cc_start: 0.8040 (m-40) cc_final: 0.7796 (m-40) REVERT: D 268 HIS cc_start: 0.8645 (m90) cc_final: 0.8403 (m90) REVERT: D 273 MET cc_start: 0.8205 (pmm) cc_final: 0.7947 (pmm) REVERT: D 307 LYS cc_start: 0.8226 (mmtt) cc_final: 0.7708 (mmtt) REVERT: D 320 LYS cc_start: 0.7969 (mtpt) cc_final: 0.7315 (mtpt) REVERT: D 324 LEU cc_start: 0.8601 (mt) cc_final: 0.8297 (mt) REVERT: D 327 MET cc_start: 0.7246 (tpp) cc_final: 0.6458 (tpp) REVERT: D 329 LYS cc_start: 0.8969 (mttt) cc_final: 0.8683 (mttt) REVERT: D 336 LYS cc_start: 0.7921 (ptpp) cc_final: 0.7710 (ptpp) REVERT: D 338 VAL cc_start: 0.8586 (t) cc_final: 0.8378 (t) REVERT: D 339 GLN cc_start: 0.8291 (pt0) cc_final: 0.7734 (pp30) REVERT: D 342 LYS cc_start: 0.7958 (tmmt) cc_final: 0.7665 (tmmt) REVERT: D 367 MET cc_start: 0.6940 (mtm) cc_final: 0.6382 (mtm) REVERT: D 372 ASN cc_start: 0.7146 (p0) cc_final: 0.6909 (p0) REVERT: D 378 LYS cc_start: 0.8829 (mttt) cc_final: 0.8379 (mttt) REVERT: D 393 ARG cc_start: 0.7817 (mtt180) cc_final: 0.7311 (ttm-80) REVERT: D 394 ASP cc_start: 0.8194 (m-30) cc_final: 0.7747 (m-30) REVERT: D 396 LEU cc_start: 0.8606 (mt) cc_final: 0.8330 (pp) REVERT: D 398 THR cc_start: 0.8042 (p) cc_final: 0.7708 (t) REVERT: D 399 LYS cc_start: 0.8135 (mmmt) cc_final: 0.7590 (mmmt) REVERT: D 403 ILE cc_start: 0.8364 (pt) cc_final: 0.7929 (pt) REVERT: D 406 GLN cc_start: 0.7250 (mt0) cc_final: 0.7021 (mt0) REVERT: D 415 PHE cc_start: 0.6688 (m-80) cc_final: 0.6472 (m-80) REVERT: D 422 LEU cc_start: 0.9053 (tp) cc_final: 0.8706 (mt) REVERT: D 429 GLU cc_start: 0.8069 (tt0) cc_final: 0.7783 (tm-30) REVERT: D 440 GLN cc_start: 0.7776 (mm-40) cc_final: 0.7209 (tp40) REVERT: D 514 LEU cc_start: 0.6761 (mt) cc_final: 0.6442 (mt) REVERT: D 530 TYR cc_start: 0.7479 (m-80) cc_final: 0.7131 (m-80) REVERT: D 534 LEU cc_start: 0.8119 (mt) cc_final: 0.7528 (tp) REVERT: D 553 MET cc_start: 0.7250 (mtm) cc_final: 0.6822 (mtm) REVERT: D 571 ARG cc_start: 0.8406 (mtt-85) cc_final: 0.8115 (mtt-85) REVERT: M 6 PHE cc_start: 0.7763 (m-80) cc_final: 0.7408 (m-10) REVERT: M 34 GLU cc_start: 0.7280 (tt0) cc_final: 0.6934 (tt0) REVERT: M 60 TYR cc_start: 0.7379 (t80) cc_final: 0.7094 (t80) REVERT: M 62 ASP cc_start: 0.8291 (m-30) cc_final: 0.8007 (m-30) REVERT: M 67 VAL cc_start: 0.7933 (t) cc_final: 0.7635 (m) REVERT: M 111 GLU cc_start: 0.8088 (tp30) cc_final: 0.7594 (tp30) REVERT: M 116 MET cc_start: 0.6890 (tpp) cc_final: 0.6495 (tpt) REVERT: M 178 GLU cc_start: 0.6514 (pt0) cc_final: 0.6220 (pt0) REVERT: M 196 SER cc_start: 0.6827 (m) cc_final: 0.6462 (p) REVERT: M 201 GLU cc_start: 0.8124 (pt0) cc_final: 0.7384 (pm20) REVERT: M 212 LEU cc_start: 0.7390 (mt) cc_final: 0.7161 (mm) REVERT: M 228 LEU cc_start: 0.8643 (mt) cc_final: 0.8350 (tp) REVERT: M 230 ASP cc_start: 0.7296 (t0) cc_final: 0.6857 (t0) REVERT: M 239 PHE cc_start: 0.8104 (t80) cc_final: 0.7593 (t80) REVERT: M 250 PHE cc_start: 0.7824 (p90) cc_final: 0.6939 (p90) REVERT: M 256 ASN cc_start: 0.7779 (t0) cc_final: 0.7470 (t0) REVERT: M 321 MET cc_start: 0.3197 (mpp) cc_final: 0.2948 (mpp) REVERT: M 333 ASP cc_start: 0.7775 (t0) cc_final: 0.7478 (t0) REVERT: M 376 GLN cc_start: 0.5992 (mm-40) cc_final: 0.5723 (mp10) REVERT: M 381 GLN cc_start: 0.7950 (tm-30) cc_final: 0.7531 (tm-30) REVERT: M 409 THR cc_start: 0.7937 (m) cc_final: 0.7435 (p) REVERT: M 410 LYS cc_start: 0.8137 (mttt) cc_final: 0.7837 (mttt) REVERT: S 7 ILE cc_start: 0.8204 (mt) cc_final: 0.7981 (mt) REVERT: S 8 PHE cc_start: 0.7058 (p90) cc_final: 0.6824 (p90) REVERT: S 17 SER cc_start: 0.7857 (t) cc_final: 0.7579 (p) REVERT: S 18 LYS cc_start: 0.8176 (tttp) cc_final: 0.7373 (tttp) REVERT: S 29 GLN cc_start: 0.8585 (mt0) cc_final: 0.8321 (mt0) REVERT: S 77 VAL cc_start: 0.7418 (m) cc_final: 0.7140 (p) REVERT: S 86 ILE cc_start: 0.7969 (mm) cc_final: 0.7720 (mm) REVERT: S 89 LEU cc_start: 0.7586 (mt) cc_final: 0.6985 (mt) REVERT: S 116 VAL cc_start: 0.7705 (t) cc_final: 0.7475 (t) REVERT: S 117 HIS cc_start: 0.8479 (m-70) cc_final: 0.8141 (m-70) REVERT: S 123 MET cc_start: 0.7472 (tpt) cc_final: 0.6833 (tpt) REVERT: S 128 MET cc_start: 0.7565 (mtp) cc_final: 0.6740 (mtp) REVERT: B 41 LEU cc_start: 0.7987 (tp) cc_final: 0.7506 (pp) REVERT: B 45 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7122 (mm-30) REVERT: B 75 ASN cc_start: 0.8233 (m110) cc_final: 0.8009 (m110) REVERT: B 96 LYS cc_start: 0.7989 (mmmt) cc_final: 0.7319 (mmmm) REVERT: B 151 MET cc_start: 0.8023 (mtm) cc_final: 0.7790 (mtt) REVERT: B 152 MET cc_start: 0.6896 (tmm) cc_final: 0.6557 (tmm) REVERT: B 153 LEU cc_start: 0.8000 (mt) cc_final: 0.7662 (mt) REVERT: B 156 LYS cc_start: 0.8202 (mtpt) cc_final: 0.7930 (mttm) REVERT: B 185 LYS cc_start: 0.7905 (tttt) cc_final: 0.7507 (mtmt) REVERT: B 187 MET cc_start: 0.8166 (mtp) cc_final: 0.7845 (mtp) REVERT: B 192 ILE cc_start: 0.7924 (mm) cc_final: 0.7705 (mt) REVERT: B 197 LYS cc_start: 0.8846 (mttp) cc_final: 0.8552 (mtmm) REVERT: B 199 LYS cc_start: 0.8356 (tmtt) cc_final: 0.8049 (tmtt) REVERT: B 213 GLU cc_start: 0.7467 (tp30) cc_final: 0.7260 (tp30) REVERT: B 239 TRP cc_start: 0.7738 (m100) cc_final: 0.7250 (m100) REVERT: B 241 GLN cc_start: 0.7810 (mt0) cc_final: 0.6991 (mt0) REVERT: B 307 LEU cc_start: 0.8617 (mt) cc_final: 0.8162 (tp) REVERT: B 323 TYR cc_start: 0.7653 (m-10) cc_final: 0.7371 (m-80) REVERT: B 360 MET cc_start: 0.7764 (mtp) cc_final: 0.7524 (mtm) REVERT: B 384 MET cc_start: 0.7759 (ptt) cc_final: 0.7555 (ptp) REVERT: B 389 LYS cc_start: 0.8554 (mttt) cc_final: 0.8172 (mmtp) REVERT: B 390 LEU cc_start: 0.8178 (tp) cc_final: 0.7719 (tt) REVERT: B 391 GLU cc_start: 0.7728 (tp30) cc_final: 0.6612 (tp30) REVERT: B 392 ILE cc_start: 0.8165 (mt) cc_final: 0.7935 (tp) REVERT: B 394 THR cc_start: 0.8322 (m) cc_final: 0.7949 (p) REVERT: B 416 GLN cc_start: 0.7209 (pt0) cc_final: 0.6681 (pt0) REVERT: B 418 LYS cc_start: 0.7220 (mtmm) cc_final: 0.6944 (mppt) REVERT: B 426 GLN cc_start: 0.8754 (mt0) cc_final: 0.8126 (mm-40) REVERT: B 433 THR cc_start: 0.8375 (t) cc_final: 0.8150 (t) REVERT: B 437 GLU cc_start: 0.7796 (pp20) cc_final: 0.7262 (tm-30) REVERT: B 440 ASP cc_start: 0.7938 (m-30) cc_final: 0.7424 (p0) REVERT: B 462 VAL cc_start: 0.8602 (t) cc_final: 0.8255 (t) REVERT: B 465 ILE cc_start: 0.8766 (mt) cc_final: 0.8394 (tp) REVERT: B 479 ILE cc_start: 0.8636 (mm) cc_final: 0.8255 (mm) REVERT: B 481 LYS cc_start: 0.8869 (mttt) cc_final: 0.8182 (mttt) REVERT: B 483 MET cc_start: 0.8519 (mmm) cc_final: 0.7571 (mmm) REVERT: B 486 LEU cc_start: 0.8320 (mt) cc_final: 0.7903 (mt) REVERT: B 499 ILE cc_start: 0.8440 (mm) cc_final: 0.7927 (tp) REVERT: B 521 MET cc_start: 0.6885 (mmp) cc_final: 0.6438 (mmm) REVERT: B 545 LEU cc_start: 0.8753 (mt) cc_final: 0.8520 (mt) REVERT: B 556 GLN cc_start: 0.8017 (mt0) cc_final: 0.7743 (mt0) REVERT: B 577 ILE cc_start: 0.8712 (mt) cc_final: 0.8054 (tp) REVERT: B 578 ARG cc_start: 0.7941 (ptt90) cc_final: 0.7698 (ptt90) REVERT: B 635 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7431 (mp0) outliers start: 1 outliers final: 1 residues processed: 580 average time/residue: 0.1577 time to fit residues: 131.8151 Evaluate side-chains 533 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 532 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 44 optimal weight: 0.0020 chunk 111 optimal weight: 2.9990 chunk 96 optimal weight: 0.4980 chunk 186 optimal weight: 0.6980 chunk 191 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 200 GLN D 214 ASN ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 559 GLN M 84 HIS ** M 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 359 ASN M 370 ASN ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 117 HIS ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.148290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.127265 restraints weight = 36226.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.131379 restraints weight = 21631.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.134219 restraints weight = 14142.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.136077 restraints weight = 9856.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.137642 restraints weight = 7403.794| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17177 Z= 0.155 Angle : 0.576 12.108 23253 Z= 0.304 Chirality : 0.043 0.305 2705 Planarity : 0.004 0.044 2931 Dihedral : 9.487 169.957 2299 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.19), residues: 2098 helix: 1.35 (0.15), residues: 1142 sheet: 0.04 (0.35), residues: 234 loop : 0.98 (0.26), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 145 TYR 0.019 0.002 TYR M 174 PHE 0.019 0.002 PHE B 368 TRP 0.023 0.002 TRP D 417 HIS 0.005 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00322 (17177) covalent geometry : angle 0.57623 (23253) hydrogen bonds : bond 0.04795 ( 996) hydrogen bonds : angle 4.93118 ( 2835) *********************** 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 555 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 555 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8314 (tttt) cc_final: 0.7842 (tttt) REVERT: A 41 GLU cc_start: 0.5509 (mm-30) cc_final: 0.5174 (mm-30) REVERT: A 61 ILE cc_start: 0.8540 (mm) cc_final: 0.8301 (mm) REVERT: A 84 ASN cc_start: 0.6977 (m-40) cc_final: 0.6441 (m-40) REVERT: C 81 TYR cc_start: 0.7857 (m-80) cc_final: 0.7520 (m-80) REVERT: C 86 GLN cc_start: 0.7083 (mt0) cc_final: 0.6315 (mt0) REVERT: C 106 GLU cc_start: 0.6967 (tp30) cc_final: 0.6702 (tp30) REVERT: C 110 MET cc_start: 0.8038 (mtm) cc_final: 0.7768 (mtp) REVERT: C 138 GLU cc_start: 0.7553 (tt0) cc_final: 0.6766 (tt0) REVERT: C 173 LEU cc_start: 0.8218 (mt) cc_final: 0.8006 (mt) REVERT: C 175 ASN cc_start: 0.7845 (m-40) cc_final: 0.7322 (t0) REVERT: C 176 GLN cc_start: 0.6854 (mm-40) cc_final: 0.6446 (mm-40) REVERT: D 1 MET cc_start: 0.4020 (ttp) cc_final: 0.3689 (ttp) REVERT: D 20 ASP cc_start: 0.7095 (t0) cc_final: 0.6663 (t0) REVERT: D 59 VAL cc_start: 0.8084 (t) cc_final: 0.7879 (t) REVERT: D 74 TRP cc_start: 0.8453 (p-90) cc_final: 0.8228 (p-90) REVERT: D 110 MET cc_start: 0.6746 (mmt) cc_final: 0.6395 (mmt) REVERT: D 126 TYR cc_start: 0.8131 (m-80) cc_final: 0.7855 (m-80) REVERT: D 128 THR cc_start: 0.7671 (m) cc_final: 0.7128 (p) REVERT: D 132 LEU cc_start: 0.7696 (mt) cc_final: 0.7187 (mt) REVERT: D 149 ASN cc_start: 0.8350 (m-40) cc_final: 0.7912 (m-40) REVERT: D 152 MET cc_start: 0.7063 (mtm) cc_final: 0.6813 (mtm) REVERT: D 154 LEU cc_start: 0.8369 (mt) cc_final: 0.8155 (mp) REVERT: D 157 HIS cc_start: 0.8341 (t-90) cc_final: 0.8073 (t70) REVERT: D 169 ILE cc_start: 0.7293 (tt) cc_final: 0.6978 (mm) REVERT: D 221 LEU cc_start: 0.7883 (mp) cc_final: 0.7180 (mp) REVERT: D 236 TRP cc_start: 0.7865 (t-100) cc_final: 0.7534 (t-100) REVERT: D 242 ILE cc_start: 0.7773 (mt) cc_final: 0.7520 (tt) REVERT: D 252 GLU cc_start: 0.6138 (tm-30) cc_final: 0.5385 (mm-30) REVERT: D 265 ASN cc_start: 0.8042 (m-40) cc_final: 0.7819 (m-40) REVERT: D 275 LEU cc_start: 0.8237 (tp) cc_final: 0.8028 (tp) REVERT: D 307 LYS cc_start: 0.8234 (mmtt) cc_final: 0.7703 (mmtt) REVERT: D 324 LEU cc_start: 0.8574 (mt) cc_final: 0.8270 (mt) REVERT: D 327 MET cc_start: 0.7175 (tpp) cc_final: 0.6444 (tpp) REVERT: D 329 LYS cc_start: 0.8942 (mttt) cc_final: 0.8691 (mttt) REVERT: D 336 LYS cc_start: 0.8031 (ptpp) cc_final: 0.7684 (ptpp) REVERT: D 339 GLN cc_start: 0.8239 (pt0) cc_final: 0.7734 (pp30) REVERT: D 342 LYS cc_start: 0.7973 (tmmt) cc_final: 0.7743 (tmmt) REVERT: D 362 ASP cc_start: 0.8569 (m-30) cc_final: 0.8226 (m-30) REVERT: D 367 MET cc_start: 0.7038 (mtm) cc_final: 0.6327 (mtm) REVERT: D 374 MET cc_start: 0.7477 (mtt) cc_final: 0.5739 (mtt) REVERT: D 378 LYS cc_start: 0.8889 (mttt) cc_final: 0.8422 (mttt) REVERT: D 381 MET cc_start: 0.7921 (mtp) cc_final: 0.7710 (mtp) REVERT: D 393 ARG cc_start: 0.7731 (mtt180) cc_final: 0.7297 (ttm-80) REVERT: D 394 ASP cc_start: 0.8172 (m-30) cc_final: 0.7723 (m-30) REVERT: D 396 LEU cc_start: 0.8657 (mt) cc_final: 0.8264 (pp) REVERT: D 399 LYS cc_start: 0.8149 (mmmt) cc_final: 0.7142 (mmmt) REVERT: D 403 ILE cc_start: 0.8489 (pt) cc_final: 0.8071 (pt) REVERT: D 418 TYR cc_start: 0.7586 (t80) cc_final: 0.7367 (t80) REVERT: D 422 LEU cc_start: 0.9010 (tp) cc_final: 0.8732 (tp) REVERT: D 440 GLN cc_start: 0.7790 (mm-40) cc_final: 0.7093 (tp40) REVERT: D 479 CYS cc_start: 0.8555 (m) cc_final: 0.8177 (p) REVERT: D 488 ILE cc_start: 0.7441 (mm) cc_final: 0.7185 (mm) REVERT: D 521 VAL cc_start: 0.8127 (p) cc_final: 0.7719 (t) REVERT: D 530 TYR cc_start: 0.7579 (m-80) cc_final: 0.7171 (m-80) REVERT: D 534 LEU cc_start: 0.8137 (mt) cc_final: 0.7642 (tp) REVERT: D 553 MET cc_start: 0.7326 (mtm) cc_final: 0.6873 (mtm) REVERT: D 571 ARG cc_start: 0.8481 (mtt-85) cc_final: 0.8257 (mtt-85) REVERT: M 17 GLU cc_start: 0.7612 (tt0) cc_final: 0.7407 (tt0) REVERT: M 44 ASN cc_start: 0.8028 (t0) cc_final: 0.7718 (t0) REVERT: M 62 ASP cc_start: 0.8386 (m-30) cc_final: 0.8177 (m-30) REVERT: M 63 LYS cc_start: 0.8625 (mttt) cc_final: 0.8054 (mttt) REVERT: M 67 VAL cc_start: 0.7915 (t) cc_final: 0.7557 (m) REVERT: M 111 GLU cc_start: 0.7949 (tp30) cc_final: 0.7276 (tp30) REVERT: M 176 ASN cc_start: 0.6603 (m-40) cc_final: 0.6358 (m-40) REVERT: M 178 GLU cc_start: 0.6580 (pt0) cc_final: 0.6246 (pt0) REVERT: M 196 SER cc_start: 0.6746 (m) cc_final: 0.6326 (p) REVERT: M 198 VAL cc_start: 0.7644 (t) cc_final: 0.7390 (t) REVERT: M 201 GLU cc_start: 0.8122 (pt0) cc_final: 0.7404 (pm20) REVERT: M 212 LEU cc_start: 0.7396 (mt) cc_final: 0.7183 (mm) REVERT: M 228 LEU cc_start: 0.8626 (mt) cc_final: 0.8366 (tp) REVERT: M 230 ASP cc_start: 0.7405 (t0) cc_final: 0.6880 (t0) REVERT: M 233 PHE cc_start: 0.7803 (m-80) cc_final: 0.7297 (m-80) REVERT: M 239 PHE cc_start: 0.8070 (t80) cc_final: 0.7688 (t80) REVERT: M 250 PHE cc_start: 0.7817 (p90) cc_final: 0.6764 (p90) REVERT: M 256 ASN cc_start: 0.7778 (t0) cc_final: 0.7437 (t0) REVERT: M 332 PHE cc_start: 0.6054 (t80) cc_final: 0.5690 (t80) REVERT: M 333 ASP cc_start: 0.7825 (t0) cc_final: 0.7411 (t0) REVERT: M 376 GLN cc_start: 0.5924 (mm-40) cc_final: 0.5713 (mp10) REVERT: M 380 GLN cc_start: 0.7798 (mt0) cc_final: 0.7374 (mt0) REVERT: M 381 GLN cc_start: 0.7852 (tm-30) cc_final: 0.7423 (tm-30) REVERT: M 394 MET cc_start: 0.7008 (tmm) cc_final: 0.6806 (tmm) REVERT: M 409 THR cc_start: 0.7954 (m) cc_final: 0.7427 (p) REVERT: M 410 LYS cc_start: 0.8141 (mttt) cc_final: 0.7867 (mttt) REVERT: S 17 SER cc_start: 0.8062 (t) cc_final: 0.7687 (p) REVERT: S 18 LYS cc_start: 0.8140 (tttp) cc_final: 0.7396 (tttp) REVERT: S 29 GLN cc_start: 0.8551 (mt0) cc_final: 0.8305 (mt0) REVERT: S 77 VAL cc_start: 0.7356 (m) cc_final: 0.7058 (p) REVERT: S 82 SER cc_start: 0.7408 (t) cc_final: 0.7042 (t) REVERT: S 86 ILE cc_start: 0.7910 (mm) cc_final: 0.7648 (mm) REVERT: S 89 LEU cc_start: 0.7513 (mt) cc_final: 0.6853 (mt) REVERT: S 117 HIS cc_start: 0.8390 (m90) cc_final: 0.8166 (m90) REVERT: S 123 MET cc_start: 0.7487 (tpt) cc_final: 0.6822 (tpt) REVERT: S 128 MET cc_start: 0.7585 (mtp) cc_final: 0.6725 (mtp) REVERT: B 41 LEU cc_start: 0.7969 (tp) cc_final: 0.7438 (pp) REVERT: B 45 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7167 (mm-30) REVERT: B 63 MET cc_start: 0.6686 (mmm) cc_final: 0.5644 (mmm) REVERT: B 75 ASN cc_start: 0.8172 (m110) cc_final: 0.7525 (m110) REVERT: B 78 GLU cc_start: 0.8089 (pm20) cc_final: 0.7841 (pm20) REVERT: B 96 LYS cc_start: 0.7878 (mmmt) cc_final: 0.7465 (tttt) REVERT: B 151 MET cc_start: 0.8037 (mtm) cc_final: 0.7808 (mtt) REVERT: B 152 MET cc_start: 0.6872 (tmm) cc_final: 0.6629 (tmm) REVERT: B 153 LEU cc_start: 0.7976 (mt) cc_final: 0.7140 (mp) REVERT: B 156 LYS cc_start: 0.8207 (mtpt) cc_final: 0.7727 (mtpp) REVERT: B 187 MET cc_start: 0.8052 (mtp) cc_final: 0.7336 (mtp) REVERT: B 190 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7975 (mt-10) REVERT: B 192 ILE cc_start: 0.7912 (mm) cc_final: 0.7642 (mt) REVERT: B 213 GLU cc_start: 0.7482 (tp30) cc_final: 0.7146 (tp30) REVERT: B 239 TRP cc_start: 0.7605 (m100) cc_final: 0.7187 (m100) REVERT: B 241 GLN cc_start: 0.7767 (mt0) cc_final: 0.6936 (mt0) REVERT: B 250 ARG cc_start: 0.7789 (tpp80) cc_final: 0.7545 (tpp80) REVERT: B 297 HIS cc_start: 0.8002 (t70) cc_final: 0.7536 (t-90) REVERT: B 307 LEU cc_start: 0.8614 (mt) cc_final: 0.8166 (tp) REVERT: B 348 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7407 (mm-30) REVERT: B 360 MET cc_start: 0.7631 (mtp) cc_final: 0.7158 (mtp) REVERT: B 365 LYS cc_start: 0.8027 (mttt) cc_final: 0.7429 (mtpp) REVERT: B 371 TYR cc_start: 0.7643 (m-80) cc_final: 0.7433 (m-80) REVERT: B 384 MET cc_start: 0.7817 (ptt) cc_final: 0.7614 (ptp) REVERT: B 386 LYS cc_start: 0.8342 (mttt) cc_final: 0.7946 (ttmt) REVERT: B 389 LYS cc_start: 0.8525 (mttt) cc_final: 0.8037 (mtpp) REVERT: B 390 LEU cc_start: 0.7979 (tp) cc_final: 0.7675 (tt) REVERT: B 391 GLU cc_start: 0.7515 (tp30) cc_final: 0.7044 (tp30) REVERT: B 392 ILE cc_start: 0.8196 (mt) cc_final: 0.7550 (tp) REVERT: B 408 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6797 (mm-30) REVERT: B 426 GLN cc_start: 0.8730 (mt0) cc_final: 0.8093 (mm-40) REVERT: B 433 THR cc_start: 0.8137 (t) cc_final: 0.7936 (t) REVERT: B 437 GLU cc_start: 0.7773 (pp20) cc_final: 0.7344 (tp30) REVERT: B 440 ASP cc_start: 0.7846 (m-30) cc_final: 0.7374 (p0) REVERT: B 450 LEU cc_start: 0.7659 (mm) cc_final: 0.7407 (mt) REVERT: B 462 VAL cc_start: 0.8591 (t) cc_final: 0.8325 (t) REVERT: B 465 ILE cc_start: 0.8652 (mt) cc_final: 0.8338 (tp) REVERT: B 479 ILE cc_start: 0.8593 (mm) cc_final: 0.8275 (mm) REVERT: B 481 LYS cc_start: 0.8902 (mttt) cc_final: 0.8317 (tptp) REVERT: B 483 MET cc_start: 0.8436 (mmm) cc_final: 0.7510 (mmm) REVERT: B 486 LEU cc_start: 0.8311 (mt) cc_final: 0.7809 (mt) REVERT: B 499 ILE cc_start: 0.8414 (mm) cc_final: 0.7815 (tp) REVERT: B 521 MET cc_start: 0.6729 (mmp) cc_final: 0.6296 (mmm) REVERT: B 545 LEU cc_start: 0.8740 (mt) cc_final: 0.8514 (mt) REVERT: B 556 GLN cc_start: 0.7990 (mt0) cc_final: 0.7729 (mt0) REVERT: B 577 ILE cc_start: 0.8813 (mt) cc_final: 0.8176 (tp) REVERT: B 635 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7450 (mp0) outliers start: 0 outliers final: 0 residues processed: 555 average time/residue: 0.1580 time to fit residues: 126.6354 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 : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 109 optimal weight: 0.9980 chunk 57 optimal weight: 0.4980 chunk 129 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 chunk 90 optimal weight: 0.0170 chunk 32 optimal weight: 1.9990 chunk 158 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 GLN ** M 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 359 ASN M 374 ASN ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.148450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.127225 restraints weight = 35967.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.131343 restraints weight = 21553.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.134207 restraints weight = 14180.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.136274 restraints weight = 9937.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.137791 restraints weight = 7275.828| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17177 Z= 0.143 Angle : 0.560 10.467 23253 Z= 0.296 Chirality : 0.043 0.163 2705 Planarity : 0.004 0.048 2931 Dihedral : 9.074 169.191 2299 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.19), residues: 2098 helix: 1.42 (0.15), residues: 1155 sheet: 0.13 (0.35), residues: 236 loop : 0.69 (0.25), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 432 TYR 0.023 0.002 TYR M 174 PHE 0.025 0.002 PHE B 211 TRP 0.022 0.002 TRP D 417 HIS 0.012 0.001 HIS D 268 Details of bonding type rmsd covalent geometry : bond 0.00291 (17177) covalent geometry : angle 0.56033 (23253) hydrogen bonds : bond 0.04524 ( 996) hydrogen bonds : angle 4.78938 ( 2835) *********************** 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 548 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 548 time to evaluate : 0.640 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: 0.8323 (tttt) cc_final: 0.7829 (tttt) REVERT: A 41 GLU cc_start: 0.5491 (mm-30) cc_final: 0.5130 (mm-30) REVERT: A 61 ILE cc_start: 0.8559 (mm) cc_final: 0.8344 (mm) REVERT: A 84 ASN cc_start: 0.6934 (m-40) cc_final: 0.6343 (m-40) REVERT: A 110 MET cc_start: 0.7795 (ttm) cc_final: 0.7578 (ttm) REVERT: C 81 TYR cc_start: 0.7845 (m-80) cc_final: 0.7589 (m-80) REVERT: C 86 GLN cc_start: 0.7056 (mt0) cc_final: 0.6209 (mt0) REVERT: C 88 LEU cc_start: 0.8215 (tt) cc_final: 0.7903 (tt) REVERT: C 106 GLU cc_start: 0.6978 (tp30) cc_final: 0.6645 (tp30) REVERT: C 110 MET cc_start: 0.8128 (mtm) cc_final: 0.7839 (mtp) REVERT: C 173 LEU cc_start: 0.8328 (mt) cc_final: 0.8067 (mt) REVERT: C 175 ASN cc_start: 0.7880 (m-40) cc_final: 0.7435 (t0) REVERT: C 176 GLN cc_start: 0.6977 (mm-40) cc_final: 0.6510 (mm-40) REVERT: D 1 MET cc_start: 0.4006 (ttp) cc_final: 0.3674 (ttp) REVERT: D 20 ASP cc_start: 0.7121 (t0) cc_final: 0.6687 (t0) REVERT: D 67 MET cc_start: 0.7564 (ttt) cc_final: 0.7185 (ttt) REVERT: D 91 LYS cc_start: 0.7293 (mtmt) cc_final: 0.6954 (mtmt) REVERT: D 110 MET cc_start: 0.6778 (mmt) cc_final: 0.6400 (mmt) REVERT: D 116 ILE cc_start: 0.8544 (mm) cc_final: 0.8238 (mm) REVERT: D 117 ARG cc_start: 0.8232 (ttm-80) cc_final: 0.8003 (mtm-85) REVERT: D 118 LYS cc_start: 0.8342 (ttmt) cc_final: 0.8076 (mtpt) REVERT: D 126 TYR cc_start: 0.8110 (m-80) cc_final: 0.7798 (m-80) REVERT: D 128 THR cc_start: 0.7486 (m) cc_final: 0.7097 (p) REVERT: D 132 LEU cc_start: 0.7743 (mt) cc_final: 0.7224 (mt) REVERT: D 149 ASN cc_start: 0.8287 (m-40) cc_final: 0.7804 (m-40) REVERT: D 154 LEU cc_start: 0.8265 (mt) cc_final: 0.8008 (mp) REVERT: D 155 MET cc_start: 0.8098 (mtm) cc_final: 0.7808 (mtm) REVERT: D 157 HIS cc_start: 0.8331 (t-90) cc_final: 0.8100 (t70) REVERT: D 169 ILE cc_start: 0.7392 (tt) cc_final: 0.7021 (mm) REVERT: D 176 LYS cc_start: 0.8120 (mmpt) cc_final: 0.7675 (mmtm) REVERT: D 221 LEU cc_start: 0.7842 (mp) cc_final: 0.7119 (mp) REVERT: D 257 LYS cc_start: 0.8182 (tttt) cc_final: 0.7688 (tttm) REVERT: D 307 LYS cc_start: 0.8238 (mmtt) cc_final: 0.7841 (mmtt) REVERT: D 324 LEU cc_start: 0.8557 (mt) cc_final: 0.8285 (mt) REVERT: D 327 MET cc_start: 0.7179 (tpp) cc_final: 0.6518 (tpp) REVERT: D 329 LYS cc_start: 0.8925 (mttt) cc_final: 0.8662 (mttt) REVERT: D 336 LYS cc_start: 0.8002 (ptpp) cc_final: 0.7611 (ptpp) REVERT: D 367 MET cc_start: 0.7111 (mtm) cc_final: 0.6493 (mtm) REVERT: D 377 VAL cc_start: 0.8892 (t) cc_final: 0.8503 (p) REVERT: D 378 LYS cc_start: 0.8860 (mttt) cc_final: 0.8344 (mttt) REVERT: D 393 ARG cc_start: 0.7787 (mtt180) cc_final: 0.7319 (ttm-80) REVERT: D 394 ASP cc_start: 0.8120 (m-30) cc_final: 0.7821 (m-30) REVERT: D 399 LYS cc_start: 0.8121 (mmmt) cc_final: 0.7164 (mmmt) REVERT: D 403 ILE cc_start: 0.8447 (pt) cc_final: 0.7954 (pt) REVERT: D 406 GLN cc_start: 0.7533 (mt0) cc_final: 0.7278 (mt0) REVERT: D 422 LEU cc_start: 0.8956 (tp) cc_final: 0.8708 (tp) REVERT: D 479 CYS cc_start: 0.8559 (m) cc_final: 0.7966 (p) REVERT: D 524 GLN cc_start: 0.7947 (pp30) cc_final: 0.7663 (pp30) REVERT: D 530 TYR cc_start: 0.7497 (m-80) cc_final: 0.7114 (m-80) REVERT: D 534 LEU cc_start: 0.8078 (mt) cc_final: 0.7618 (tp) REVERT: D 553 MET cc_start: 0.7354 (mtm) cc_final: 0.6945 (mtm) REVERT: D 571 ARG cc_start: 0.8423 (mtt-85) cc_final: 0.8141 (mtt-85) REVERT: M 44 ASN cc_start: 0.8135 (t0) cc_final: 0.7750 (t0) REVERT: M 63 LYS cc_start: 0.8578 (mttt) cc_final: 0.8047 (mttt) REVERT: M 67 VAL cc_start: 0.7922 (t) cc_final: 0.7546 (m) REVERT: M 88 ASP cc_start: 0.7997 (m-30) cc_final: 0.7726 (m-30) REVERT: M 111 GLU cc_start: 0.8015 (tp30) cc_final: 0.6776 (tp30) REVERT: M 116 MET cc_start: 0.7031 (tpp) cc_final: 0.6759 (tpt) REVERT: M 176 ASN cc_start: 0.6517 (m-40) cc_final: 0.5612 (m-40) REVERT: M 196 SER cc_start: 0.6690 (m) cc_final: 0.6286 (p) REVERT: M 201 GLU cc_start: 0.8131 (pt0) cc_final: 0.7740 (pt0) REVERT: M 212 LEU cc_start: 0.7415 (mt) cc_final: 0.7195 (mm) REVERT: M 230 ASP cc_start: 0.7451 (t0) cc_final: 0.6906 (t0) REVERT: M 233 PHE cc_start: 0.7733 (m-80) cc_final: 0.7272 (m-80) REVERT: M 239 PHE cc_start: 0.8015 (t80) cc_final: 0.7630 (t80) REVERT: M 250 PHE cc_start: 0.7746 (p90) cc_final: 0.6658 (p90) REVERT: M 256 ASN cc_start: 0.7747 (t0) cc_final: 0.7438 (t0) REVERT: M 333 ASP cc_start: 0.7928 (t0) cc_final: 0.7485 (t0) REVERT: M 376 GLN cc_start: 0.5882 (mm-40) cc_final: 0.5673 (mp10) REVERT: M 380 GLN cc_start: 0.7700 (mt0) cc_final: 0.7271 (mt0) REVERT: M 381 GLN cc_start: 0.7882 (tm-30) cc_final: 0.7389 (tm-30) REVERT: M 406 LYS cc_start: 0.8176 (mtpt) cc_final: 0.7775 (mtmt) REVERT: M 409 THR cc_start: 0.7952 (m) cc_final: 0.7475 (p) REVERT: M 410 LYS cc_start: 0.8148 (mttt) cc_final: 0.7920 (mttt) REVERT: S 17 SER cc_start: 0.8081 (t) cc_final: 0.7584 (p) REVERT: S 18 LYS cc_start: 0.8181 (tttp) cc_final: 0.7367 (tttp) REVERT: S 29 GLN cc_start: 0.8568 (mt0) cc_final: 0.8064 (mm-40) REVERT: S 77 VAL cc_start: 0.7293 (m) cc_final: 0.7005 (p) REVERT: S 82 SER cc_start: 0.7268 (t) cc_final: 0.6681 (p) REVERT: S 86 ILE cc_start: 0.7829 (mm) cc_final: 0.7479 (mm) REVERT: S 89 LEU cc_start: 0.7431 (mt) cc_final: 0.6722 (mt) REVERT: S 97 LEU cc_start: 0.7923 (mt) cc_final: 0.7362 (mt) REVERT: S 117 HIS cc_start: 0.8392 (m90) cc_final: 0.8186 (m90) REVERT: S 123 MET cc_start: 0.7479 (tpt) cc_final: 0.6800 (tpt) REVERT: S 125 MET cc_start: 0.7764 (ttm) cc_final: 0.7544 (ttm) REVERT: S 128 MET cc_start: 0.7607 (mtp) cc_final: 0.6881 (mtp) REVERT: B 75 ASN cc_start: 0.8066 (m110) cc_final: 0.7375 (m110) REVERT: B 96 LYS cc_start: 0.7838 (mmmt) cc_final: 0.7534 (tttp) REVERT: B 126 ASP cc_start: 0.7509 (t70) cc_final: 0.7232 (t70) REVERT: B 129 GLN cc_start: 0.8474 (pm20) cc_final: 0.7984 (pt0) REVERT: B 151 MET cc_start: 0.7946 (mtm) cc_final: 0.7670 (mtt) REVERT: B 152 MET cc_start: 0.6928 (tmm) cc_final: 0.6665 (tmm) REVERT: B 153 LEU cc_start: 0.7974 (mt) cc_final: 0.7112 (mp) REVERT: B 156 LYS cc_start: 0.8175 (mtpt) cc_final: 0.7711 (mtpp) REVERT: B 187 MET cc_start: 0.8050 (mtp) cc_final: 0.7320 (mtp) REVERT: B 192 ILE cc_start: 0.7857 (mm) cc_final: 0.7607 (mt) REVERT: B 197 LYS cc_start: 0.8730 (mttp) cc_final: 0.8268 (mtmm) REVERT: B 213 GLU cc_start: 0.7555 (tp30) cc_final: 0.7204 (tp30) REVERT: B 239 TRP cc_start: 0.7562 (m100) cc_final: 0.7146 (m100) REVERT: B 241 GLN cc_start: 0.7817 (mt0) cc_final: 0.6977 (mt0) REVERT: B 297 HIS cc_start: 0.7819 (t-90) cc_final: 0.7216 (t-90) REVERT: B 307 LEU cc_start: 0.8468 (mt) cc_final: 0.8123 (tp) REVERT: B 360 MET cc_start: 0.7621 (mtp) cc_final: 0.7201 (mtp) REVERT: B 362 ILE cc_start: 0.7708 (mm) cc_final: 0.7475 (mm) REVERT: B 365 LYS cc_start: 0.8358 (mttt) cc_final: 0.7723 (mtpp) REVERT: B 371 TYR cc_start: 0.7708 (m-80) cc_final: 0.7373 (m-80) REVERT: B 384 MET cc_start: 0.7779 (ptt) cc_final: 0.7572 (ptp) REVERT: B 389 LYS cc_start: 0.8475 (mttt) cc_final: 0.8078 (mmtp) REVERT: B 390 LEU cc_start: 0.8046 (tp) cc_final: 0.7730 (tt) REVERT: B 391 GLU cc_start: 0.7322 (tp30) cc_final: 0.7003 (tp30) REVERT: B 392 ILE cc_start: 0.8011 (mt) cc_final: 0.7510 (tp) REVERT: B 399 GLU cc_start: 0.7969 (pm20) cc_final: 0.7559 (pp20) REVERT: B 405 LEU cc_start: 0.7839 (tp) cc_final: 0.7592 (tp) REVERT: B 408 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7115 (tp30) REVERT: B 426 GLN cc_start: 0.8623 (mt0) cc_final: 0.8109 (mm-40) REVERT: B 433 THR cc_start: 0.7979 (t) cc_final: 0.7771 (t) REVERT: B 437 GLU cc_start: 0.7656 (pp20) cc_final: 0.7421 (tp30) REVERT: B 440 ASP cc_start: 0.7850 (m-30) cc_final: 0.7307 (p0) REVERT: B 462 VAL cc_start: 0.8588 (t) cc_final: 0.8307 (t) REVERT: B 465 ILE cc_start: 0.8674 (mt) cc_final: 0.8327 (tp) REVERT: B 466 LYS cc_start: 0.8201 (ttpp) cc_final: 0.7844 (ttpp) REVERT: B 481 LYS cc_start: 0.8914 (mttt) cc_final: 0.8315 (tptp) REVERT: B 483 MET cc_start: 0.8416 (mmm) cc_final: 0.7786 (mmm) REVERT: B 498 SER cc_start: 0.8518 (m) cc_final: 0.8239 (p) REVERT: B 499 ILE cc_start: 0.8385 (mm) cc_final: 0.7738 (tp) REVERT: B 521 MET cc_start: 0.6874 (mmp) cc_final: 0.6484 (mmm) REVERT: B 556 GLN cc_start: 0.7986 (mt0) cc_final: 0.7740 (mt0) REVERT: B 572 ASP cc_start: 0.7359 (t70) cc_final: 0.6966 (t70) REVERT: B 577 ILE cc_start: 0.8851 (mt) cc_final: 0.8166 (tp) REVERT: B 635 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7408 (mp0) REVERT: B 649 ARG cc_start: 0.6044 (mmp80) cc_final: 0.5120 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 548 average time/residue: 0.1584 time to fit residues: 124.8086 Evaluate side-chains 518 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 518 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 120 optimal weight: 0.9980 chunk 122 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 chunk 202 optimal weight: 0.0370 chunk 93 optimal weight: 0.0470 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 169 optimal weight: 0.0070 overall best weight: 0.2974 ------------------------------------------------------------------------------- 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 ** D 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 HIS ** M 119 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** ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.149540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.128370 restraints weight = 35650.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.132536 restraints weight = 21371.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.135458 restraints weight = 13991.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.137422 restraints weight = 9748.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.138957 restraints weight = 7186.683| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17177 Z= 0.123 Angle : 0.554 8.542 23253 Z= 0.289 Chirality : 0.043 0.167 2705 Planarity : 0.004 0.047 2931 Dihedral : 8.805 167.289 2299 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.19), residues: 2098 helix: 1.53 (0.15), residues: 1145 sheet: 0.13 (0.34), residues: 240 loop : 0.76 (0.25), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 79 TYR 0.019 0.002 TYR M 174 PHE 0.019 0.002 PHE S 49 TRP 0.033 0.002 TRP D 236 HIS 0.014 0.001 HIS D 268 Details of bonding type rmsd covalent geometry : bond 0.00260 (17177) covalent geometry : angle 0.55365 (23253) hydrogen bonds : bond 0.04226 ( 996) hydrogen bonds : angle 4.62137 ( 2835) *********************** 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 : 0.659 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: 0.8312 (tttt) cc_final: 0.7823 (tttt) REVERT: A 41 GLU cc_start: 0.5281 (mm-30) cc_final: 0.4940 (mm-30) REVERT: A 61 ILE cc_start: 0.8564 (mm) cc_final: 0.8327 (mm) REVERT: A 84 ASN cc_start: 0.6850 (m-40) cc_final: 0.6279 (m-40) REVERT: A 102 GLU cc_start: 0.8319 (tt0) cc_final: 0.7651 (tm-30) REVERT: C 22 MET cc_start: 0.7615 (ttm) cc_final: 0.7091 (ttm) REVERT: C 81 TYR cc_start: 0.7776 (m-80) cc_final: 0.7552 (m-80) REVERT: C 86 GLN cc_start: 0.7011 (mt0) cc_final: 0.6174 (mt0) REVERT: C 88 LEU cc_start: 0.8178 (tt) cc_final: 0.7903 (tt) REVERT: C 97 ARG cc_start: 0.8509 (mtp85) cc_final: 0.8294 (mtp85) REVERT: C 106 GLU cc_start: 0.6948 (tp30) cc_final: 0.6622 (tp30) REVERT: C 149 ARG cc_start: 0.6950 (ttm-80) cc_final: 0.6645 (mmm160) REVERT: C 173 LEU cc_start: 0.8348 (mt) cc_final: 0.8092 (mt) REVERT: C 175 ASN cc_start: 0.7785 (m-40) cc_final: 0.7272 (t0) REVERT: C 176 GLN cc_start: 0.6883 (mm-40) cc_final: 0.6460 (mm-40) REVERT: D 1 MET cc_start: 0.3991 (ttp) cc_final: 0.3646 (ttp) REVERT: D 20 ASP cc_start: 0.7104 (t0) cc_final: 0.6810 (t0) REVERT: D 77 PHE cc_start: 0.7345 (t80) cc_final: 0.7038 (t80) REVERT: D 83 MET cc_start: 0.7871 (mtt) cc_final: 0.7284 (mtt) REVERT: D 110 MET cc_start: 0.6813 (mmt) cc_final: 0.6447 (mmt) REVERT: D 116 ILE cc_start: 0.8451 (mm) cc_final: 0.8227 (mm) REVERT: D 117 ARG cc_start: 0.8182 (ttm-80) cc_final: 0.7938 (mtm-85) REVERT: D 118 LYS cc_start: 0.8315 (ttmt) cc_final: 0.8032 (mtpt) REVERT: D 126 TYR cc_start: 0.8065 (m-80) cc_final: 0.7791 (m-80) REVERT: D 128 THR cc_start: 0.7406 (m) cc_final: 0.6986 (p) REVERT: D 132 LEU cc_start: 0.7743 (mt) cc_final: 0.7374 (mt) REVERT: D 149 ASN cc_start: 0.8246 (m-40) cc_final: 0.7763 (m-40) REVERT: D 155 MET cc_start: 0.7978 (mtm) cc_final: 0.7521 (mtm) REVERT: D 157 HIS cc_start: 0.8330 (t-90) cc_final: 0.8088 (t70) REVERT: D 169 ILE cc_start: 0.7317 (tt) cc_final: 0.6848 (pt) REVERT: D 176 LYS cc_start: 0.8171 (mmpt) cc_final: 0.7461 (mmtm) REVERT: D 221 LEU cc_start: 0.7847 (mp) cc_final: 0.7056 (mp) REVERT: D 257 LYS cc_start: 0.8108 (tttt) cc_final: 0.7575 (tttm) REVERT: D 307 LYS cc_start: 0.8227 (mmtt) cc_final: 0.7800 (mmtt) REVERT: D 320 LYS cc_start: 0.7963 (mtpt) cc_final: 0.7260 (mtmm) REVERT: D 324 LEU cc_start: 0.8623 (mt) cc_final: 0.8332 (mt) REVERT: D 327 MET cc_start: 0.7174 (tpp) cc_final: 0.6566 (tpp) REVERT: D 329 LYS cc_start: 0.8918 (mttt) cc_final: 0.8650 (mttt) REVERT: D 336 LYS cc_start: 0.7939 (ptpp) cc_final: 0.7644 (ptpp) REVERT: D 339 GLN cc_start: 0.8284 (pt0) cc_final: 0.7829 (pp30) REVERT: D 367 MET cc_start: 0.7103 (mtm) cc_final: 0.6509 (mtm) REVERT: D 374 MET cc_start: 0.7352 (mtt) cc_final: 0.6164 (mtt) REVERT: D 377 VAL cc_start: 0.8880 (t) cc_final: 0.8476 (p) REVERT: D 378 LYS cc_start: 0.8861 (mttt) cc_final: 0.8339 (mttt) REVERT: D 393 ARG cc_start: 0.7714 (mtt180) cc_final: 0.7387 (ttm-80) REVERT: D 394 ASP cc_start: 0.8074 (m-30) cc_final: 0.7758 (m-30) REVERT: D 396 LEU cc_start: 0.8769 (pp) cc_final: 0.8524 (pp) REVERT: D 399 LYS cc_start: 0.8029 (mmmt) cc_final: 0.7605 (mmmt) REVERT: D 403 ILE cc_start: 0.8456 (pt) cc_final: 0.8000 (pt) REVERT: D 406 GLN cc_start: 0.7530 (mt0) cc_final: 0.7231 (mt0) REVERT: D 413 THR cc_start: 0.7470 (p) cc_final: 0.7194 (p) REVERT: D 422 LEU cc_start: 0.8899 (tp) cc_final: 0.8660 (tp) REVERT: D 440 GLN cc_start: 0.7681 (mm-40) cc_final: 0.6963 (tp40) REVERT: D 521 VAL cc_start: 0.8102 (p) cc_final: 0.7880 (t) REVERT: D 524 GLN cc_start: 0.7899 (pp30) cc_final: 0.7644 (pp30) REVERT: D 530 TYR cc_start: 0.7482 (m-80) cc_final: 0.7143 (m-80) REVERT: D 532 SER cc_start: 0.7625 (m) cc_final: 0.7280 (p) REVERT: D 534 LEU cc_start: 0.8127 (mt) cc_final: 0.7539 (tp) REVERT: D 553 MET cc_start: 0.7451 (mtm) cc_final: 0.6874 (mtm) REVERT: D 571 ARG cc_start: 0.8445 (mtt-85) cc_final: 0.8182 (mtt-85) REVERT: M 44 ASN cc_start: 0.8025 (t0) cc_final: 0.7667 (t0) REVERT: M 63 LYS cc_start: 0.8494 (mttt) cc_final: 0.8003 (mttt) REVERT: M 67 VAL cc_start: 0.7868 (t) cc_final: 0.7477 (m) REVERT: M 88 ASP cc_start: 0.7849 (m-30) cc_final: 0.7526 (m-30) REVERT: M 111 GLU cc_start: 0.7956 (tp30) cc_final: 0.7689 (tp30) REVERT: M 114 GLU cc_start: 0.7613 (tp30) cc_final: 0.7386 (tp30) REVERT: M 176 ASN cc_start: 0.6457 (m-40) cc_final: 0.5566 (m-40) REVERT: M 196 SER cc_start: 0.6575 (m) cc_final: 0.6160 (p) REVERT: M 201 GLU cc_start: 0.8083 (pt0) cc_final: 0.7682 (pt0) REVERT: M 212 LEU cc_start: 0.7414 (mt) cc_final: 0.7207 (mm) REVERT: M 228 LEU cc_start: 0.8635 (mt) cc_final: 0.8389 (mt) REVERT: M 230 ASP cc_start: 0.7494 (t0) cc_final: 0.6982 (t0) REVERT: M 233 PHE cc_start: 0.7817 (m-80) cc_final: 0.7446 (m-80) REVERT: M 239 PHE cc_start: 0.7919 (t80) cc_final: 0.7628 (t80) REVERT: M 250 PHE cc_start: 0.7773 (p90) cc_final: 0.6598 (p90) REVERT: M 256 ASN cc_start: 0.7687 (t0) cc_final: 0.7421 (t0) REVERT: M 333 ASP cc_start: 0.7965 (t0) cc_final: 0.7440 (t0) REVERT: M 380 GLN cc_start: 0.7684 (mt0) cc_final: 0.7201 (mt0) REVERT: M 381 GLN cc_start: 0.7875 (tm-30) cc_final: 0.7394 (tm-30) REVERT: M 406 LYS cc_start: 0.8034 (mtpt) cc_final: 0.7627 (ttmt) REVERT: M 409 THR cc_start: 0.7930 (m) cc_final: 0.7425 (p) REVERT: M 410 LYS cc_start: 0.8096 (mttt) cc_final: 0.7880 (mttt) REVERT: S 17 SER cc_start: 0.8034 (t) cc_final: 0.7571 (p) REVERT: S 18 LYS cc_start: 0.8051 (tttp) cc_final: 0.7354 (tttp) REVERT: S 29 GLN cc_start: 0.8526 (mt0) cc_final: 0.8046 (mm-40) REVERT: S 77 VAL cc_start: 0.7276 (m) cc_final: 0.6986 (p) REVERT: S 82 SER cc_start: 0.7406 (t) cc_final: 0.6644 (t) REVERT: S 86 ILE cc_start: 0.7856 (mm) cc_final: 0.7594 (mm) REVERT: S 97 LEU cc_start: 0.7896 (mt) cc_final: 0.7353 (mt) REVERT: S 123 MET cc_start: 0.7518 (tpt) cc_final: 0.6923 (tpt) REVERT: B 86 ASN cc_start: 0.7915 (t0) cc_final: 0.7682 (t0) REVERT: B 126 ASP cc_start: 0.7474 (t70) cc_final: 0.7153 (t70) REVERT: B 129 GLN cc_start: 0.8464 (pm20) cc_final: 0.7963 (pt0) REVERT: B 151 MET cc_start: 0.7910 (mtm) cc_final: 0.7705 (mtt) REVERT: B 152 MET cc_start: 0.6901 (tmm) cc_final: 0.6635 (tmm) REVERT: B 153 LEU cc_start: 0.8034 (mt) cc_final: 0.7156 (mp) REVERT: B 156 LYS cc_start: 0.8025 (mtpt) cc_final: 0.7563 (mtpp) REVERT: B 187 MET cc_start: 0.7793 (mtp) cc_final: 0.7435 (mtp) REVERT: B 197 LYS cc_start: 0.8703 (mttp) cc_final: 0.8281 (mtmm) REVERT: B 199 LYS cc_start: 0.8586 (pptt) cc_final: 0.8241 (pptt) REVERT: B 213 GLU cc_start: 0.7531 (tp30) cc_final: 0.7172 (tp30) REVERT: B 239 TRP cc_start: 0.7385 (m100) cc_final: 0.6921 (m100) REVERT: B 241 GLN cc_start: 0.7848 (mt0) cc_final: 0.7046 (mt0) REVERT: B 293 MET cc_start: 0.6879 (ttt) cc_final: 0.6297 (ttt) REVERT: B 297 HIS cc_start: 0.7819 (t-90) cc_final: 0.7261 (t-90) REVERT: B 307 LEU cc_start: 0.8436 (mt) cc_final: 0.8041 (tp) REVERT: B 330 SER cc_start: 0.7989 (t) cc_final: 0.7629 (t) REVERT: B 342 LEU cc_start: 0.8452 (mt) cc_final: 0.8241 (mm) REVERT: B 345 SER cc_start: 0.8260 (t) cc_final: 0.8058 (t) REVERT: B 360 MET cc_start: 0.7577 (mtp) cc_final: 0.7260 (mtp) REVERT: B 365 LYS cc_start: 0.8355 (mttt) cc_final: 0.7656 (mtpp) REVERT: B 371 TYR cc_start: 0.7662 (m-80) cc_final: 0.7300 (m-80) REVERT: B 384 MET cc_start: 0.7856 (ptt) cc_final: 0.7637 (ptp) REVERT: B 389 LYS cc_start: 0.8492 (mttt) cc_final: 0.7885 (mtpp) REVERT: B 390 LEU cc_start: 0.8111 (tp) cc_final: 0.7854 (tt) REVERT: B 391 GLU cc_start: 0.7321 (tp30) cc_final: 0.7044 (tp30) REVERT: B 392 ILE cc_start: 0.8027 (mt) cc_final: 0.7483 (tp) REVERT: B 399 GLU cc_start: 0.8037 (pm20) cc_final: 0.7603 (pp20) REVERT: B 408 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7162 (tp30) REVERT: B 426 GLN cc_start: 0.8599 (mt0) cc_final: 0.8070 (mm-40) REVERT: B 433 THR cc_start: 0.7907 (t) cc_final: 0.7670 (t) REVERT: B 437 GLU cc_start: 0.7630 (pp20) cc_final: 0.7409 (tp30) REVERT: B 440 ASP cc_start: 0.7752 (m-30) cc_final: 0.7249 (p0) REVERT: B 450 LEU cc_start: 0.7622 (mm) cc_final: 0.7307 (mt) REVERT: B 462 VAL cc_start: 0.8514 (t) cc_final: 0.8244 (t) REVERT: B 465 ILE cc_start: 0.8638 (mt) cc_final: 0.8378 (tp) REVERT: B 466 LYS cc_start: 0.8164 (ttpp) cc_final: 0.7749 (ttpp) REVERT: B 481 LYS cc_start: 0.8869 (mttt) cc_final: 0.8280 (mttt) REVERT: B 483 MET cc_start: 0.8435 (mmm) cc_final: 0.7674 (mmm) REVERT: B 498 SER cc_start: 0.8502 (m) cc_final: 0.8266 (p) REVERT: B 499 ILE cc_start: 0.8383 (mm) cc_final: 0.7735 (tp) REVERT: B 521 MET cc_start: 0.6703 (mmp) cc_final: 0.6278 (mmm) REVERT: B 556 GLN cc_start: 0.7960 (mt0) cc_final: 0.7663 (mt0) REVERT: B 572 ASP cc_start: 0.7313 (t70) cc_final: 0.7016 (t0) REVERT: B 577 ILE cc_start: 0.8847 (mt) cc_final: 0.8189 (tp) REVERT: B 649 ARG cc_start: 0.6059 (mmp80) cc_final: 0.5143 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 549 average time/residue: 0.1607 time to fit residues: 127.0486 Evaluate side-chains 515 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 515 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 109 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 110 optimal weight: 0.4980 chunk 124 optimal weight: 0.0870 chunk 142 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 90 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 200 GLN D 214 ASN ** M 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 359 ASN ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.148184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.126522 restraints weight = 35658.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.130701 restraints weight = 21449.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.133601 restraints weight = 14080.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.135689 restraints weight = 9873.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.137086 restraints weight = 7284.063| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17177 Z= 0.145 Angle : 0.570 10.055 23253 Z= 0.298 Chirality : 0.043 0.245 2705 Planarity : 0.004 0.050 2931 Dihedral : 8.677 170.088 2299 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.19), residues: 2098 helix: 1.48 (0.15), residues: 1152 sheet: 0.28 (0.35), residues: 234 loop : 0.58 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 212 TYR 0.020 0.002 TYR B 105 PHE 0.043 0.002 PHE D 245 TRP 0.024 0.002 TRP D 236 HIS 0.011 0.001 HIS D 268 Details of bonding type rmsd covalent geometry : bond 0.00301 (17177) covalent geometry : angle 0.56965 (23253) hydrogen bonds : bond 0.04489 ( 996) hydrogen bonds : angle 4.72581 ( 2835) *********************** 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 543 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 543 time to evaluate : 0.757 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: 0.8373 (tttt) cc_final: 0.7911 (tttt) REVERT: A 41 GLU cc_start: 0.5531 (mm-30) cc_final: 0.5192 (mm-30) REVERT: A 61 ILE cc_start: 0.8596 (mm) cc_final: 0.8364 (mm) REVERT: A 84 ASN cc_start: 0.6886 (m-40) cc_final: 0.6301 (m-40) REVERT: A 102 GLU cc_start: 0.8392 (tt0) cc_final: 0.7708 (tm-30) REVERT: C 81 TYR cc_start: 0.7911 (m-80) cc_final: 0.7711 (m-80) REVERT: C 86 GLN cc_start: 0.7129 (mt0) cc_final: 0.6328 (mt0) REVERT: C 88 LEU cc_start: 0.8040 (tt) cc_final: 0.7526 (tt) REVERT: C 106 GLU cc_start: 0.7105 (tp30) cc_final: 0.6771 (tp30) REVERT: C 149 ARG cc_start: 0.7039 (ttm-80) cc_final: 0.6746 (mmm160) REVERT: C 173 LEU cc_start: 0.8368 (mt) cc_final: 0.8092 (mt) REVERT: C 175 ASN cc_start: 0.7960 (m-40) cc_final: 0.7498 (t0) REVERT: C 176 GLN cc_start: 0.6912 (mm-40) cc_final: 0.6529 (mm-40) REVERT: D 1 MET cc_start: 0.4042 (ttp) cc_final: 0.3672 (ttp) REVERT: D 20 ASP cc_start: 0.7104 (t0) cc_final: 0.6836 (t0) REVERT: D 77 PHE cc_start: 0.7378 (t80) cc_final: 0.7085 (t80) REVERT: D 83 MET cc_start: 0.8040 (mtt) cc_final: 0.7532 (mtt) REVERT: D 110 MET cc_start: 0.6830 (mmt) cc_final: 0.6479 (mmt) REVERT: D 116 ILE cc_start: 0.8460 (mm) cc_final: 0.8139 (mm) REVERT: D 117 ARG cc_start: 0.8188 (ttm-80) cc_final: 0.7963 (mtm-85) REVERT: D 128 THR cc_start: 0.7350 (m) cc_final: 0.6922 (p) REVERT: D 132 LEU cc_start: 0.7701 (mt) cc_final: 0.7343 (mt) REVERT: D 149 ASN cc_start: 0.8321 (m-40) cc_final: 0.7835 (m-40) REVERT: D 154 LEU cc_start: 0.8149 (mt) cc_final: 0.7856 (mp) REVERT: D 155 MET cc_start: 0.7934 (mtm) cc_final: 0.7556 (mtm) REVERT: D 157 HIS cc_start: 0.8355 (t-90) cc_final: 0.8130 (t70) REVERT: D 169 ILE cc_start: 0.7346 (tt) cc_final: 0.6714 (pt) REVERT: D 176 LYS cc_start: 0.8284 (mmpt) cc_final: 0.7157 (tppt) REVERT: D 179 GLU cc_start: 0.8092 (mp0) cc_final: 0.6495 (mp0) REVERT: D 189 LYS cc_start: 0.8067 (mtmt) cc_final: 0.7752 (mtmt) REVERT: D 200 GLN cc_start: 0.7099 (mm110) cc_final: 0.6802 (mm-40) REVERT: D 221 LEU cc_start: 0.7839 (mp) cc_final: 0.7060 (mp) REVERT: D 236 TRP cc_start: 0.7607 (t-100) cc_final: 0.7319 (t-100) REVERT: D 240 LYS cc_start: 0.8108 (mtpp) cc_final: 0.7591 (mttt) REVERT: D 242 ILE cc_start: 0.7728 (mt) cc_final: 0.7410 (tt) REVERT: D 257 LYS cc_start: 0.8137 (tttt) cc_final: 0.7594 (tttm) REVERT: D 302 GLN cc_start: 0.8669 (pt0) cc_final: 0.8143 (pp30) REVERT: D 307 LYS cc_start: 0.8200 (mmtt) cc_final: 0.7829 (mmtt) REVERT: D 320 LYS cc_start: 0.7997 (mtpt) cc_final: 0.7311 (mtmm) REVERT: D 324 LEU cc_start: 0.8631 (mt) cc_final: 0.8309 (mt) REVERT: D 327 MET cc_start: 0.7198 (tpp) cc_final: 0.6643 (tpp) REVERT: D 329 LYS cc_start: 0.8943 (mttt) cc_final: 0.8733 (mttt) REVERT: D 336 LYS cc_start: 0.7971 (ptpp) cc_final: 0.7578 (ptpp) REVERT: D 362 ASP cc_start: 0.8582 (m-30) cc_final: 0.8358 (m-30) REVERT: D 367 MET cc_start: 0.7179 (mtm) cc_final: 0.6730 (mtm) REVERT: D 374 MET cc_start: 0.7403 (mtt) cc_final: 0.6094 (mtt) REVERT: D 377 VAL cc_start: 0.8858 (t) cc_final: 0.8486 (p) REVERT: D 378 LYS cc_start: 0.8887 (mttt) cc_final: 0.8342 (mttt) REVERT: D 383 HIS cc_start: 0.7615 (t70) cc_final: 0.7238 (t70) REVERT: D 393 ARG cc_start: 0.7831 (mtt180) cc_final: 0.7503 (ttm-80) REVERT: D 394 ASP cc_start: 0.8097 (m-30) cc_final: 0.7873 (m-30) REVERT: D 396 LEU cc_start: 0.8774 (pp) cc_final: 0.8536 (pp) REVERT: D 399 LYS cc_start: 0.7992 (mmmt) cc_final: 0.7548 (mmmt) REVERT: D 403 ILE cc_start: 0.8492 (pt) cc_final: 0.8040 (pt) REVERT: D 406 GLN cc_start: 0.7567 (mt0) cc_final: 0.7300 (mt0) REVERT: D 413 THR cc_start: 0.7544 (p) cc_final: 0.7324 (p) REVERT: D 422 LEU cc_start: 0.9044 (tp) cc_final: 0.8841 (tp) REVERT: D 530 TYR cc_start: 0.7599 (m-80) cc_final: 0.7255 (m-80) REVERT: D 532 SER cc_start: 0.7732 (m) cc_final: 0.7364 (p) REVERT: D 534 LEU cc_start: 0.8131 (mt) cc_final: 0.7619 (tt) REVERT: D 547 GLN cc_start: 0.7637 (mm110) cc_final: 0.7091 (tp40) REVERT: D 553 MET cc_start: 0.7532 (mtm) cc_final: 0.6895 (mtm) REVERT: D 571 ARG cc_start: 0.8474 (mtt-85) cc_final: 0.8247 (mtt-85) REVERT: M 44 ASN cc_start: 0.8150 (t0) cc_final: 0.7760 (t0) REVERT: M 67 VAL cc_start: 0.7934 (t) cc_final: 0.7561 (m) REVERT: M 111 GLU cc_start: 0.8009 (tp30) cc_final: 0.7681 (tp30) REVERT: M 114 GLU cc_start: 0.7569 (tp30) cc_final: 0.7316 (tp30) REVERT: M 176 ASN cc_start: 0.6476 (m-40) cc_final: 0.5661 (m-40) REVERT: M 196 SER cc_start: 0.6543 (m) cc_final: 0.6165 (p) REVERT: M 212 LEU cc_start: 0.7502 (mt) cc_final: 0.7249 (mm) REVERT: M 228 LEU cc_start: 0.8575 (mt) cc_final: 0.8371 (mt) REVERT: M 230 ASP cc_start: 0.7541 (t0) cc_final: 0.7058 (t0) REVERT: M 233 PHE cc_start: 0.7842 (m-80) cc_final: 0.7548 (m-80) REVERT: M 239 PHE cc_start: 0.7939 (t80) cc_final: 0.7667 (t80) REVERT: M 250 PHE cc_start: 0.7742 (p90) cc_final: 0.7529 (p90) REVERT: M 256 ASN cc_start: 0.7624 (t0) cc_final: 0.7420 (t0) REVERT: M 333 ASP cc_start: 0.8084 (t0) cc_final: 0.7624 (t0) REVERT: M 380 GLN cc_start: 0.7672 (mt0) cc_final: 0.7171 (mt0) REVERT: M 381 GLN cc_start: 0.7952 (tm-30) cc_final: 0.7399 (tm-30) REVERT: M 394 MET cc_start: 0.6874 (tmm) cc_final: 0.6551 (tmm) REVERT: M 406 LYS cc_start: 0.8018 (mtpt) cc_final: 0.7648 (ttmt) REVERT: M 409 THR cc_start: 0.7914 (m) cc_final: 0.7405 (p) REVERT: M 410 LYS cc_start: 0.8111 (mttt) cc_final: 0.7869 (mttt) REVERT: S 17 SER cc_start: 0.8024 (t) cc_final: 0.7742 (p) REVERT: S 18 LYS cc_start: 0.8037 (tttp) cc_final: 0.7233 (tttp) REVERT: S 29 GLN cc_start: 0.8607 (mt0) cc_final: 0.8349 (mt0) REVERT: S 77 VAL cc_start: 0.7264 (m) cc_final: 0.6916 (p) REVERT: S 82 SER cc_start: 0.7459 (t) cc_final: 0.6855 (t) REVERT: S 89 LEU cc_start: 0.7867 (mt) cc_final: 0.6925 (mt) REVERT: S 97 LEU cc_start: 0.7924 (mt) cc_final: 0.7384 (mt) REVERT: S 123 MET cc_start: 0.7509 (tpt) cc_final: 0.6822 (tpt) REVERT: S 125 MET cc_start: 0.7851 (ttm) cc_final: 0.7417 (ttm) REVERT: S 128 MET cc_start: 0.7632 (mtp) cc_final: 0.6634 (mtp) REVERT: B 75 ASN cc_start: 0.7996 (m110) cc_final: 0.7645 (m110) REVERT: B 78 GLU cc_start: 0.8233 (pm20) cc_final: 0.7960 (pm20) REVERT: B 129 GLN cc_start: 0.8490 (pm20) cc_final: 0.8027 (mt0) REVERT: B 151 MET cc_start: 0.7927 (mtm) cc_final: 0.7702 (mtt) REVERT: B 152 MET cc_start: 0.6976 (tmm) cc_final: 0.6730 (tmm) REVERT: B 153 LEU cc_start: 0.7995 (mt) cc_final: 0.7156 (mp) REVERT: B 156 LYS cc_start: 0.8044 (mtpt) cc_final: 0.7676 (mtpp) REVERT: B 185 LYS cc_start: 0.7793 (mtpt) cc_final: 0.7461 (mmmt) REVERT: B 187 MET cc_start: 0.7847 (mtp) cc_final: 0.7409 (mtp) REVERT: B 197 LYS cc_start: 0.8693 (mttp) cc_final: 0.8256 (mtmm) REVERT: B 199 LYS cc_start: 0.8646 (pptt) cc_final: 0.8257 (pptt) REVERT: B 202 LEU cc_start: 0.8199 (mt) cc_final: 0.7975 (mm) REVERT: B 213 GLU cc_start: 0.7509 (tp30) cc_final: 0.7207 (tp30) REVERT: B 239 TRP cc_start: 0.7585 (m100) cc_final: 0.7261 (m100) REVERT: B 297 HIS cc_start: 0.7891 (t-90) cc_final: 0.7649 (t-90) REVERT: B 307 LEU cc_start: 0.8514 (mt) cc_final: 0.8163 (tp) REVERT: B 322 LEU cc_start: 0.8023 (tp) cc_final: 0.7807 (tp) REVERT: B 330 SER cc_start: 0.7786 (t) cc_final: 0.7330 (t) REVERT: B 331 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7078 (mm-30) REVERT: B 345 SER cc_start: 0.8348 (t) cc_final: 0.8113 (t) REVERT: B 348 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7378 (mm-30) REVERT: B 360 MET cc_start: 0.7637 (mtp) cc_final: 0.7259 (mtp) REVERT: B 365 LYS cc_start: 0.8450 (mttt) cc_final: 0.7752 (mtpp) REVERT: B 371 TYR cc_start: 0.7734 (m-80) cc_final: 0.7417 (m-80) REVERT: B 389 LYS cc_start: 0.8543 (mttt) cc_final: 0.8153 (mttp) REVERT: B 390 LEU cc_start: 0.8111 (tp) cc_final: 0.7738 (tt) REVERT: B 391 GLU cc_start: 0.7349 (tp30) cc_final: 0.6935 (tp30) REVERT: B 399 GLU cc_start: 0.7974 (pm20) cc_final: 0.7636 (pp20) REVERT: B 408 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7322 (tp30) REVERT: B 426 GLN cc_start: 0.8576 (mt0) cc_final: 0.8061 (mm-40) REVERT: B 428 ILE cc_start: 0.7394 (mt) cc_final: 0.7059 (pt) REVERT: B 433 THR cc_start: 0.7910 (t) cc_final: 0.7697 (t) REVERT: B 465 ILE cc_start: 0.8656 (mt) cc_final: 0.8426 (mm) REVERT: B 481 LYS cc_start: 0.8875 (mttt) cc_final: 0.8294 (mttt) REVERT: B 483 MET cc_start: 0.8434 (mmm) cc_final: 0.7492 (mmm) REVERT: B 498 SER cc_start: 0.8520 (m) cc_final: 0.8235 (p) REVERT: B 499 ILE cc_start: 0.8392 (mm) cc_final: 0.7748 (tp) REVERT: B 521 MET cc_start: 0.6854 (mmp) cc_final: 0.6422 (mmm) REVERT: B 556 GLN cc_start: 0.7982 (mt0) cc_final: 0.7680 (mt0) REVERT: B 577 ILE cc_start: 0.8891 (mt) cc_final: 0.8275 (tp) REVERT: B 649 ARG cc_start: 0.6077 (mmp80) cc_final: 0.5207 (mmt90) outliers start: 0 outliers final: 0 residues processed: 543 average time/residue: 0.1582 time to fit residues: 124.3516 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 : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 75 optimal weight: 0.3980 chunk 0 optimal weight: 6.9990 chunk 177 optimal weight: 0.2980 chunk 199 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 562 GLN ** M 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.147183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.125358 restraints weight = 35778.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.129553 restraints weight = 21509.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.132505 restraints weight = 14118.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.134508 restraints weight = 9867.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.136039 restraints weight = 7299.798| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17177 Z= 0.169 Angle : 0.602 10.699 23253 Z= 0.318 Chirality : 0.044 0.161 2705 Planarity : 0.004 0.050 2931 Dihedral : 8.651 174.376 2299 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.19), residues: 2098 helix: 1.39 (0.15), residues: 1148 sheet: 0.19 (0.34), residues: 238 loop : 0.49 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 212 TYR 0.022 0.002 TYR M 174 PHE 0.018 0.002 PHE M 78 TRP 0.020 0.002 TRP D 236 HIS 0.011 0.001 HIS D 268 Details of bonding type rmsd covalent geometry : bond 0.00340 (17177) covalent geometry : angle 0.60193 (23253) hydrogen bonds : bond 0.04709 ( 996) hydrogen bonds : angle 4.83846 ( 2835) *********************** 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 559 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 559 time to evaluate : 0.663 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: 0.8386 (tttt) cc_final: 0.7930 (tttt) REVERT: A 41 GLU cc_start: 0.5650 (mm-30) cc_final: 0.5317 (mm-30) REVERT: A 61 ILE cc_start: 0.8635 (mm) cc_final: 0.8400 (mm) REVERT: A 84 ASN cc_start: 0.6998 (m-40) cc_final: 0.6393 (m-40) REVERT: A 102 GLU cc_start: 0.8468 (tt0) cc_final: 0.7709 (tm-30) REVERT: C 38 LYS cc_start: 0.8433 (tmtt) cc_final: 0.8170 (tmtt) REVERT: C 39 LEU cc_start: 0.8575 (mp) cc_final: 0.7630 (mp) REVERT: C 86 GLN cc_start: 0.7117 (mt0) cc_final: 0.6374 (mt0) REVERT: C 106 GLU cc_start: 0.7296 (tp30) cc_final: 0.6925 (tp30) REVERT: C 110 MET cc_start: 0.8373 (ttp) cc_final: 0.8025 (ttp) REVERT: C 149 ARG cc_start: 0.7083 (ttm-80) cc_final: 0.6679 (mmm160) REVERT: C 173 LEU cc_start: 0.8439 (mt) cc_final: 0.8155 (mt) REVERT: C 175 ASN cc_start: 0.7987 (m-40) cc_final: 0.7596 (t0) REVERT: C 176 GLN cc_start: 0.7008 (mm-40) cc_final: 0.6563 (mm-40) REVERT: D 1 MET cc_start: 0.4001 (ttp) cc_final: 0.3623 (ttp) REVERT: D 63 THR cc_start: 0.7564 (m) cc_final: 0.7300 (p) REVERT: D 74 TRP cc_start: 0.8418 (p-90) cc_final: 0.8055 (p-90) REVERT: D 83 MET cc_start: 0.8039 (mtt) cc_final: 0.7505 (mtt) REVERT: D 110 MET cc_start: 0.6927 (mmt) cc_final: 0.6556 (mmt) REVERT: D 112 THR cc_start: 0.7480 (p) cc_final: 0.6807 (m) REVERT: D 116 ILE cc_start: 0.8461 (mm) cc_final: 0.8089 (mm) REVERT: D 117 ARG cc_start: 0.8197 (ttm-80) cc_final: 0.7912 (mtm-85) REVERT: D 118 LYS cc_start: 0.8469 (ttmt) cc_final: 0.8174 (mtpt) REVERT: D 126 TYR cc_start: 0.7941 (m-80) cc_final: 0.7608 (m-80) REVERT: D 132 LEU cc_start: 0.7727 (mt) cc_final: 0.7405 (mt) REVERT: D 149 ASN cc_start: 0.8315 (m-40) cc_final: 0.7849 (m-40) REVERT: D 155 MET cc_start: 0.7964 (mtm) cc_final: 0.7571 (mtm) REVERT: D 157 HIS cc_start: 0.8363 (t-90) cc_final: 0.8143 (t70) REVERT: D 165 LYS cc_start: 0.7547 (mmtt) cc_final: 0.7318 (mmtt) REVERT: D 169 ILE cc_start: 0.7419 (tt) cc_final: 0.6759 (pt) REVERT: D 176 LYS cc_start: 0.8362 (mmpt) cc_final: 0.7176 (tppt) REVERT: D 179 GLU cc_start: 0.8148 (mp0) cc_final: 0.6719 (mp0) REVERT: D 189 LYS cc_start: 0.8073 (mtmt) cc_final: 0.7794 (mtmt) REVERT: D 221 LEU cc_start: 0.7601 (mp) cc_final: 0.7106 (mp) REVERT: D 236 TRP cc_start: 0.7549 (t-100) cc_final: 0.7286 (t-100) REVERT: D 242 ILE cc_start: 0.7778 (mt) cc_final: 0.7496 (tt) REVERT: D 257 LYS cc_start: 0.8137 (tttt) cc_final: 0.7622 (tttm) REVERT: D 275 LEU cc_start: 0.7997 (tp) cc_final: 0.7632 (tp) REVERT: D 302 GLN cc_start: 0.8666 (pt0) cc_final: 0.8148 (pp30) REVERT: D 307 LYS cc_start: 0.8215 (mmtt) cc_final: 0.7874 (mmtt) REVERT: D 320 LYS cc_start: 0.8009 (mtpt) cc_final: 0.7338 (mtmm) REVERT: D 324 LEU cc_start: 0.8629 (mt) cc_final: 0.8326 (mt) REVERT: D 327 MET cc_start: 0.7205 (tpp) cc_final: 0.6752 (tpp) REVERT: D 329 LYS cc_start: 0.8942 (mttt) cc_final: 0.8658 (mttt) REVERT: D 339 GLN cc_start: 0.8384 (pt0) cc_final: 0.7966 (pp30) REVERT: D 367 MET cc_start: 0.7132 (mtm) cc_final: 0.6761 (mtm) REVERT: D 373 LEU cc_start: 0.8572 (tp) cc_final: 0.8181 (pp) REVERT: D 374 MET cc_start: 0.7154 (mtt) cc_final: 0.5863 (mtt) REVERT: D 377 VAL cc_start: 0.8864 (t) cc_final: 0.8481 (p) REVERT: D 378 LYS cc_start: 0.8864 (mttt) cc_final: 0.8328 (mttt) REVERT: D 383 HIS cc_start: 0.7643 (t70) cc_final: 0.7272 (t70) REVERT: D 393 ARG cc_start: 0.7852 (mtt180) cc_final: 0.7494 (ttm-80) REVERT: D 399 LYS cc_start: 0.8011 (mmmt) cc_final: 0.7622 (mmmt) REVERT: D 403 ILE cc_start: 0.8436 (pt) cc_final: 0.7961 (pt) REVERT: D 413 THR cc_start: 0.7497 (p) cc_final: 0.7281 (p) REVERT: D 429 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7184 (tm-30) REVERT: D 440 GLN cc_start: 0.7594 (mm-40) cc_final: 0.6787 (mm-40) REVERT: D 530 TYR cc_start: 0.7473 (m-80) cc_final: 0.7036 (m-80) REVERT: D 532 SER cc_start: 0.7745 (m) cc_final: 0.7362 (p) REVERT: D 534 LEU cc_start: 0.8144 (mt) cc_final: 0.7669 (tt) REVERT: D 547 GLN cc_start: 0.7592 (mm110) cc_final: 0.7304 (tp40) REVERT: D 553 MET cc_start: 0.7498 (mtm) cc_final: 0.6915 (mtm) REVERT: D 571 ARG cc_start: 0.8488 (mtt-85) cc_final: 0.8243 (mtt-85) REVERT: M 6 PHE cc_start: 0.7863 (m-80) cc_final: 0.7388 (m-80) REVERT: M 43 GLU cc_start: 0.8512 (mm-30) cc_final: 0.7984 (mm-30) REVERT: M 67 VAL cc_start: 0.7991 (t) cc_final: 0.7614 (m) REVERT: M 111 GLU cc_start: 0.8022 (tp30) cc_final: 0.7664 (tp30) REVERT: M 114 GLU cc_start: 0.7578 (tp30) cc_final: 0.7295 (tp30) REVERT: M 116 MET cc_start: 0.7042 (mmm) cc_final: 0.6829 (tpt) REVERT: M 167 TRP cc_start: 0.7945 (p90) cc_final: 0.7081 (p90) REVERT: M 176 ASN cc_start: 0.6454 (m-40) cc_final: 0.5687 (m110) REVERT: M 196 SER cc_start: 0.6609 (m) cc_final: 0.6137 (p) REVERT: M 212 LEU cc_start: 0.7561 (mt) cc_final: 0.7285 (mm) REVERT: M 230 ASP cc_start: 0.7575 (t0) cc_final: 0.7145 (t0) REVERT: M 239 PHE cc_start: 0.7905 (t80) cc_final: 0.7683 (t80) REVERT: M 250 PHE cc_start: 0.7851 (p90) cc_final: 0.6790 (p90) REVERT: M 256 ASN cc_start: 0.7681 (t0) cc_final: 0.7442 (t0) REVERT: M 333 ASP cc_start: 0.8135 (t0) cc_final: 0.7703 (t0) REVERT: M 380 GLN cc_start: 0.7706 (mt0) cc_final: 0.7178 (mt0) REVERT: M 381 GLN cc_start: 0.7912 (tm-30) cc_final: 0.7401 (tm-30) REVERT: M 406 LYS cc_start: 0.8052 (mtpt) cc_final: 0.7653 (ttmt) REVERT: M 409 THR cc_start: 0.7892 (m) cc_final: 0.7393 (p) REVERT: M 410 LYS cc_start: 0.8109 (mttt) cc_final: 0.7895 (mttt) REVERT: S 17 SER cc_start: 0.8129 (t) cc_final: 0.7904 (p) REVERT: S 18 LYS cc_start: 0.8061 (tttp) cc_final: 0.7222 (tttp) REVERT: S 29 GLN cc_start: 0.8618 (mt0) cc_final: 0.8382 (mt0) REVERT: S 89 LEU cc_start: 0.7485 (mt) cc_final: 0.6581 (mt) REVERT: S 97 LEU cc_start: 0.7981 (mt) cc_final: 0.7462 (mt) REVERT: S 123 MET cc_start: 0.7475 (tpt) cc_final: 0.6931 (tpt) REVERT: S 125 MET cc_start: 0.7876 (ttm) cc_final: 0.7359 (ttm) REVERT: S 128 MET cc_start: 0.7184 (mtp) cc_final: 0.6389 (mtp) REVERT: B 75 ASN cc_start: 0.7933 (m110) cc_final: 0.7587 (m110) REVERT: B 78 GLU cc_start: 0.8178 (pm20) cc_final: 0.7844 (pm20) REVERT: B 129 GLN cc_start: 0.8498 (pm20) cc_final: 0.8193 (mt0) REVERT: B 151 MET cc_start: 0.7954 (mtm) cc_final: 0.7667 (mtt) REVERT: B 152 MET cc_start: 0.7039 (tmm) cc_final: 0.6826 (tmm) REVERT: B 156 LYS cc_start: 0.8007 (mtpt) cc_final: 0.7797 (mttm) REVERT: B 185 LYS cc_start: 0.7790 (mtpt) cc_final: 0.7388 (mmmt) REVERT: B 187 MET cc_start: 0.7811 (mtp) cc_final: 0.7526 (mtp) REVERT: B 197 LYS cc_start: 0.8808 (mttp) cc_final: 0.8384 (mtmm) REVERT: B 199 LYS cc_start: 0.8645 (pptt) cc_final: 0.8266 (pptt) REVERT: B 239 TRP cc_start: 0.7509 (m100) cc_final: 0.7216 (m100) REVERT: B 307 LEU cc_start: 0.8677 (mt) cc_final: 0.8332 (tp) REVERT: B 330 SER cc_start: 0.7681 (t) cc_final: 0.6697 (t) REVERT: B 331 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6575 (mm-30) REVERT: B 365 LYS cc_start: 0.8469 (mttt) cc_final: 0.7787 (mtpp) REVERT: B 371 TYR cc_start: 0.7711 (m-80) cc_final: 0.7350 (m-80) REVERT: B 389 LYS cc_start: 0.8569 (mttt) cc_final: 0.8251 (mttt) REVERT: B 390 LEU cc_start: 0.8010 (tp) cc_final: 0.7717 (tt) REVERT: B 391 GLU cc_start: 0.7352 (tp30) cc_final: 0.6835 (tp30) REVERT: B 399 GLU cc_start: 0.8093 (pm20) cc_final: 0.7874 (pp20) REVERT: B 408 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7199 (tp30) REVERT: B 426 GLN cc_start: 0.8544 (mt0) cc_final: 0.8016 (mm-40) REVERT: B 431 CYS cc_start: 0.8307 (p) cc_final: 0.7942 (p) REVERT: B 433 THR cc_start: 0.7927 (t) cc_final: 0.7666 (t) REVERT: B 437 GLU cc_start: 0.7522 (tp30) cc_final: 0.7191 (tp30) REVERT: B 481 LYS cc_start: 0.8864 (mttt) cc_final: 0.8325 (mttt) REVERT: B 483 MET cc_start: 0.8454 (mmm) cc_final: 0.7769 (mmm) REVERT: B 499 ILE cc_start: 0.8391 (mm) cc_final: 0.7786 (tp) REVERT: B 521 MET cc_start: 0.6927 (mmp) cc_final: 0.6443 (mmm) REVERT: B 543 LEU cc_start: 0.7451 (pp) cc_final: 0.7194 (pp) REVERT: B 556 GLN cc_start: 0.7992 (mt0) cc_final: 0.7681 (mt0) REVERT: B 577 ILE cc_start: 0.8862 (mt) cc_final: 0.8304 (tp) REVERT: B 617 PHE cc_start: 0.5367 (m-80) cc_final: 0.5154 (m-80) REVERT: B 649 ARG cc_start: 0.6098 (mmp80) cc_final: 0.5395 (mmt90) outliers start: 0 outliers final: 0 residues processed: 559 average time/residue: 0.1363 time to fit residues: 110.2048 Evaluate side-chains 527 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 527 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 85 optimal weight: 0.0970 chunk 151 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 146 optimal weight: 0.8980 chunk 107 optimal weight: 0.0060 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 207 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.4394 ------------------------------------------------------------------------------- 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 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 303 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.148035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.126211 restraints weight = 35209.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.130405 restraints weight = 21106.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.133288 restraints weight = 13824.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.135424 restraints weight = 9711.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.136832 restraints weight = 7102.935| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.5349 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= 0.141 Angle : 0.591 9.249 23253 Z= 0.307 Chirality : 0.044 0.168 2705 Planarity : 0.004 0.050 2931 Dihedral : 8.605 175.787 2299 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.19), residues: 2098 helix: 1.38 (0.15), residues: 1150 sheet: 0.28 (0.35), residues: 234 loop : 0.50 (0.25), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 212 TYR 0.017 0.001 TYR M 93 PHE 0.015 0.002 PHE D 245 TRP 0.020 0.002 TRP D 74 HIS 0.010 0.001 HIS D 268 Details of bonding type rmsd covalent geometry : bond 0.00294 (17177) covalent geometry : angle 0.59077 (23253) hydrogen bonds : bond 0.04375 ( 996) hydrogen bonds : angle 4.75048 ( 2835) *********************** 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 553 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 553 time to evaluate : 0.559 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8400 (tttt) cc_final: 0.7926 (tttt) REVERT: A 41 GLU cc_start: 0.5566 (mm-30) cc_final: 0.5251 (mm-30) REVERT: A 61 ILE cc_start: 0.8631 (mm) cc_final: 0.8367 (mm) REVERT: A 84 ASN cc_start: 0.6984 (m-40) cc_final: 0.6393 (m-40) REVERT: A 102 GLU cc_start: 0.8437 (tt0) cc_final: 0.7675 (tm-30) REVERT: C 38 LYS cc_start: 0.8477 (tmtt) cc_final: 0.8167 (tmtt) REVERT: C 39 LEU cc_start: 0.8579 (mp) cc_final: 0.7648 (mp) REVERT: C 86 GLN cc_start: 0.7103 (mt0) cc_final: 0.6322 (mt0) REVERT: C 88 LEU cc_start: 0.8186 (tt) cc_final: 0.7785 (tt) REVERT: C 97 ARG cc_start: 0.8676 (mtp85) cc_final: 0.8357 (mtp85) REVERT: C 106 GLU cc_start: 0.7299 (tp30) cc_final: 0.6980 (tp30) REVERT: C 149 ARG cc_start: 0.7140 (ttm-80) cc_final: 0.6800 (mmm160) REVERT: C 173 LEU cc_start: 0.8431 (mt) cc_final: 0.8148 (mt) REVERT: C 175 ASN cc_start: 0.7974 (m-40) cc_final: 0.7516 (t0) REVERT: C 176 GLN cc_start: 0.6938 (mm-40) cc_final: 0.6544 (mm-40) REVERT: D 1 MET cc_start: 0.4004 (ttp) cc_final: 0.3644 (ttp) REVERT: D 95 TYR cc_start: 0.7601 (m-80) cc_final: 0.7369 (m-10) REVERT: D 110 MET cc_start: 0.6874 (mmt) cc_final: 0.6451 (mmt) REVERT: D 116 ILE cc_start: 0.8518 (mm) cc_final: 0.7854 (mm) REVERT: D 117 ARG cc_start: 0.8176 (ttm-80) cc_final: 0.7856 (mtm-85) REVERT: D 118 LYS cc_start: 0.8434 (ttmt) cc_final: 0.8150 (mtpt) REVERT: D 126 TYR cc_start: 0.8038 (m-80) cc_final: 0.7790 (m-80) REVERT: D 128 THR cc_start: 0.7177 (m) cc_final: 0.6822 (p) REVERT: D 132 LEU cc_start: 0.7706 (mt) cc_final: 0.7373 (mt) REVERT: D 149 ASN cc_start: 0.8290 (m-40) cc_final: 0.7819 (m-40) REVERT: D 155 MET cc_start: 0.8006 (mtm) cc_final: 0.7629 (mtm) REVERT: D 165 LYS cc_start: 0.7438 (mmtt) cc_final: 0.7189 (mmtt) REVERT: D 169 ILE cc_start: 0.7370 (tt) cc_final: 0.6740 (pt) REVERT: D 176 LYS cc_start: 0.8395 (mmpt) cc_final: 0.7285 (tppt) REVERT: D 221 LEU cc_start: 0.7814 (mp) cc_final: 0.6983 (mp) REVERT: D 236 TRP cc_start: 0.7550 (t-100) cc_final: 0.7198 (t-100) REVERT: D 257 LYS cc_start: 0.8101 (tttt) cc_final: 0.7617 (tttm) REVERT: D 273 MET cc_start: 0.8233 (pmm) cc_final: 0.7985 (pmm) REVERT: D 275 LEU cc_start: 0.7983 (tp) cc_final: 0.7640 (tp) REVERT: D 302 GLN cc_start: 0.8623 (pt0) cc_final: 0.8182 (pp30) REVERT: D 307 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7858 (mmtt) REVERT: D 320 LYS cc_start: 0.7987 (mtpt) cc_final: 0.7303 (mtmm) REVERT: D 324 LEU cc_start: 0.8621 (mt) cc_final: 0.8328 (mt) REVERT: D 327 MET cc_start: 0.7166 (tpp) cc_final: 0.6695 (tpp) REVERT: D 329 LYS cc_start: 0.8932 (mttt) cc_final: 0.8628 (mttt) REVERT: D 339 GLN cc_start: 0.8409 (pt0) cc_final: 0.8195 (pp30) REVERT: D 367 MET cc_start: 0.7006 (mtm) cc_final: 0.6646 (mtm) REVERT: D 373 LEU cc_start: 0.8565 (tp) cc_final: 0.8224 (pp) REVERT: D 374 MET cc_start: 0.7039 (mtt) cc_final: 0.5691 (mtt) REVERT: D 377 VAL cc_start: 0.8817 (t) cc_final: 0.8476 (p) REVERT: D 378 LYS cc_start: 0.8862 (mttt) cc_final: 0.8299 (mttt) REVERT: D 383 HIS cc_start: 0.7664 (t70) cc_final: 0.7298 (t70) REVERT: D 393 ARG cc_start: 0.7813 (mtt180) cc_final: 0.7482 (ttm-80) REVERT: D 399 LYS cc_start: 0.7966 (mmmt) cc_final: 0.7625 (mmmt) REVERT: D 403 ILE cc_start: 0.8467 (pt) cc_final: 0.8067 (pt) REVERT: D 421 ILE cc_start: 0.8500 (mm) cc_final: 0.8154 (mm) REVERT: D 427 ARG cc_start: 0.8372 (mtp180) cc_final: 0.7687 (mtp180) REVERT: D 429 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7141 (tm-30) REVERT: D 440 GLN cc_start: 0.7568 (mm-40) cc_final: 0.6827 (mm-40) REVERT: D 479 CYS cc_start: 0.8678 (m) cc_final: 0.8445 (m) REVERT: D 524 GLN cc_start: 0.8158 (tm-30) cc_final: 0.7933 (tm-30) REVERT: D 530 TYR cc_start: 0.7408 (m-80) cc_final: 0.7024 (m-80) REVERT: D 532 SER cc_start: 0.7773 (m) cc_final: 0.7378 (p) REVERT: D 534 LEU cc_start: 0.8122 (mt) cc_final: 0.7643 (tt) REVERT: D 553 MET cc_start: 0.7406 (mtm) cc_final: 0.6810 (mtm) REVERT: D 594 GLU cc_start: 0.7126 (pm20) cc_final: 0.6806 (pm20) REVERT: M 6 PHE cc_start: 0.7784 (m-80) cc_final: 0.7314 (m-80) REVERT: M 43 GLU cc_start: 0.8523 (mm-30) cc_final: 0.7859 (mm-30) REVERT: M 67 VAL cc_start: 0.7932 (t) cc_final: 0.7587 (m) REVERT: M 111 GLU cc_start: 0.8002 (tp30) cc_final: 0.7613 (tp30) REVERT: M 114 GLU cc_start: 0.7566 (tp30) cc_final: 0.7344 (tp30) REVERT: M 167 TRP cc_start: 0.7912 (p90) cc_final: 0.7024 (p90) REVERT: M 176 ASN cc_start: 0.6388 (m-40) cc_final: 0.5672 (m110) REVERT: M 178 GLU cc_start: 0.6470 (pt0) cc_final: 0.6266 (pt0) REVERT: M 196 SER cc_start: 0.6605 (m) cc_final: 0.6177 (p) REVERT: M 201 GLU cc_start: 0.8101 (pt0) cc_final: 0.7616 (pt0) REVERT: M 212 LEU cc_start: 0.7502 (mt) cc_final: 0.7149 (mm) REVERT: M 250 PHE cc_start: 0.7839 (p90) cc_final: 0.6723 (p90) REVERT: M 333 ASP cc_start: 0.8161 (t0) cc_final: 0.7768 (t0) REVERT: M 380 GLN cc_start: 0.7689 (mt0) cc_final: 0.7174 (mt0) REVERT: M 381 GLN cc_start: 0.7898 (tm-30) cc_final: 0.7358 (tm-30) REVERT: M 394 MET cc_start: 0.6808 (tmm) cc_final: 0.6489 (tmm) REVERT: M 406 LYS cc_start: 0.8060 (mtpt) cc_final: 0.7672 (ttmt) REVERT: M 409 THR cc_start: 0.7863 (m) cc_final: 0.7400 (p) REVERT: S 17 SER cc_start: 0.8100 (t) cc_final: 0.7884 (p) REVERT: S 18 LYS cc_start: 0.7994 (tttp) cc_final: 0.7178 (tttp) REVERT: S 29 GLN cc_start: 0.8574 (mt0) cc_final: 0.8354 (mt0) REVERT: S 89 LEU cc_start: 0.7693 (mt) cc_final: 0.6774 (mt) REVERT: S 97 LEU cc_start: 0.7968 (mt) cc_final: 0.7400 (mt) REVERT: S 123 MET cc_start: 0.7480 (tpt) cc_final: 0.6845 (tpt) REVERT: S 128 MET cc_start: 0.7251 (mtp) cc_final: 0.6470 (mtp) REVERT: B 75 ASN cc_start: 0.7906 (m110) cc_final: 0.7527 (m110) REVERT: B 78 GLU cc_start: 0.8071 (pm20) cc_final: 0.7776 (pm20) REVERT: B 89 SER cc_start: 0.8598 (t) cc_final: 0.8372 (t) REVERT: B 129 GLN cc_start: 0.8458 (pm20) cc_final: 0.8069 (mt0) REVERT: B 151 MET cc_start: 0.7926 (mtm) cc_final: 0.7634 (mtt) REVERT: B 152 MET cc_start: 0.7045 (tmm) cc_final: 0.6789 (tmm) REVERT: B 156 LYS cc_start: 0.7979 (mtpt) cc_final: 0.7779 (mttm) REVERT: B 185 LYS cc_start: 0.7774 (mtpt) cc_final: 0.7570 (mtpt) REVERT: B 187 MET cc_start: 0.7854 (mtp) cc_final: 0.7548 (mtp) REVERT: B 197 LYS cc_start: 0.8782 (mttp) cc_final: 0.8417 (mtmm) REVERT: B 199 LYS cc_start: 0.8622 (pptt) cc_final: 0.8271 (pptt) REVERT: B 209 MET cc_start: 0.7808 (tpp) cc_final: 0.7210 (tmm) REVERT: B 307 LEU cc_start: 0.8630 (mt) cc_final: 0.8290 (tp) REVERT: B 331 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6839 (mm-30) REVERT: B 365 LYS cc_start: 0.8409 (mttt) cc_final: 0.7660 (mtpp) REVERT: B 367 MET cc_start: 0.7716 (ttp) cc_final: 0.7462 (ttp) REVERT: B 371 TYR cc_start: 0.7635 (m-80) cc_final: 0.7269 (m-80) REVERT: B 375 PHE cc_start: 0.7823 (m-80) cc_final: 0.7593 (m-80) REVERT: B 389 LYS cc_start: 0.8582 (mttt) cc_final: 0.8147 (mtpp) REVERT: B 390 LEU cc_start: 0.8062 (tp) cc_final: 0.7710 (tt) REVERT: B 391 GLU cc_start: 0.7374 (tp30) cc_final: 0.6812 (tp30) REVERT: B 408 GLU cc_start: 0.7554 (mm-30) cc_final: 0.6920 (tp30) REVERT: B 426 GLN cc_start: 0.8605 (mt0) cc_final: 0.8022 (mm-40) REVERT: B 431 CYS cc_start: 0.8257 (p) cc_final: 0.8009 (p) REVERT: B 437 GLU cc_start: 0.7526 (tp30) cc_final: 0.7197 (tp30) REVERT: B 456 ILE cc_start: 0.8280 (mt) cc_final: 0.7485 (mm) REVERT: B 466 LYS cc_start: 0.8126 (ttpp) cc_final: 0.7790 (ttpp) REVERT: B 481 LYS cc_start: 0.8846 (mttt) cc_final: 0.8277 (mttt) REVERT: B 483 MET cc_start: 0.8380 (mmm) cc_final: 0.7735 (mmm) REVERT: B 498 SER cc_start: 0.8498 (m) cc_final: 0.8267 (p) REVERT: B 499 ILE cc_start: 0.8472 (mm) cc_final: 0.7770 (tp) REVERT: B 521 MET cc_start: 0.6840 (mmp) cc_final: 0.6383 (mmm) REVERT: B 556 GLN cc_start: 0.7967 (mt0) cc_final: 0.7635 (mt0) REVERT: B 577 ILE cc_start: 0.8829 (mt) cc_final: 0.8292 (tp) outliers start: 0 outliers final: 0 residues processed: 553 average time/residue: 0.1396 time to fit residues: 112.7271 Evaluate side-chains 520 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 520 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 61 optimal weight: 0.0060 chunk 193 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 chunk 46 optimal weight: 0.1980 chunk 141 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 132 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 157 HIS D 214 ASN M 3 HIS ** M 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 303 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.148816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.126990 restraints weight = 35292.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.131118 restraints weight = 21178.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.134045 restraints weight = 13920.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.136125 restraints weight = 9775.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.137647 restraints weight = 7182.927| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.5491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17177 Z= 0.138 Angle : 0.592 8.179 23253 Z= 0.308 Chirality : 0.044 0.299 2705 Planarity : 0.004 0.052 2931 Dihedral : 8.542 176.813 2299 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.19), residues: 2098 helix: 1.36 (0.15), residues: 1151 sheet: 0.28 (0.35), residues: 235 loop : 0.53 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 571 TYR 0.019 0.002 TYR A 154 PHE 0.017 0.002 PHE S 73 TRP 0.060 0.002 TRP B 239 HIS 0.009 0.001 HIS D 268 Details of bonding type rmsd covalent geometry : bond 0.00294 (17177) covalent geometry : angle 0.59169 (23253) hydrogen bonds : bond 0.04349 ( 996) hydrogen bonds : angle 4.75401 ( 2835) ********************** 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 537 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 537 time to evaluate : 0.606 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: 0.8367 (tttt) cc_final: 0.7885 (tttt) REVERT: A 41 GLU cc_start: 0.5519 (mm-30) cc_final: 0.5227 (mm-30) REVERT: A 61 ILE cc_start: 0.8630 (mm) cc_final: 0.8375 (mm) REVERT: A 84 ASN cc_start: 0.6936 (m-40) cc_final: 0.6336 (m-40) REVERT: A 102 GLU cc_start: 0.8496 (tt0) cc_final: 0.7797 (tm-30) REVERT: C 38 LYS cc_start: 0.8488 (tmtt) cc_final: 0.8176 (tmtt) REVERT: C 39 LEU cc_start: 0.8595 (mp) cc_final: 0.7664 (mp) REVERT: C 86 GLN cc_start: 0.7151 (mt0) cc_final: 0.6336 (mt0) REVERT: C 88 LEU cc_start: 0.8118 (tt) cc_final: 0.7703 (tt) REVERT: C 97 ARG cc_start: 0.8735 (mtp85) cc_final: 0.8430 (mtp85) REVERT: C 106 GLU cc_start: 0.7276 (tp30) cc_final: 0.6979 (tp30) REVERT: C 149 ARG cc_start: 0.7141 (ttm-80) cc_final: 0.6865 (mmm160) REVERT: C 173 LEU cc_start: 0.8433 (mt) cc_final: 0.8144 (mt) REVERT: C 175 ASN cc_start: 0.7949 (m-40) cc_final: 0.7521 (t0) REVERT: C 176 GLN cc_start: 0.6958 (mm-40) cc_final: 0.6615 (mm-40) REVERT: D 1 MET cc_start: 0.3987 (ttp) cc_final: 0.3605 (ttp) REVERT: D 74 TRP cc_start: 0.8386 (p-90) cc_final: 0.8089 (p-90) REVERT: D 83 MET cc_start: 0.8082 (mtt) cc_final: 0.7432 (mtt) REVERT: D 95 TYR cc_start: 0.7642 (m-80) cc_final: 0.7234 (m-10) REVERT: D 110 MET cc_start: 0.6873 (mmt) cc_final: 0.6445 (mmt) REVERT: D 116 ILE cc_start: 0.8423 (mm) cc_final: 0.8082 (mm) REVERT: D 117 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7837 (mtm-85) REVERT: D 118 LYS cc_start: 0.8436 (ttmt) cc_final: 0.8150 (mtpt) REVERT: D 128 THR cc_start: 0.7184 (m) cc_final: 0.6837 (p) REVERT: D 132 LEU cc_start: 0.7714 (mt) cc_final: 0.7370 (mt) REVERT: D 149 ASN cc_start: 0.8261 (m-40) cc_final: 0.7807 (m-40) REVERT: D 155 MET cc_start: 0.7972 (mtm) cc_final: 0.7609 (mtm) REVERT: D 157 HIS cc_start: 0.8412 (t-90) cc_final: 0.8073 (t70) REVERT: D 169 ILE cc_start: 0.7348 (tt) cc_final: 0.6753 (pt) REVERT: D 176 LYS cc_start: 0.8417 (mmpt) cc_final: 0.7324 (tppt) REVERT: D 179 GLU cc_start: 0.8074 (mp0) cc_final: 0.6321 (mp0) REVERT: D 221 LEU cc_start: 0.7738 (mp) cc_final: 0.7009 (mp) REVERT: D 236 TRP cc_start: 0.7554 (t-100) cc_final: 0.7221 (t-100) REVERT: D 240 LYS cc_start: 0.7962 (mtpp) cc_final: 0.7551 (mmmm) REVERT: D 273 MET cc_start: 0.8240 (pmm) cc_final: 0.8011 (pmm) REVERT: D 275 LEU cc_start: 0.7944 (tp) cc_final: 0.7624 (tp) REVERT: D 302 GLN cc_start: 0.8571 (pt0) cc_final: 0.8148 (pp30) REVERT: D 307 LYS cc_start: 0.8225 (mmtt) cc_final: 0.7879 (mmtt) REVERT: D 320 LYS cc_start: 0.8008 (mtpt) cc_final: 0.7326 (mtmm) REVERT: D 324 LEU cc_start: 0.8610 (mt) cc_final: 0.8304 (mt) REVERT: D 327 MET cc_start: 0.7157 (tpp) cc_final: 0.6660 (tpp) REVERT: D 329 LYS cc_start: 0.8901 (mttt) cc_final: 0.8600 (mttt) REVERT: D 367 MET cc_start: 0.7005 (mtm) cc_final: 0.6657 (mtm) REVERT: D 373 LEU cc_start: 0.8557 (tp) cc_final: 0.8240 (pp) REVERT: D 374 MET cc_start: 0.7031 (mtt) cc_final: 0.5841 (mtt) REVERT: D 377 VAL cc_start: 0.8803 (t) cc_final: 0.8398 (p) REVERT: D 378 LYS cc_start: 0.8863 (mttt) cc_final: 0.8289 (mttt) REVERT: D 381 MET cc_start: 0.7936 (mtp) cc_final: 0.7649 (mtp) REVERT: D 383 HIS cc_start: 0.7689 (t70) cc_final: 0.7272 (t70) REVERT: D 393 ARG cc_start: 0.7797 (mtt180) cc_final: 0.7483 (ttm-80) REVERT: D 403 ILE cc_start: 0.8409 (pt) cc_final: 0.7918 (pt) REVERT: D 406 GLN cc_start: 0.7536 (mt0) cc_final: 0.7323 (mt0) REVERT: D 429 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7130 (tm-30) REVERT: D 530 TYR cc_start: 0.7455 (m-80) cc_final: 0.7053 (m-80) REVERT: D 532 SER cc_start: 0.7687 (m) cc_final: 0.7297 (p) REVERT: D 534 LEU cc_start: 0.8101 (mt) cc_final: 0.7623 (tt) REVERT: D 553 MET cc_start: 0.7516 (mtm) cc_final: 0.6925 (mtm) REVERT: D 567 GLU cc_start: 0.7891 (tp30) cc_final: 0.7589 (tp30) REVERT: D 571 ARG cc_start: 0.8650 (mtt-85) cc_final: 0.8427 (mtt-85) REVERT: M 6 PHE cc_start: 0.7829 (m-80) cc_final: 0.7481 (m-10) REVERT: M 43 GLU cc_start: 0.8478 (mm-30) cc_final: 0.7884 (mm-30) REVERT: M 59 ILE cc_start: 0.8234 (mp) cc_final: 0.7780 (mm) REVERT: M 67 VAL cc_start: 0.7952 (t) cc_final: 0.7542 (m) REVERT: M 85 ARG cc_start: 0.8324 (tpp80) cc_final: 0.8084 (tpp80) REVERT: M 111 GLU cc_start: 0.7976 (tp30) cc_final: 0.7611 (tp30) REVERT: M 114 GLU cc_start: 0.7568 (tp30) cc_final: 0.7294 (tp30) REVERT: M 167 TRP cc_start: 0.7834 (p90) cc_final: 0.7094 (p90) REVERT: M 176 ASN cc_start: 0.6360 (m-40) cc_final: 0.5633 (m110) REVERT: M 212 LEU cc_start: 0.7406 (mt) cc_final: 0.7150 (mm) REVERT: M 380 GLN cc_start: 0.7568 (mt0) cc_final: 0.6978 (mt0) REVERT: M 381 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7336 (tm-30) REVERT: M 394 MET cc_start: 0.6827 (tmm) cc_final: 0.6540 (tmm) REVERT: M 406 LYS cc_start: 0.8037 (mtpt) cc_final: 0.7672 (ttmt) REVERT: S 17 SER cc_start: 0.8100 (t) cc_final: 0.7847 (p) REVERT: S 18 LYS cc_start: 0.7992 (tttp) cc_final: 0.7141 (tttp) REVERT: S 29 GLN cc_start: 0.8557 (mt0) cc_final: 0.8338 (mt0) REVERT: S 89 LEU cc_start: 0.7699 (mt) cc_final: 0.6793 (mt) REVERT: S 97 LEU cc_start: 0.7970 (mt) cc_final: 0.7396 (mt) REVERT: S 123 MET cc_start: 0.7438 (tpt) cc_final: 0.6784 (tpt) REVERT: S 128 MET cc_start: 0.7275 (mtp) cc_final: 0.6403 (mtp) REVERT: B 50 MET cc_start: 0.7533 (ptp) cc_final: 0.7327 (ptp) REVERT: B 75 ASN cc_start: 0.7965 (m110) cc_final: 0.7615 (m110) REVERT: B 78 GLU cc_start: 0.8025 (pm20) cc_final: 0.7773 (pm20) REVERT: B 129 GLN cc_start: 0.8493 (pm20) cc_final: 0.8143 (mt0) REVERT: B 142 ILE cc_start: 0.7959 (tp) cc_final: 0.7561 (mm) REVERT: B 151 MET cc_start: 0.7911 (mtm) cc_final: 0.7660 (mtt) REVERT: B 152 MET cc_start: 0.7060 (tmm) cc_final: 0.6787 (tmm) REVERT: B 156 LYS cc_start: 0.7978 (mtpt) cc_final: 0.7770 (mttm) REVERT: B 185 LYS cc_start: 0.7776 (mtpt) cc_final: 0.7574 (mtpt) REVERT: B 187 MET cc_start: 0.7852 (mtp) cc_final: 0.7538 (mtp) REVERT: B 197 LYS cc_start: 0.8793 (mttp) cc_final: 0.8400 (mtmm) REVERT: B 199 LYS cc_start: 0.8622 (pptt) cc_final: 0.8271 (pptt) REVERT: B 209 MET cc_start: 0.7833 (tpp) cc_final: 0.7199 (tmm) REVERT: B 297 HIS cc_start: 0.7654 (t70) cc_final: 0.7315 (t-90) REVERT: B 307 LEU cc_start: 0.8670 (mt) cc_final: 0.8317 (tp) REVERT: B 331 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6687 (mm-30) REVERT: B 345 SER cc_start: 0.8308 (t) cc_final: 0.8100 (t) REVERT: B 365 LYS cc_start: 0.8341 (mttt) cc_final: 0.7588 (mtpp) REVERT: B 367 MET cc_start: 0.7662 (ttp) cc_final: 0.7439 (ttp) REVERT: B 371 TYR cc_start: 0.7619 (m-80) cc_final: 0.7282 (m-80) REVERT: B 389 LYS cc_start: 0.8559 (mttt) cc_final: 0.8133 (mtpp) REVERT: B 390 LEU cc_start: 0.8044 (tp) cc_final: 0.7735 (tt) REVERT: B 391 GLU cc_start: 0.7377 (tp30) cc_final: 0.6888 (tp30) REVERT: B 408 GLU cc_start: 0.7571 (mm-30) cc_final: 0.6833 (tp30) REVERT: B 426 GLN cc_start: 0.8551 (mt0) cc_final: 0.8018 (mm-40) REVERT: B 437 GLU cc_start: 0.7556 (tp30) cc_final: 0.7257 (tp30) REVERT: B 456 ILE cc_start: 0.8299 (mt) cc_final: 0.7564 (mm) REVERT: B 466 LYS cc_start: 0.8131 (ttpp) cc_final: 0.7759 (ttpp) REVERT: B 481 LYS cc_start: 0.8832 (mttt) cc_final: 0.8396 (tmtt) REVERT: B 483 MET cc_start: 0.8397 (mmm) cc_final: 0.8082 (mmm) REVERT: B 498 SER cc_start: 0.8507 (m) cc_final: 0.8201 (p) REVERT: B 499 ILE cc_start: 0.8429 (mm) cc_final: 0.7772 (tp) REVERT: B 521 MET cc_start: 0.6900 (mmp) cc_final: 0.6440 (mmm) REVERT: B 556 GLN cc_start: 0.7949 (mt0) cc_final: 0.7640 (mt0) REVERT: B 577 ILE cc_start: 0.8860 (mt) cc_final: 0.8344 (tp) outliers start: 0 outliers final: 0 residues processed: 537 average time/residue: 0.1369 time to fit residues: 107.4836 Evaluate side-chains 505 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 505 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 62 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 143 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 103 optimal weight: 0.0870 chunk 124 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 ** M 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 140 GLN ** B 86 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** B 297 HIS B 303 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.148302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.126493 restraints weight = 35337.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.130605 restraints weight = 21270.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.133490 restraints weight = 13999.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.135559 restraints weight = 9825.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.136975 restraints weight = 7229.586| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.5674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17177 Z= 0.149 Angle : 0.590 8.622 23253 Z= 0.310 Chirality : 0.044 0.250 2705 Planarity : 0.004 0.051 2931 Dihedral : 8.496 179.843 2299 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.19), residues: 2098 helix: 1.33 (0.15), residues: 1149 sheet: 0.28 (0.34), residues: 237 loop : 0.42 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 79 TYR 0.016 0.002 TYR B 226 PHE 0.015 0.002 PHE M 78 TRP 0.048 0.002 TRP B 239 HIS 0.006 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00309 (17177) covalent geometry : angle 0.59008 (23253) hydrogen bonds : bond 0.04464 ( 996) hydrogen bonds : angle 4.78772 ( 2835) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3291.93 seconds wall clock time: 57 minutes 43.72 seconds (3463.72 seconds total)