Starting phenix.real_space_refine on Tue Nov 18 19:16:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6d83_7453/11_2025/6d83_7453.cif Found real_map, /net/cci-nas-00/data/ceres_data/6d83_7453/11_2025/6d83_7453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6d83_7453/11_2025/6d83_7453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6d83_7453/11_2025/6d83_7453.map" model { file = "/net/cci-nas-00/data/ceres_data/6d83_7453/11_2025/6d83_7453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6d83_7453/11_2025/6d83_7453.cif" } resolution = 4.27 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= 0.000 sd= 0.003 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 99 5.16 5 C 10538 2.51 5 N 2821 2.21 5 O 3122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16588 Number of models: 1 Model: "" Number of chains: 10 Chain: "T" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 1, 'TRANS': 11} Chain: "L" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 70 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "B" Number of atoms: 4513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4513 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 25, 'TRANS': 544} Chain: "C" 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: "G" Number of atoms: 4633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4633 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 13, 'TRANS': 571} Chain: "H" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 3, 'TRANS': 159} Chain: "M" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3362 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 20, 'TRANS': 394} Chain breaks: 1 Chain: "S" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1197 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 1, 'TRANS': 140} 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} Chain: "H" 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: 3.99, per 1000 atoms: 0.24 Number of scatterers: 16588 At special positions: 0 Unit cell: (164.318, 133.375, 126.973, 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 99 16.00 P 6 15.00 Mg 2 11.99 O 3122 8.00 N 2821 7.00 C 10538 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: 1.35 Conformation dependent library (CDL) restraints added in 694.3 milliseconds 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3954 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 13 sheets defined 55.7% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'B' and resid 15 through 23 Processing helix chain 'B' and resid 26 through 44 removed outlier: 4.224A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 55 removed outlier: 3.673A pdb=" N VAL B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 59 removed outlier: 4.216A pdb=" N GLN B 59 " --> pdb=" O ASN B 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 59' Processing helix chain 'B' and resid 65 through 76 Processing helix chain 'B' and resid 83 through 86 removed outlier: 3.768A pdb=" N MET B 86 " --> pdb=" O MET B 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 83 through 86' Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 99 through 113 removed outlier: 3.927A pdb=" N ARG B 103 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N CYS B 112 " --> pdb=" O ARG B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 131 removed outlier: 3.762A pdb=" N LEU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 152 removed outlier: 3.775A pdb=" N ARG B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 159 removed outlier: 3.769A pdb=" N VAL B 156 " --> pdb=" O ASN B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 168 removed outlier: 3.984A pdb=" N THR B 164 " --> pdb=" O GLY B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 191 removed outlier: 4.259A pdb=" N VAL B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 210 Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 234 through 245 removed outlier: 3.934A pdb=" N ARG B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 250 removed outlier: 3.615A pdb=" N HIS B 250 " --> pdb=" O ARG B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 267 Processing helix chain 'B' and resid 275 through 291 removed outlier: 3.580A pdb=" N THR B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA B 285 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Proline residue: B 286 - end of helix Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 295 through 313 removed outlier: 3.859A pdb=" N GLN B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR B 300 " --> pdb=" O PRO B 296 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN B 311 " --> pdb=" O ASN B 307 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 325 removed outlier: 3.786A pdb=" N PHE B 325 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 removed outlier: 4.276A pdb=" N GLU B 337 " --> pdb=" O TYR B 333 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 360 removed outlier: 3.830A pdb=" N VAL B 354 " --> pdb=" O ASN B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 384 Processing helix chain 'B' and resid 387 through 400 Processing helix chain 'B' and resid 403 through 421 removed outlier: 4.415A pdb=" N VAL B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 removed outlier: 3.601A pdb=" N LEU B 432 " --> pdb=" O VAL B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 455 removed outlier: 3.773A pdb=" N ALA B 446 " --> pdb=" O PRO B 442 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ALA B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR B 455 " --> pdb=" O ILE B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 467 removed outlier: 3.662A pdb=" N LEU B 465 " --> pdb=" O ASN B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.734A pdb=" N ASP B 475 " --> pdb=" O GLY B 472 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS B 476 " --> pdb=" O PHE B 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 472 through 476' Processing helix chain 'B' and resid 478 through 495 removed outlier: 3.691A pdb=" N VAL B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 512 removed outlier: 3.785A pdb=" N GLN B 504 " --> pdb=" O GLN B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 533 Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'B' and resid 556 through 565 removed outlier: 3.868A pdb=" N CYS B 565 " --> pdb=" O ASP B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 573 removed outlier: 3.532A pdb=" N VAL B 573 " --> pdb=" O LEU B 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 39 Processing helix chain 'C' and resid 74 through 79 removed outlier: 3.673A pdb=" N TRP C 78 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG C 79 " --> pdb=" O PRO C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 111 removed outlier: 4.296A pdb=" N ASN C 101 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU C 102 " --> pdb=" O GLU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 144 Processing helix chain 'C' and resid 145 through 148 removed outlier: 3.601A pdb=" N LEU C 148 " --> pdb=" O LEU C 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 145 through 148' Processing helix chain 'C' and resid 165 through 178 Processing helix chain 'G' and resid 6 through 16 Processing helix chain 'G' and resid 19 through 39 removed outlier: 4.659A pdb=" N GLU G 25 " --> pdb=" O ALA G 21 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU G 30 " --> pdb=" O MET G 26 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG G 39 " --> pdb=" O ARG G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 60 removed outlier: 3.686A pdb=" N LEU G 59 " --> pdb=" O TYR G 55 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY G 60 " --> pdb=" O MET G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 75 Processing helix chain 'G' and resid 78 through 93 removed outlier: 3.518A pdb=" N LYS G 82 " --> pdb=" O LYS G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 98 removed outlier: 3.717A pdb=" N GLN G 97 " --> pdb=" O ASP G 94 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP G 98 " --> pdb=" O GLU G 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 94 through 98' Processing helix chain 'G' and resid 99 through 101 No H-bonds generated for 'chain 'G' and resid 99 through 101' Processing helix chain 'G' and resid 102 through 111 removed outlier: 4.637A pdb=" N CYS G 106 " --> pdb=" O LEU G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 130 removed outlier: 4.002A pdb=" N LEU G 126 " --> pdb=" O ALA G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 143 removed outlier: 3.670A pdb=" N ARG G 136 " --> pdb=" O SER G 132 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP G 137 " --> pdb=" O GLU G 133 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N GLY G 140 " --> pdb=" O ARG G 136 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLU G 141 " --> pdb=" O ASP G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 147 Processing helix chain 'G' and resid 150 through 168 removed outlier: 3.944A pdb=" N LYS G 155 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS G 156 " --> pdb=" O TYR G 152 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU G 159 " --> pdb=" O LYS G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 172 removed outlier: 3.870A pdb=" N MET G 172 " --> pdb=" O PRO G 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 169 through 172' Processing helix chain 'G' and resid 187 through 205 Processing helix chain 'G' and resid 205 through 213 removed outlier: 4.011A pdb=" N HIS G 211 " --> pdb=" O ASP G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 228 removed outlier: 3.529A pdb=" N LEU G 219 " --> pdb=" O LEU G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 242 through 255 removed outlier: 3.769A pdb=" N ARG G 248 " --> pdb=" O PHE G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 261 through 267 Processing helix chain 'G' and resid 267 through 275 removed outlier: 3.890A pdb=" N LEU G 271 " --> pdb=" O MET G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 299 removed outlier: 4.106A pdb=" N ASN G 286 " --> pdb=" O LYS G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 317 removed outlier: 3.634A pdb=" N ARG G 306 " --> pdb=" O GLU G 302 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU G 308 " --> pdb=" O GLY G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 335 Processing helix chain 'G' and resid 339 through 344 removed outlier: 3.856A pdb=" N VAL G 343 " --> pdb=" O ASP G 339 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN G 344 " --> pdb=" O HIS G 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 339 through 344' Processing helix chain 'G' and resid 346 through 353 Processing helix chain 'G' and resid 354 through 356 No H-bonds generated for 'chain 'G' and resid 354 through 356' Processing helix chain 'G' and resid 358 through 373 Processing helix chain 'G' and resid 377 through 391 removed outlier: 3.668A pdb=" N MET G 381 " --> pdb=" O ASN G 377 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET G 382 " --> pdb=" O ILE G 378 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS G 383 " --> pdb=" O ARG G 379 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU G 384 " --> pdb=" O GLY G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 411 removed outlier: 3.631A pdb=" N PHE G 405 " --> pdb=" O ALA G 401 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS G 410 " --> pdb=" O LEU G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 429 Processing helix chain 'G' and resid 437 through 448 Processing helix chain 'G' and resid 452 through 464 removed outlier: 3.962A pdb=" N ARG G 458 " --> pdb=" O TYR G 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 469 through 488 removed outlier: 4.101A pdb=" N TRP G 478 " --> pdb=" O GLN G 474 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASP G 485 " --> pdb=" O GLY G 481 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU G 486 " --> pdb=" O GLU G 482 " (cutoff:3.500A) Processing helix chain 'G' and resid 503 through 515 removed outlier: 4.030A pdb=" N LEU G 509 " --> pdb=" O VAL G 505 " (cutoff:3.500A) Processing helix chain 'G' and resid 521 through 537 removed outlier: 3.788A pdb=" N SER G 534 " --> pdb=" O ILE G 530 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N THR G 535 " --> pdb=" O MET G 531 " (cutoff:3.500A) Processing helix chain 'G' and resid 543 through 551 Processing helix chain 'G' and resid 556 through 573 removed outlier: 3.737A pdb=" N LEU G 569 " --> pdb=" O GLU G 565 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR G 573 " --> pdb=" O LEU G 569 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 39 Processing helix chain 'H' and resid 74 through 82 removed outlier: 3.708A pdb=" N TRP H 78 " --> pdb=" O ARG H 75 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG H 79 " --> pdb=" O PRO H 76 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS H 80 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 98 No H-bonds generated for 'chain 'H' and resid 96 through 98' Processing helix chain 'H' and resid 99 through 111 Processing helix chain 'H' and resid 135 through 144 removed outlier: 3.626A pdb=" N ILE H 139 " --> pdb=" O ASN H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 148 Processing helix chain 'H' and resid 165 through 178 removed outlier: 4.027A pdb=" N ARG H 178 " --> pdb=" O SER H 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 31 removed outlier: 3.727A pdb=" N VAL M 30 " --> pdb=" O MET M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 42 Processing helix chain 'M' and resid 76 through 95 Processing helix chain 'M' and resid 99 through 104 removed outlier: 3.730A pdb=" N ILE M 103 " --> pdb=" O GLU M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 117 removed outlier: 4.056A pdb=" N TYR M 111 " --> pdb=" O PHE M 107 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU M 112 " --> pdb=" O VAL M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 133 removed outlier: 3.663A pdb=" N GLU M 133 " --> pdb=" O LYS M 129 " (cutoff:3.500A) Processing helix chain 'M' and resid 150 through 154 Processing helix chain 'M' and resid 216 through 224 Processing helix chain 'M' and resid 243 through 251 Processing helix chain 'S' and resid 24 through 41 removed outlier: 3.564A pdb=" N SER S 41 " --> pdb=" O GLN S 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 96 removed outlier: 3.587A pdb=" N LEU S 81 " --> pdb=" O GLU S 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 106 Processing helix chain 'S' and resid 106 through 116 Processing helix chain 'S' and resid 129 through 142 Processing sheet with id=AA1, first strand: chain 'T' and resid 9 through 10 Processing sheet with id=AA2, first strand: chain 'M' and resid 236 through 238 removed outlier: 6.857A pdb=" N ILE M 198 " --> pdb=" O LEU M 264 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER M 266 " --> pdb=" O GLY M 196 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLY M 196 " --> pdb=" O SER M 266 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG M 268 " --> pdb=" O ILE M 194 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE M 194 " --> pdb=" O ARG M 268 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ASN M 270 " --> pdb=" O SER M 192 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N SER M 192 " --> pdb=" O ASN M 270 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG M 191 " --> pdb=" O LEU M 182 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU M 182 " --> pdb=" O ARG M 191 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N LEU M 181 " --> pdb=" O GLY M 416 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR M 418 " --> pdb=" O LEU M 181 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL M 183 " --> pdb=" O TYR M 418 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LEU M 420 " --> pdb=" O VAL M 183 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 19 through 22 Processing sheet with id=AA4, first strand: chain 'C' and resid 90 through 93 removed outlier: 3.667A pdb=" N PHE C 124 " --> pdb=" O PHE C 90 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN C 126 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL C 123 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N THR C 158 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ALA C 125 " --> pdb=" O THR C 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 236 through 237 removed outlier: 3.614A pdb=" N VAL G 237 " --> pdb=" O ILE G 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 51 through 57 removed outlier: 5.891A pdb=" N MET H 18 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TRP H 66 " --> pdb=" O MET H 18 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE H 20 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL H 68 " --> pdb=" O ILE H 20 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N MET H 22 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG H 19 " --> pdb=" O GLY H 87 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE H 89 " --> pdb=" O ARG H 19 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU H 21 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL H 91 " --> pdb=" O LEU H 21 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL H 23 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N GLN H 156 " --> pdb=" O LEU H 121 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL H 123 " --> pdb=" O GLN H 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 15 through 20 removed outlier: 4.210A pdb=" N ALA M 5 " --> pdb=" O THR M 70 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR M 66 " --> pdb=" O LEU M 9 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER M 71 " --> pdb=" O ARG M 56 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'M' and resid 253 through 255 removed outlier: 4.818A pdb=" N ILE M 253 " --> pdb=" O LEU M 212 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLU M 209 " --> pdb=" O ILE M 397 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE M 397 " --> pdb=" O GLU M 209 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ARG M 211 " --> pdb=" O LEU M 395 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU M 395 " --> pdb=" O ARG M 211 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLY M 213 " --> pdb=" O ARG M 393 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 277 through 280 removed outlier: 6.976A pdb=" N ARG M 357 " --> pdb=" O PHE M 325 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N PHE M 325 " --> pdb=" O ARG M 357 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N HIS M 359 " --> pdb=" O PRO M 323 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 306 through 315 removed outlier: 6.502A pdb=" N LYS M 346 " --> pdb=" O ASN M 309 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLU M 311 " --> pdb=" O SER M 344 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER M 344 " --> pdb=" O GLU M 311 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N HIS M 313 " --> pdb=" O VAL M 342 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL M 342 " --> pdb=" O HIS M 313 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLU M 340 " --> pdb=" O PRO M 315 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 14 through 19 removed outlier: 6.489A pdb=" N LEU S 7 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN S 17 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE S 5 " --> pdb=" O GLN S 17 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE S 4 " --> pdb=" O ALA S 70 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE S 71 " --> pdb=" O LYS S 56 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS S 56 " --> pdb=" O ILE S 71 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 118 through 119 removed outlier: 3.919A pdb=" N ILE S 119 " --> pdb=" O GLU S 122 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU S 122 " --> pdb=" O ILE S 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 776 hydrogen bonds defined for protein. 2256 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: 2.78 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5389 1.34 - 1.46: 2858 1.46 - 1.58: 8455 1.58 - 1.69: 10 1.69 - 1.81: 161 Bond restraints: 16873 Sorted by residual: bond pdb=" C THR B 245 " pdb=" N PRO B 246 " ideal model delta sigma weight residual 1.337 1.371 -0.034 1.11e-02 8.12e+03 9.54e+00 bond pdb=" C ILE H 46 " pdb=" N PRO H 47 " ideal model delta sigma weight residual 1.333 1.354 -0.020 1.01e-02 9.80e+03 4.11e+00 bond pdb=" CA GLN B 400 " pdb=" C GLN B 400 " ideal model delta sigma weight residual 1.523 1.548 -0.025 1.34e-02 5.57e+03 3.40e+00 bond pdb=" C VAL G 216 " pdb=" N PRO G 217 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.25e-02 6.40e+03 3.24e+00 bond pdb=" CA VAL M 273 " pdb=" CB VAL M 273 " ideal model delta sigma weight residual 1.542 1.563 -0.021 1.26e-02 6.30e+03 2.76e+00 ... (remaining 16868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 21847 1.97 - 3.94: 836 3.94 - 5.91: 98 5.91 - 7.88: 40 7.88 - 9.86: 6 Bond angle restraints: 22827 Sorted by residual: angle pdb=" N VAL B 334 " pdb=" CA VAL B 334 " pdb=" C VAL B 334 " ideal model delta sigma weight residual 112.96 106.91 6.05 1.00e+00 1.00e+00 3.66e+01 angle pdb=" N ARG G 543 " pdb=" CA ARG G 543 " pdb=" C ARG G 543 " ideal model delta sigma weight residual 114.04 106.62 7.42 1.24e+00 6.50e-01 3.58e+01 angle pdb=" C LYS H 59 " pdb=" N ASN H 60 " pdb=" CA ASN H 60 " ideal model delta sigma weight residual 121.54 130.76 -9.22 1.91e+00 2.74e-01 2.33e+01 angle pdb=" C ASN M 308 " pdb=" N ASN M 309 " pdb=" CA ASN M 309 " ideal model delta sigma weight residual 121.54 130.18 -8.64 1.91e+00 2.74e-01 2.05e+01 angle pdb=" CA GLN B 400 " pdb=" C GLN B 400 " pdb=" N THR B 401 " ideal model delta sigma weight residual 116.84 123.65 -6.81 1.71e+00 3.42e-01 1.59e+01 ... (remaining 22822 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.15: 10206 30.15 - 60.30: 119 60.30 - 90.45: 14 90.45 - 120.61: 2 120.61 - 150.76: 7 Dihedral angle restraints: 10348 sinusoidal: 4265 harmonic: 6083 Sorted by residual: dihedral pdb=" O5' GTP H1001 " pdb=" O3A GTP H1001 " pdb=" PA GTP H1001 " pdb=" PB GTP H1001 " ideal model delta sinusoidal sigma weight residual -85.88 64.88 -150.76 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" CA GLU B 295 " pdb=" C GLU B 295 " pdb=" N PRO B 296 " pdb=" CA PRO B 296 " ideal model delta harmonic sigma weight residual 180.00 -146.57 -33.43 0 5.00e+00 4.00e-02 4.47e+01 dihedral pdb=" O3B GTP C1001 " pdb=" O3A GTP C1001 " pdb=" PB GTP C1001 " pdb=" PA GTP C1001 " ideal model delta sinusoidal sigma weight residual 291.08 146.93 144.15 1 2.00e+01 2.50e-03 4.35e+01 ... (remaining 10345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2215 0.071 - 0.143: 390 0.143 - 0.214: 25 0.214 - 0.285: 3 0.285 - 0.356: 1 Chirality restraints: 2634 Sorted by residual: chirality pdb=" CB VAL B 47 " pdb=" CA VAL B 47 " pdb=" CG1 VAL B 47 " pdb=" CG2 VAL B 47 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CG LEU B 197 " pdb=" CB LEU B 197 " pdb=" CD1 LEU B 197 " pdb=" CD2 LEU B 197 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA ASN H 60 " pdb=" N ASN H 60 " pdb=" C ASN H 60 " pdb=" CB ASN H 60 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2631 not shown) Planarity restraints: 2890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO M 374 " 0.047 5.00e-02 4.00e+02 7.13e-02 8.14e+00 pdb=" N PRO M 375 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO M 375 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO M 375 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 75 " 0.038 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO H 76 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO H 76 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO H 76 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 97 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.92e+00 pdb=" N PRO B 98 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 98 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 98 " 0.031 5.00e-02 4.00e+02 ... (remaining 2887 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 90 2.50 - 3.10: 11307 3.10 - 3.70: 25438 3.70 - 4.30: 36242 4.30 - 4.90: 59071 Nonbonded interactions: 132148 Sorted by model distance: nonbonded pdb=" O2G GTP C1001 " pdb="MG MG C1002 " model vdw 1.904 2.170 nonbonded pdb=" O2G GTP H1001 " pdb="MG MG H1002 " model vdw 1.907 2.170 nonbonded pdb=" O1G GTP H1001 " pdb="MG MG H1002 " model vdw 1.954 2.170 nonbonded pdb=" CG2 THR H 31 " pdb="MG MG H1002 " model vdw 2.113 2.590 nonbonded pdb=" PG GTP H1001 " pdb="MG MG H1002 " model vdw 2.192 2.530 ... (remaining 132143 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 'C' and (resid 17 through 179 or resid 1001 through 1002)) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.460 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 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 : 0.005 0.061 16873 Z= 0.230 Angle : 0.922 9.855 22827 Z= 0.525 Chirality : 0.053 0.356 2634 Planarity : 0.006 0.071 2890 Dihedral : 11.341 150.758 6394 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.04 % Favored : 94.91 % Rotamer: Outliers : 0.05 % Allowed : 2.82 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.30 (0.15), residues: 2045 helix: -2.79 (0.11), residues: 1039 sheet: -3.08 (0.30), residues: 246 loop : -2.53 (0.19), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 201 TYR 0.022 0.003 TYR G 61 PHE 0.029 0.003 PHE B 91 TRP 0.031 0.003 TRP B 450 HIS 0.008 0.002 HIS G 418 Details of bonding type rmsd covalent geometry : bond 0.00491 (16873) covalent geometry : angle 0.92154 (22827) hydrogen bonds : bond 0.18880 ( 776) hydrogen bonds : angle 7.74424 ( 2256) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 724 time to evaluate : 0.697 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: B 71 LEU cc_start: 0.9469 (tp) cc_final: 0.9074 (tp) REVERT: B 109 THR cc_start: 0.8736 (m) cc_final: 0.8278 (p) REVERT: B 126 LEU cc_start: 0.8932 (tp) cc_final: 0.8564 (tt) REVERT: B 147 LYS cc_start: 0.8826 (mttt) cc_final: 0.8275 (mmtp) REVERT: B 165 LEU cc_start: 0.8766 (tp) cc_final: 0.8523 (tp) REVERT: B 211 LEU cc_start: 0.8137 (tp) cc_final: 0.7869 (tp) REVERT: B 283 LYS cc_start: 0.8725 (mttt) cc_final: 0.8410 (mttm) REVERT: B 293 SER cc_start: 0.9291 (m) cc_final: 0.8898 (t) REVERT: B 295 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7387 (mt-10) REVERT: B 333 TYR cc_start: 0.8730 (p90) cc_final: 0.8374 (p90) REVERT: B 361 TYR cc_start: 0.7747 (m-10) cc_final: 0.7463 (m-80) REVERT: B 382 ILE cc_start: 0.9247 (mt) cc_final: 0.8996 (pt) REVERT: B 404 ASN cc_start: 0.7655 (p0) cc_final: 0.6994 (t0) REVERT: B 435 ASN cc_start: 0.7828 (p0) cc_final: 0.7457 (p0) REVERT: C 72 ASP cc_start: 0.8401 (t0) cc_final: 0.8182 (t70) REVERT: C 89 ILE cc_start: 0.9197 (mt) cc_final: 0.8979 (mm) REVERT: C 151 ARG cc_start: 0.5682 (mmt180) cc_final: 0.5118 (mmt-90) REVERT: C 175 ASN cc_start: 0.8272 (m110) cc_final: 0.7874 (m110) REVERT: G 54 LEU cc_start: 0.9460 (mt) cc_final: 0.9129 (tt) REVERT: G 110 ASP cc_start: 0.7685 (m-30) cc_final: 0.7478 (m-30) REVERT: G 124 CYS cc_start: 0.8109 (t) cc_final: 0.7536 (t) REVERT: G 134 MET cc_start: 0.8667 (mtp) cc_final: 0.7845 (mtp) REVERT: G 137 ASP cc_start: 0.8332 (m-30) cc_final: 0.7628 (t0) REVERT: G 303 SER cc_start: 0.8776 (m) cc_final: 0.8285 (p) REVERT: G 310 ILE cc_start: 0.8696 (mm) cc_final: 0.8482 (pt) REVERT: G 320 ASN cc_start: 0.7878 (m-40) cc_final: 0.7255 (p0) REVERT: G 323 ASN cc_start: 0.7189 (m-40) cc_final: 0.6906 (m-40) REVERT: G 363 ARG cc_start: 0.8581 (ttm-80) cc_final: 0.8279 (ttm110) REVERT: G 364 ARG cc_start: 0.8624 (mmt180) cc_final: 0.7711 (mmt90) REVERT: G 389 LEU cc_start: 0.8622 (tp) cc_final: 0.8165 (pp) REVERT: G 395 GLU cc_start: 0.8108 (pt0) cc_final: 0.7639 (mp0) REVERT: G 475 VAL cc_start: 0.9252 (t) cc_final: 0.9048 (p) REVERT: H 23 VAL cc_start: 0.8403 (m) cc_final: 0.7272 (m) REVERT: H 64 THR cc_start: 0.8785 (m) cc_final: 0.8491 (t) REVERT: H 115 GLU cc_start: 0.6952 (pt0) cc_final: 0.6673 (pm20) REVERT: H 142 LYS cc_start: 0.8340 (mtmt) cc_final: 0.8079 (ptpt) REVERT: M 58 MET cc_start: 0.8180 (mpp) cc_final: 0.7816 (mtm) REVERT: M 74 ASN cc_start: 0.8478 (t0) cc_final: 0.7958 (t0) REVERT: M 130 ILE cc_start: 0.8577 (mm) cc_final: 0.8180 (mm) REVERT: M 134 TYR cc_start: 0.7451 (p90) cc_final: 0.6842 (p90) REVERT: M 174 ASP cc_start: 0.6704 (m-30) cc_final: 0.6492 (m-30) REVERT: M 248 GLU cc_start: 0.7323 (tp30) cc_final: 0.6535 (tm-30) REVERT: M 321 ASP cc_start: 0.7525 (p0) cc_final: 0.7280 (p0) REVERT: S 7 LEU cc_start: 0.8784 (mp) cc_final: 0.8532 (mt) REVERT: S 22 THR cc_start: 0.6216 (p) cc_final: 0.5330 (p) REVERT: S 93 LYS cc_start: 0.8755 (tttp) cc_final: 0.8417 (tppt) REVERT: S 116 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6743 (tp30) REVERT: S 119 ILE cc_start: 0.7844 (pp) cc_final: 0.7372 (pp) REVERT: S 130 ILE cc_start: 0.8623 (mt) cc_final: 0.8185 (mt) REVERT: S 140 MET cc_start: 0.7053 (tpt) cc_final: 0.6731 (tpp) outliers start: 1 outliers final: 0 residues processed: 725 average time/residue: 0.1624 time to fit residues: 166.8679 Evaluate side-chains 358 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 0.0970 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.0670 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 overall best weight: 0.5716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN B 173 ASN B 319 HIS ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN B 483 GLN B 505 GLN B 575 HIS C 95 ASN C 128 GLN C 150 HIS C 180 GLN G 97 GLN ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 GLN G 235 HIS ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 452 HIS ** G 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 GLN ** G 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 HIS H 156 GLN H 176 GLN M 239 HIS M 240 GLN M 286 HIS M 300 GLN S 3 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.095364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.081703 restraints weight = 52440.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.083824 restraints weight = 31077.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.085287 restraints weight = 20718.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.086209 restraints weight = 15062.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.087073 restraints weight = 12002.649| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16873 Z= 0.142 Angle : 0.683 14.595 22827 Z= 0.346 Chirality : 0.045 0.195 2634 Planarity : 0.007 0.196 2890 Dihedral : 10.167 145.714 2272 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.16 % Allowed : 3.26 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.17), residues: 2045 helix: -1.26 (0.14), residues: 1067 sheet: -2.96 (0.28), residues: 254 loop : -2.10 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 96 TYR 0.014 0.001 TYR C 81 PHE 0.031 0.002 PHE B 91 TRP 0.015 0.001 TRP C 66 HIS 0.006 0.001 HIS G 235 Details of bonding type rmsd covalent geometry : bond 0.00314 (16873) covalent geometry : angle 0.68255 (22827) hydrogen bonds : bond 0.04315 ( 776) hydrogen bonds : angle 5.34063 ( 2256) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 504 time to evaluate : 0.687 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: B 71 LEU cc_start: 0.9439 (tp) cc_final: 0.8788 (tp) REVERT: B 155 LEU cc_start: 0.9107 (tp) cc_final: 0.8699 (tp) REVERT: B 243 ARG cc_start: 0.8173 (mtm180) cc_final: 0.7779 (ptp-170) REVERT: B 283 LYS cc_start: 0.8964 (mttt) cc_final: 0.8663 (mttm) REVERT: B 323 VAL cc_start: 0.9014 (m) cc_final: 0.8587 (p) REVERT: B 382 ILE cc_start: 0.9151 (mt) cc_final: 0.8909 (pt) REVERT: B 398 LEU cc_start: 0.9254 (mt) cc_final: 0.9001 (mt) REVERT: B 404 ASN cc_start: 0.7574 (p0) cc_final: 0.7145 (t0) REVERT: B 435 ASN cc_start: 0.8134 (p0) cc_final: 0.7335 (p0) REVERT: C 72 ASP cc_start: 0.8662 (t0) cc_final: 0.8416 (t70) REVERT: C 142 LYS cc_start: 0.8899 (mttt) cc_final: 0.7979 (mtmt) REVERT: C 151 ARG cc_start: 0.5888 (mmt180) cc_final: 0.5453 (mmt-90) REVERT: C 175 ASN cc_start: 0.8102 (m110) cc_final: 0.7689 (m110) REVERT: G 110 ASP cc_start: 0.7876 (m-30) cc_final: 0.7665 (m-30) REVERT: G 226 LEU cc_start: 0.8608 (tp) cc_final: 0.8377 (tp) REVERT: G 303 SER cc_start: 0.9007 (m) cc_final: 0.8612 (p) REVERT: G 320 ASN cc_start: 0.7923 (m-40) cc_final: 0.7303 (p0) REVERT: G 360 SER cc_start: 0.9059 (m) cc_final: 0.8468 (t) REVERT: G 364 ARG cc_start: 0.8456 (mmt180) cc_final: 0.8064 (mmt90) REVERT: G 366 MET cc_start: 0.8405 (ptt) cc_final: 0.8167 (ptt) REVERT: G 395 GLU cc_start: 0.8233 (pt0) cc_final: 0.7811 (mp0) REVERT: H 64 THR cc_start: 0.8496 (m) cc_final: 0.8282 (t) REVERT: H 124 PHE cc_start: 0.7741 (OUTLIER) cc_final: 0.7525 (m-10) REVERT: H 145 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.6948 (mp) REVERT: H 155 ILE cc_start: 0.9067 (tt) cc_final: 0.8823 (tt) REVERT: M 58 MET cc_start: 0.8459 (mpp) cc_final: 0.8229 (mtm) REVERT: M 74 ASN cc_start: 0.8437 (t0) cc_final: 0.7803 (t0) REVERT: M 119 ASP cc_start: 0.8162 (t0) cc_final: 0.7855 (t0) REVERT: M 134 TYR cc_start: 0.7589 (p90) cc_final: 0.6971 (p90) REVERT: M 159 TRP cc_start: 0.8283 (p90) cc_final: 0.7904 (p90) REVERT: M 243 ARG cc_start: 0.7453 (mmp80) cc_final: 0.7014 (mmm160) REVERT: M 294 MET cc_start: 0.7134 (tmm) cc_final: 0.6895 (tmm) REVERT: M 343 TRP cc_start: 0.8857 (t60) cc_final: 0.8577 (t60) REVERT: M 356 MET cc_start: 0.6971 (tmm) cc_final: 0.6579 (tmm) REVERT: S 22 THR cc_start: 0.7281 (p) cc_final: 0.6947 (p) REVERT: S 32 THR cc_start: 0.9414 (p) cc_final: 0.9132 (p) REVERT: S 33 ARG cc_start: 0.8153 (mmp80) cc_final: 0.7822 (mmp80) REVERT: S 39 ILE cc_start: 0.8868 (mm) cc_final: 0.8530 (tt) REVERT: S 61 ARG cc_start: 0.8044 (ttt-90) cc_final: 0.7541 (ptm-80) REVERT: S 93 LYS cc_start: 0.8650 (tttp) cc_final: 0.8253 (tppt) REVERT: S 99 CYS cc_start: 0.6677 (t) cc_final: 0.6145 (t) REVERT: S 116 GLU cc_start: 0.7439 (mm-30) cc_final: 0.6912 (tp30) REVERT: S 119 ILE cc_start: 0.8167 (pt) cc_final: 0.7909 (mt) REVERT: S 133 LYS cc_start: 0.9188 (mtmt) cc_final: 0.8652 (mtmm) outliers start: 3 outliers final: 0 residues processed: 505 average time/residue: 0.1534 time to fit residues: 111.8292 Evaluate side-chains 312 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 310 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 195 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 199 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN B 319 HIS ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN G 97 GLN ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 470 GLN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 GLN M 52 HIS ** M 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 239 HIS M 288 HIS ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.092590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.079096 restraints weight = 54752.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.081116 restraints weight = 32475.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.082549 restraints weight = 21931.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.083523 restraints weight = 16039.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.084262 restraints weight = 12659.354| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 16873 Z= 0.160 Angle : 0.667 14.192 22827 Z= 0.338 Chirality : 0.045 0.228 2634 Planarity : 0.006 0.160 2890 Dihedral : 9.980 148.263 2272 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.05 % Allowed : 3.15 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.18), residues: 2045 helix: -0.53 (0.15), residues: 1071 sheet: -2.71 (0.29), residues: 253 loop : -1.75 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 96 TYR 0.015 0.002 TYR M 166 PHE 0.033 0.002 PHE B 91 TRP 0.016 0.001 TRP C 66 HIS 0.005 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00362 (16873) covalent geometry : angle 0.66725 (22827) hydrogen bonds : bond 0.03871 ( 776) hydrogen bonds : angle 5.04024 ( 2256) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 433 time to evaluate : 0.704 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: B 71 LEU cc_start: 0.9455 (tp) cc_final: 0.9078 (tp) REVERT: B 109 THR cc_start: 0.8760 (m) cc_final: 0.8323 (p) REVERT: B 147 LYS cc_start: 0.8768 (mmtm) cc_final: 0.7696 (mmtm) REVERT: B 155 LEU cc_start: 0.9050 (tp) cc_final: 0.8708 (tp) REVERT: B 165 LEU cc_start: 0.9102 (tp) cc_final: 0.8901 (tp) REVERT: B 267 MET cc_start: 0.6753 (tmm) cc_final: 0.6274 (tmm) REVERT: B 283 LYS cc_start: 0.9014 (mttt) cc_final: 0.8626 (mttm) REVERT: B 323 VAL cc_start: 0.8998 (m) cc_final: 0.8694 (p) REVERT: B 404 ASN cc_start: 0.7583 (p0) cc_final: 0.7117 (t0) REVERT: B 435 ASN cc_start: 0.8207 (p0) cc_final: 0.7257 (p0) REVERT: C 20 ILE cc_start: 0.9169 (tp) cc_final: 0.8895 (tp) REVERT: C 67 ASP cc_start: 0.6977 (t70) cc_final: 0.6539 (t0) REVERT: C 72 ASP cc_start: 0.8651 (t0) cc_final: 0.8372 (t70) REVERT: C 151 ARG cc_start: 0.6002 (mmt180) cc_final: 0.5488 (mmp80) REVERT: C 175 ASN cc_start: 0.8111 (m110) cc_final: 0.7658 (m110) REVERT: G 24 ARG cc_start: 0.8707 (tpp80) cc_final: 0.8345 (ttp80) REVERT: G 201 MET cc_start: 0.8604 (mmm) cc_final: 0.8326 (mmp) REVERT: G 226 LEU cc_start: 0.8717 (tp) cc_final: 0.8485 (tp) REVERT: G 303 SER cc_start: 0.8899 (m) cc_final: 0.8501 (p) REVERT: G 320 ASN cc_start: 0.8015 (m-40) cc_final: 0.7376 (p0) REVERT: G 366 MET cc_start: 0.8433 (ptt) cc_final: 0.8203 (ptt) REVERT: G 395 GLU cc_start: 0.8346 (pt0) cc_final: 0.7693 (mp0) REVERT: G 513 LEU cc_start: 0.8721 (mt) cc_final: 0.8116 (tt) REVERT: H 64 THR cc_start: 0.8489 (m) cc_final: 0.8275 (t) REVERT: H 135 ASN cc_start: 0.8249 (p0) cc_final: 0.8025 (p0) REVERT: H 145 LEU cc_start: 0.8559 (mp) cc_final: 0.8234 (mp) REVERT: M 74 ASN cc_start: 0.8415 (t0) cc_final: 0.7765 (t0) REVERT: M 159 TRP cc_start: 0.8289 (p90) cc_final: 0.7960 (p90) REVERT: M 207 MET cc_start: 0.8560 (mmm) cc_final: 0.8273 (mmt) REVERT: M 243 ARG cc_start: 0.7388 (mmp80) cc_final: 0.6820 (mmm-85) REVERT: M 294 MET cc_start: 0.7216 (tmm) cc_final: 0.6814 (tmm) REVERT: S 16 LEU cc_start: 0.8145 (tt) cc_final: 0.7611 (tp) REVERT: S 17 GLN cc_start: 0.7735 (pt0) cc_final: 0.7365 (pm20) REVERT: S 22 THR cc_start: 0.7637 (p) cc_final: 0.7339 (p) REVERT: S 32 THR cc_start: 0.9380 (p) cc_final: 0.9066 (p) REVERT: S 33 ARG cc_start: 0.8281 (mmp80) cc_final: 0.7941 (mmp80) REVERT: S 39 ILE cc_start: 0.8963 (mm) cc_final: 0.8579 (tt) REVERT: S 46 THR cc_start: 0.7268 (p) cc_final: 0.6981 (p) REVERT: S 61 ARG cc_start: 0.8016 (ttt-90) cc_final: 0.7543 (ptm-80) REVERT: S 93 LYS cc_start: 0.8508 (tttp) cc_final: 0.8171 (tppt) REVERT: S 116 GLU cc_start: 0.7490 (mm-30) cc_final: 0.6956 (tp30) REVERT: S 133 LYS cc_start: 0.9194 (mtmt) cc_final: 0.8744 (mtmm) outliers start: 1 outliers final: 1 residues processed: 434 average time/residue: 0.1332 time to fit residues: 86.6252 Evaluate side-chains 299 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 298 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 167 optimal weight: 0.1980 chunk 150 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 155 optimal weight: 0.2980 chunk 79 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 191 optimal weight: 2.9990 chunk 73 optimal weight: 20.0000 chunk 16 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN B 319 HIS ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 HIS M 239 HIS ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.094864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.081608 restraints weight = 53549.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.083467 restraints weight = 32973.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.084873 restraints weight = 22744.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.085866 restraints weight = 16896.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.086457 restraints weight = 13470.770| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16873 Z= 0.125 Angle : 0.642 13.629 22827 Z= 0.319 Chirality : 0.044 0.205 2634 Planarity : 0.005 0.141 2890 Dihedral : 9.754 153.493 2272 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.18), residues: 2045 helix: -0.18 (0.16), residues: 1068 sheet: -2.49 (0.30), residues: 258 loop : -1.45 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 315 TYR 0.036 0.002 TYR B 361 PHE 0.035 0.002 PHE B 91 TRP 0.018 0.001 TRP C 66 HIS 0.005 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00279 (16873) covalent geometry : angle 0.64200 (22827) hydrogen bonds : bond 0.03594 ( 776) hydrogen bonds : angle 4.83471 ( 2256) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 442 time to evaluate : 0.541 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: B 71 LEU cc_start: 0.9501 (tp) cc_final: 0.9277 (tp) REVERT: B 147 LYS cc_start: 0.8128 (mmmm) cc_final: 0.7550 (mmtm) REVERT: B 155 LEU cc_start: 0.9055 (tp) cc_final: 0.8697 (tp) REVERT: B 165 LEU cc_start: 0.9027 (tp) cc_final: 0.8798 (tp) REVERT: B 267 MET cc_start: 0.6780 (tmm) cc_final: 0.6371 (tmm) REVERT: B 283 LYS cc_start: 0.8986 (mttt) cc_final: 0.8679 (mttm) REVERT: B 323 VAL cc_start: 0.8932 (m) cc_final: 0.8667 (p) REVERT: B 361 TYR cc_start: 0.7895 (m-80) cc_final: 0.7612 (m-80) REVERT: B 404 ASN cc_start: 0.7621 (p0) cc_final: 0.7095 (t0) REVERT: B 435 ASN cc_start: 0.8029 (p0) cc_final: 0.7045 (p0) REVERT: C 20 ILE cc_start: 0.9148 (tp) cc_final: 0.8895 (tp) REVERT: C 71 LEU cc_start: 0.8456 (mm) cc_final: 0.8216 (mt) REVERT: C 72 ASP cc_start: 0.8542 (t0) cc_final: 0.8225 (t70) REVERT: C 151 ARG cc_start: 0.5762 (mmt180) cc_final: 0.5355 (mmt-90) REVERT: C 175 ASN cc_start: 0.8119 (m110) cc_final: 0.7651 (m110) REVERT: G 26 MET cc_start: 0.7778 (ptm) cc_final: 0.7330 (ppp) REVERT: G 91 LEU cc_start: 0.9012 (mm) cc_final: 0.8679 (mm) REVERT: G 110 ASP cc_start: 0.7818 (m-30) cc_final: 0.7613 (m-30) REVERT: G 303 SER cc_start: 0.8777 (m) cc_final: 0.8419 (p) REVERT: G 320 ASN cc_start: 0.7966 (m-40) cc_final: 0.7424 (p0) REVERT: G 366 MET cc_start: 0.8409 (ptt) cc_final: 0.8172 (ptt) REVERT: G 395 GLU cc_start: 0.8169 (pt0) cc_final: 0.7583 (mp0) REVERT: G 513 LEU cc_start: 0.8656 (mt) cc_final: 0.8217 (tt) REVERT: H 145 LEU cc_start: 0.8618 (mp) cc_final: 0.7782 (mp) REVERT: M 74 ASN cc_start: 0.8399 (t0) cc_final: 0.7704 (t0) REVERT: M 134 TYR cc_start: 0.8036 (p90) cc_final: 0.7169 (p90) REVERT: M 159 TRP cc_start: 0.8302 (p90) cc_final: 0.8021 (p90) REVERT: M 207 MET cc_start: 0.8514 (mmm) cc_final: 0.8155 (mmt) REVERT: M 243 ARG cc_start: 0.7240 (mmp80) cc_final: 0.6878 (mmm-85) REVERT: M 248 GLU cc_start: 0.8302 (tp30) cc_final: 0.7130 (tm-30) REVERT: M 294 MET cc_start: 0.7178 (tmm) cc_final: 0.6761 (tmm) REVERT: M 354 TYR cc_start: 0.7616 (m-80) cc_final: 0.7358 (m-80) REVERT: M 368 GLU cc_start: 0.6912 (tt0) cc_final: 0.6588 (mt-10) REVERT: S 28 ARG cc_start: 0.8712 (mmm-85) cc_final: 0.8424 (mmm-85) REVERT: S 32 THR cc_start: 0.9387 (p) cc_final: 0.9114 (p) REVERT: S 33 ARG cc_start: 0.8328 (mmp80) cc_final: 0.8077 (mmp80) REVERT: S 39 ILE cc_start: 0.8902 (mm) cc_final: 0.8541 (tt) REVERT: S 61 ARG cc_start: 0.7972 (ttt-90) cc_final: 0.7404 (ptm-80) REVERT: S 93 LYS cc_start: 0.8519 (tttp) cc_final: 0.8185 (tppt) REVERT: S 116 GLU cc_start: 0.7535 (mm-30) cc_final: 0.6922 (tp30) REVERT: S 133 LYS cc_start: 0.9127 (mtmt) cc_final: 0.8583 (mtmm) outliers start: 0 outliers final: 0 residues processed: 442 average time/residue: 0.1308 time to fit residues: 87.0806 Evaluate side-chains 297 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 1 optimal weight: 0.0040 chunk 84 optimal weight: 3.9990 chunk 189 optimal weight: 6.9990 chunk 144 optimal weight: 0.0060 chunk 22 optimal weight: 0.8980 chunk 111 optimal weight: 9.9990 chunk 184 optimal weight: 7.9990 chunk 182 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.9810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN B 252 ASN B 319 HIS ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 ASN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 239 HIS ** M 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.093800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.080744 restraints weight = 53687.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.082628 restraints weight = 33280.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.083895 restraints weight = 22967.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.084883 restraints weight = 17285.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.085506 restraints weight = 13755.930| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16873 Z= 0.135 Angle : 0.648 13.608 22827 Z= 0.321 Chirality : 0.045 0.194 2634 Planarity : 0.005 0.082 2890 Dihedral : 9.636 159.424 2272 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.19), residues: 2045 helix: 0.01 (0.16), residues: 1060 sheet: -2.43 (0.30), residues: 258 loop : -1.34 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 96 TYR 0.027 0.002 TYR B 361 PHE 0.024 0.002 PHE G 570 TRP 0.018 0.001 TRP H 153 HIS 0.005 0.001 HIS G 100 Details of bonding type rmsd covalent geometry : bond 0.00309 (16873) covalent geometry : angle 0.64820 (22827) hydrogen bonds : bond 0.03501 ( 776) hydrogen bonds : angle 4.76656 ( 2256) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 0.709 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: B 25 ASP cc_start: 0.7935 (m-30) cc_final: 0.7660 (t0) REVERT: B 147 LYS cc_start: 0.8289 (mmmm) cc_final: 0.7842 (mmtp) REVERT: B 155 LEU cc_start: 0.9034 (tp) cc_final: 0.8659 (tp) REVERT: B 165 LEU cc_start: 0.9031 (tp) cc_final: 0.8828 (tp) REVERT: B 175 MET cc_start: 0.7268 (ttm) cc_final: 0.7065 (tpp) REVERT: B 283 LYS cc_start: 0.8977 (mttt) cc_final: 0.8619 (mttm) REVERT: B 323 VAL cc_start: 0.8898 (m) cc_final: 0.8640 (p) REVERT: B 361 TYR cc_start: 0.7786 (m-80) cc_final: 0.7574 (m-80) REVERT: B 404 ASN cc_start: 0.7686 (p0) cc_final: 0.7100 (t0) REVERT: B 435 ASN cc_start: 0.8027 (p0) cc_final: 0.7082 (p0) REVERT: C 151 ARG cc_start: 0.5732 (mmt180) cc_final: 0.5411 (mmt-90) REVERT: C 175 ASN cc_start: 0.8126 (m110) cc_final: 0.7652 (m110) REVERT: G 91 LEU cc_start: 0.9009 (mm) cc_final: 0.8747 (mm) REVERT: G 201 MET cc_start: 0.8444 (mmm) cc_final: 0.8227 (mmp) REVERT: G 303 SER cc_start: 0.8766 (m) cc_final: 0.8403 (p) REVERT: G 320 ASN cc_start: 0.8046 (m-40) cc_final: 0.7396 (p0) REVERT: G 366 MET cc_start: 0.8421 (ptt) cc_final: 0.8219 (ptt) REVERT: G 395 GLU cc_start: 0.8066 (pt0) cc_final: 0.7510 (mp0) REVERT: G 513 LEU cc_start: 0.8661 (mt) cc_final: 0.8048 (tt) REVERT: G 531 MET cc_start: 0.9486 (mmm) cc_final: 0.9090 (mmm) REVERT: H 135 ASN cc_start: 0.7920 (p0) cc_final: 0.7650 (p0) REVERT: M 74 ASN cc_start: 0.8410 (t0) cc_final: 0.7632 (t0) REVERT: M 159 TRP cc_start: 0.8279 (p90) cc_final: 0.7931 (p90) REVERT: M 207 MET cc_start: 0.8453 (mmm) cc_final: 0.8191 (mmp) REVERT: M 243 ARG cc_start: 0.7135 (mmp80) cc_final: 0.6816 (mmm-85) REVERT: M 294 MET cc_start: 0.7191 (tmm) cc_final: 0.6813 (tmm) REVERT: S 32 THR cc_start: 0.9409 (p) cc_final: 0.9102 (p) REVERT: S 33 ARG cc_start: 0.8348 (mmp80) cc_final: 0.8117 (mmp80) REVERT: S 39 ILE cc_start: 0.8958 (mm) cc_final: 0.8592 (tt) REVERT: S 61 ARG cc_start: 0.8042 (ttt-90) cc_final: 0.7415 (ptm-80) REVERT: S 93 LYS cc_start: 0.8522 (tttp) cc_final: 0.8191 (tppt) REVERT: S 116 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7058 (tp30) REVERT: S 133 LYS cc_start: 0.9119 (mtmt) cc_final: 0.8602 (mtmm) outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.1358 time to fit residues: 80.5544 Evaluate side-chains 296 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 170 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 123 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 65 optimal weight: 0.5980 chunk 197 optimal weight: 0.0270 chunk 24 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 188 optimal weight: 0.0030 overall best weight: 0.8050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN B 319 HIS ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS G 43 ASN ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 HIS M 239 HIS ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.094236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.081507 restraints weight = 53880.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.083056 restraints weight = 33235.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.085179 restraints weight = 22418.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.085760 restraints weight = 14712.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.085820 restraints weight = 12937.021| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16873 Z= 0.127 Angle : 0.641 14.215 22827 Z= 0.316 Chirality : 0.044 0.198 2634 Planarity : 0.004 0.080 2890 Dihedral : 9.469 166.935 2272 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.19), residues: 2045 helix: 0.18 (0.16), residues: 1063 sheet: -2.30 (0.31), residues: 250 loop : -1.24 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 96 TYR 0.045 0.002 TYR M 111 PHE 0.027 0.002 PHE B 91 TRP 0.014 0.001 TRP C 66 HIS 0.004 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00291 (16873) covalent geometry : angle 0.64143 (22827) hydrogen bonds : bond 0.03410 ( 776) hydrogen bonds : angle 4.73665 ( 2256) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 0.649 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: B 126 LEU cc_start: 0.8997 (tt) cc_final: 0.8780 (tp) REVERT: B 155 LEU cc_start: 0.9092 (tp) cc_final: 0.8690 (tp) REVERT: B 250 HIS cc_start: 0.7955 (t-90) cc_final: 0.7568 (t-90) REVERT: B 267 MET cc_start: 0.7486 (ttt) cc_final: 0.7272 (tmm) REVERT: B 283 LYS cc_start: 0.8988 (mttt) cc_final: 0.8617 (mttm) REVERT: B 323 VAL cc_start: 0.8844 (m) cc_final: 0.8583 (p) REVERT: B 404 ASN cc_start: 0.7724 (p0) cc_final: 0.7095 (t0) REVERT: B 435 ASN cc_start: 0.8012 (p0) cc_final: 0.7110 (p0) REVERT: C 99 ARG cc_start: 0.8383 (ttp-170) cc_final: 0.8066 (ttp80) REVERT: C 142 LYS cc_start: 0.8139 (mttt) cc_final: 0.7892 (mttt) REVERT: C 151 ARG cc_start: 0.5748 (mmt180) cc_final: 0.5372 (mmt-90) REVERT: C 171 ASP cc_start: 0.8474 (t0) cc_final: 0.8248 (t0) REVERT: C 175 ASN cc_start: 0.8095 (m110) cc_final: 0.7617 (m110) REVERT: G 110 ASP cc_start: 0.7772 (m-30) cc_final: 0.7524 (m-30) REVERT: G 201 MET cc_start: 0.8470 (mmm) cc_final: 0.8228 (mmp) REVERT: G 303 SER cc_start: 0.8904 (m) cc_final: 0.8527 (p) REVERT: G 320 ASN cc_start: 0.8008 (m-40) cc_final: 0.7389 (p0) REVERT: G 395 GLU cc_start: 0.8027 (pt0) cc_final: 0.7471 (mp0) REVERT: G 531 MET cc_start: 0.9525 (mmm) cc_final: 0.9109 (mmm) REVERT: H 38 LYS cc_start: 0.9288 (tptt) cc_final: 0.9067 (tppt) REVERT: M 27 MET cc_start: 0.7986 (mmt) cc_final: 0.7421 (mmp) REVERT: M 74 ASN cc_start: 0.8393 (t0) cc_final: 0.7654 (t0) REVERT: M 159 TRP cc_start: 0.8299 (p90) cc_final: 0.7902 (p90) REVERT: M 207 MET cc_start: 0.8377 (mmm) cc_final: 0.8084 (mmp) REVERT: M 243 ARG cc_start: 0.7083 (mmp80) cc_final: 0.6827 (mmm-85) REVERT: M 294 MET cc_start: 0.7198 (tmm) cc_final: 0.6781 (tmm) REVERT: M 368 GLU cc_start: 0.6938 (tt0) cc_final: 0.6640 (mt-10) REVERT: S 32 THR cc_start: 0.9414 (p) cc_final: 0.9101 (p) REVERT: S 33 ARG cc_start: 0.8325 (mmp80) cc_final: 0.8109 (mmp80) REVERT: S 39 ILE cc_start: 0.8944 (mm) cc_final: 0.8600 (tt) REVERT: S 61 ARG cc_start: 0.8028 (ttt-90) cc_final: 0.7371 (ptm-80) REVERT: S 93 LYS cc_start: 0.8499 (tttp) cc_final: 0.8176 (tppt) REVERT: S 133 LYS cc_start: 0.9155 (mtmt) cc_final: 0.8659 (mtmm) outliers start: 0 outliers final: 0 residues processed: 396 average time/residue: 0.1370 time to fit residues: 81.0085 Evaluate side-chains 294 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 156 optimal weight: 0.4980 chunk 132 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 chunk 28 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 174 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN B 319 HIS ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.095030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.082343 restraints weight = 53220.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.084284 restraints weight = 33045.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.086239 restraints weight = 20986.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.086697 restraints weight = 13741.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.086844 restraints weight = 12253.047| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16873 Z= 0.122 Angle : 0.645 14.579 22827 Z= 0.314 Chirality : 0.044 0.168 2634 Planarity : 0.004 0.067 2890 Dihedral : 9.244 179.111 2272 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.19), residues: 2045 helix: 0.29 (0.16), residues: 1056 sheet: -2.17 (0.32), residues: 252 loop : -1.14 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 96 TYR 0.029 0.002 TYR M 111 PHE 0.025 0.001 PHE B 91 TRP 0.025 0.001 TRP C 66 HIS 0.003 0.001 HIS G 64 Details of bonding type rmsd covalent geometry : bond 0.00278 (16873) covalent geometry : angle 0.64455 (22827) hydrogen bonds : bond 0.03342 ( 776) hydrogen bonds : angle 4.68265 ( 2256) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 0.509 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: B 155 LEU cc_start: 0.9049 (tp) cc_final: 0.8642 (tp) REVERT: B 165 LEU cc_start: 0.9075 (tp) cc_final: 0.8867 (tp) REVERT: B 250 HIS cc_start: 0.8065 (t-90) cc_final: 0.7586 (t-90) REVERT: B 267 MET cc_start: 0.7489 (ttt) cc_final: 0.7228 (tmm) REVERT: B 283 LYS cc_start: 0.9001 (mttt) cc_final: 0.8609 (mttm) REVERT: B 323 VAL cc_start: 0.8746 (m) cc_final: 0.8503 (p) REVERT: B 404 ASN cc_start: 0.7709 (p0) cc_final: 0.7097 (t0) REVERT: C 35 TYR cc_start: 0.8693 (m-80) cc_final: 0.8316 (m-80) REVERT: C 58 TYR cc_start: 0.5452 (t80) cc_final: 0.5079 (t80) REVERT: C 67 ASP cc_start: 0.8026 (t70) cc_final: 0.7402 (t0) REVERT: C 142 LYS cc_start: 0.8091 (mttt) cc_final: 0.7877 (mttt) REVERT: C 151 ARG cc_start: 0.5790 (mmt180) cc_final: 0.5436 (mmt-90) REVERT: C 175 ASN cc_start: 0.8147 (m110) cc_final: 0.7717 (m110) REVERT: G 24 ARG cc_start: 0.8446 (tpt90) cc_final: 0.8113 (tpt90) REVERT: G 303 SER cc_start: 0.8823 (m) cc_final: 0.8448 (p) REVERT: G 320 ASN cc_start: 0.7980 (m-40) cc_final: 0.7344 (p0) REVERT: G 323 ASN cc_start: 0.7879 (m-40) cc_final: 0.7649 (m-40) REVERT: G 381 MET cc_start: 0.7973 (ptm) cc_final: 0.7442 (ptt) REVERT: G 395 GLU cc_start: 0.8030 (pt0) cc_final: 0.7494 (mp0) REVERT: G 513 LEU cc_start: 0.8544 (mt) cc_final: 0.8106 (tt) REVERT: G 531 MET cc_start: 0.9440 (mmm) cc_final: 0.9079 (mmm) REVERT: H 135 ASN cc_start: 0.8068 (p0) cc_final: 0.7805 (p0) REVERT: M 74 ASN cc_start: 0.8337 (t0) cc_final: 0.7653 (t0) REVERT: M 159 TRP cc_start: 0.8257 (p90) cc_final: 0.7869 (p90) REVERT: M 207 MET cc_start: 0.8362 (mmm) cc_final: 0.8111 (mmp) REVERT: M 243 ARG cc_start: 0.7001 (mmp80) cc_final: 0.6761 (mmm-85) REVERT: M 294 MET cc_start: 0.7139 (tmm) cc_final: 0.6713 (tmm) REVERT: M 368 GLU cc_start: 0.6922 (tt0) cc_final: 0.6538 (mt-10) REVERT: S 32 THR cc_start: 0.9373 (p) cc_final: 0.9090 (p) REVERT: S 61 ARG cc_start: 0.7958 (ttt-90) cc_final: 0.7304 (ptm-80) REVERT: S 93 LYS cc_start: 0.8480 (tttp) cc_final: 0.8204 (tppt) REVERT: S 109 LYS cc_start: 0.8216 (mmtp) cc_final: 0.7774 (mttm) REVERT: S 116 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7105 (tp30) REVERT: S 133 LYS cc_start: 0.9177 (mtmt) cc_final: 0.8691 (mtmm) outliers start: 0 outliers final: 0 residues processed: 407 average time/residue: 0.1355 time to fit residues: 82.0479 Evaluate side-chains 291 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 80 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 136 optimal weight: 0.0570 chunk 78 optimal weight: 0.7980 chunk 119 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 182 optimal weight: 0.0980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 ASN B 173 ASN B 319 HIS ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 ASN ** G 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 HIS ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.095184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.082991 restraints weight = 53938.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.084579 restraints weight = 33809.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.086192 restraints weight = 23126.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.086443 restraints weight = 15867.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.086596 restraints weight = 14936.637| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.5447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16873 Z= 0.120 Angle : 0.646 14.246 22827 Z= 0.317 Chirality : 0.044 0.179 2634 Planarity : 0.004 0.057 2890 Dihedral : 8.892 164.649 2272 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.19), residues: 2045 helix: 0.33 (0.16), residues: 1061 sheet: -2.04 (0.33), residues: 241 loop : -1.18 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 96 TYR 0.033 0.002 TYR M 111 PHE 0.023 0.001 PHE B 91 TRP 0.045 0.002 TRP S 19 HIS 0.004 0.001 HIS G 100 Details of bonding type rmsd covalent geometry : bond 0.00273 (16873) covalent geometry : angle 0.64584 (22827) hydrogen bonds : bond 0.03272 ( 776) hydrogen bonds : angle 4.62918 ( 2256) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 0.676 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: B 124 GLU cc_start: 0.7358 (tp30) cc_final: 0.6950 (tp30) REVERT: B 126 LEU cc_start: 0.8974 (tt) cc_final: 0.8741 (tp) REVERT: B 128 LYS cc_start: 0.8643 (mppt) cc_final: 0.8305 (mmtm) REVERT: B 155 LEU cc_start: 0.9031 (tp) cc_final: 0.8593 (tp) REVERT: B 165 LEU cc_start: 0.9023 (tp) cc_final: 0.8814 (tp) REVERT: B 250 HIS cc_start: 0.7973 (t-90) cc_final: 0.7634 (t-90) REVERT: B 283 LYS cc_start: 0.8948 (mttt) cc_final: 0.8536 (mttm) REVERT: B 303 LEU cc_start: 0.9169 (mm) cc_final: 0.8897 (tt) REVERT: B 323 VAL cc_start: 0.8695 (m) cc_final: 0.8453 (p) REVERT: B 404 ASN cc_start: 0.7631 (p0) cc_final: 0.7078 (t0) REVERT: C 58 TYR cc_start: 0.5013 (t80) cc_final: 0.4559 (t80) REVERT: C 66 TRP cc_start: 0.7834 (m100) cc_final: 0.7524 (m100) REVERT: C 151 ARG cc_start: 0.5688 (mmt180) cc_final: 0.5122 (mmt-90) REVERT: C 171 ASP cc_start: 0.8446 (t0) cc_final: 0.8127 (t0) REVERT: C 175 ASN cc_start: 0.8091 (m110) cc_final: 0.7626 (m110) REVERT: G 303 SER cc_start: 0.8801 (m) cc_final: 0.8408 (p) REVERT: G 320 ASN cc_start: 0.8029 (m-40) cc_final: 0.7380 (p0) REVERT: G 366 MET cc_start: 0.8389 (ptt) cc_final: 0.8065 (ptt) REVERT: G 376 ASN cc_start: 0.7343 (p0) cc_final: 0.6908 (m-40) REVERT: G 381 MET cc_start: 0.7827 (ptm) cc_final: 0.7365 (ptt) REVERT: G 395 GLU cc_start: 0.7983 (pt0) cc_final: 0.7430 (mp0) REVERT: G 513 LEU cc_start: 0.8540 (mt) cc_final: 0.8035 (tt) REVERT: G 531 MET cc_start: 0.9401 (mmm) cc_final: 0.9062 (mmm) REVERT: H 32 THR cc_start: 0.8067 (m) cc_final: 0.7866 (p) REVERT: H 38 LYS cc_start: 0.9357 (tptp) cc_final: 0.9134 (tppt) REVERT: M 74 ASN cc_start: 0.8314 (t0) cc_final: 0.7600 (t0) REVERT: M 159 TRP cc_start: 0.8237 (p90) cc_final: 0.8020 (p90) REVERT: M 262 PHE cc_start: 0.7713 (p90) cc_final: 0.7170 (m-80) REVERT: M 294 MET cc_start: 0.7169 (tmm) cc_final: 0.6729 (tmm) REVERT: M 311 GLU cc_start: 0.7944 (tt0) cc_final: 0.7441 (tt0) REVERT: M 368 GLU cc_start: 0.7062 (tt0) cc_final: 0.6571 (mt-10) REVERT: S 1 MET cc_start: 0.8298 (tpt) cc_final: 0.7510 (tpt) REVERT: S 61 ARG cc_start: 0.7893 (ttt-90) cc_final: 0.7335 (ptm-80) REVERT: S 93 LYS cc_start: 0.8526 (tttp) cc_final: 0.8197 (tppt) REVERT: S 109 LYS cc_start: 0.8237 (mmtp) cc_final: 0.7786 (mttm) REVERT: S 133 LYS cc_start: 0.9172 (mtmt) cc_final: 0.8635 (mtmm) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.1351 time to fit residues: 82.1136 Evaluate side-chains 301 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 78 optimal weight: 0.4980 chunk 137 optimal weight: 1.9990 chunk 178 optimal weight: 0.3980 chunk 34 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 146 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 ASN B 319 HIS ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 ASN ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 443 GLN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.094527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.082170 restraints weight = 54480.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.083598 restraints weight = 37489.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.085122 restraints weight = 24961.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.085802 restraints weight = 19164.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.086035 restraints weight = 15756.751| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.5599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16873 Z= 0.129 Angle : 0.657 14.460 22827 Z= 0.323 Chirality : 0.045 0.196 2634 Planarity : 0.004 0.054 2890 Dihedral : 8.761 166.849 2272 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.19), residues: 2045 helix: 0.38 (0.16), residues: 1065 sheet: -1.97 (0.33), residues: 243 loop : -1.16 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 35 TYR 0.034 0.002 TYR M 111 PHE 0.026 0.002 PHE M 120 TRP 0.020 0.002 TRP C 66 HIS 0.004 0.001 HIS G 100 Details of bonding type rmsd covalent geometry : bond 0.00298 (16873) covalent geometry : angle 0.65697 (22827) hydrogen bonds : bond 0.03285 ( 776) hydrogen bonds : angle 4.62688 ( 2256) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 0.718 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: B 126 LEU cc_start: 0.8989 (tt) cc_final: 0.8775 (tp) REVERT: B 155 LEU cc_start: 0.9043 (tp) cc_final: 0.8599 (tp) REVERT: B 165 LEU cc_start: 0.9020 (tp) cc_final: 0.8808 (tp) REVERT: B 250 HIS cc_start: 0.7996 (t-90) cc_final: 0.7667 (t-90) REVERT: B 283 LYS cc_start: 0.8947 (mttt) cc_final: 0.8543 (mttm) REVERT: B 323 VAL cc_start: 0.8698 (m) cc_final: 0.8443 (p) REVERT: B 449 ILE cc_start: 0.8543 (mm) cc_final: 0.8215 (mm) REVERT: C 58 TYR cc_start: 0.4943 (t80) cc_final: 0.4307 (t80) REVERT: C 156 GLN cc_start: 0.8020 (tp-100) cc_final: 0.7359 (tm-30) REVERT: C 175 ASN cc_start: 0.8159 (m110) cc_final: 0.7882 (m110) REVERT: G 201 MET cc_start: 0.8480 (mmt) cc_final: 0.8103 (mmm) REVERT: G 245 LEU cc_start: 0.7693 (mt) cc_final: 0.6771 (tt) REVERT: G 267 MET cc_start: 0.7591 (mtm) cc_final: 0.7381 (mtm) REVERT: G 303 SER cc_start: 0.8824 (m) cc_final: 0.8426 (p) REVERT: G 320 ASN cc_start: 0.8082 (m-40) cc_final: 0.7397 (p0) REVERT: G 366 MET cc_start: 0.8429 (ptt) cc_final: 0.8114 (ptt) REVERT: G 376 ASN cc_start: 0.7364 (p0) cc_final: 0.7043 (m-40) REVERT: G 381 MET cc_start: 0.7825 (ptm) cc_final: 0.7361 (ptt) REVERT: G 395 GLU cc_start: 0.7980 (pt0) cc_final: 0.7490 (mp0) REVERT: H 32 THR cc_start: 0.8160 (m) cc_final: 0.7956 (p) REVERT: H 38 LYS cc_start: 0.9371 (tptp) cc_final: 0.9169 (tppt) REVERT: H 135 ASN cc_start: 0.7998 (p0) cc_final: 0.7796 (p0) REVERT: M 74 ASN cc_start: 0.8313 (t0) cc_final: 0.7600 (t0) REVERT: M 159 TRP cc_start: 0.8408 (p90) cc_final: 0.8153 (p90) REVERT: M 200 MET cc_start: 0.7673 (mtm) cc_final: 0.7341 (mtp) REVERT: M 262 PHE cc_start: 0.7678 (p90) cc_final: 0.7123 (m-80) REVERT: M 294 MET cc_start: 0.7031 (tmm) cc_final: 0.6587 (tmm) REVERT: M 311 GLU cc_start: 0.7983 (tt0) cc_final: 0.7426 (tt0) REVERT: M 368 GLU cc_start: 0.6973 (tt0) cc_final: 0.6561 (mt-10) REVERT: S 1 MET cc_start: 0.8332 (tpt) cc_final: 0.7493 (tpt) REVERT: S 7 LEU cc_start: 0.8341 (mm) cc_final: 0.7652 (mm) REVERT: S 8 PHE cc_start: 0.8594 (p90) cc_final: 0.8350 (p90) REVERT: S 61 ARG cc_start: 0.7982 (ttt-90) cc_final: 0.7338 (ptm-80) REVERT: S 93 LYS cc_start: 0.8532 (tttp) cc_final: 0.8224 (tppt) REVERT: S 109 LYS cc_start: 0.8268 (mmtp) cc_final: 0.8041 (mttm) REVERT: S 133 LYS cc_start: 0.9158 (mtmt) cc_final: 0.8665 (mtmm) outliers start: 0 outliers final: 0 residues processed: 385 average time/residue: 0.1349 time to fit residues: 78.2192 Evaluate side-chains 289 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 52 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 203 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 182 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 ASN B 173 ASN B 319 HIS ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 500 GLN ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 418 HIS ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 HIS ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.091410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.079066 restraints weight = 55276.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.080500 restraints weight = 35388.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.082357 restraints weight = 24388.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.082974 restraints weight = 16334.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.083111 restraints weight = 13655.583| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 16873 Z= 0.180 Angle : 0.712 15.182 22827 Z= 0.353 Chirality : 0.046 0.192 2634 Planarity : 0.005 0.122 2890 Dihedral : 8.847 175.443 2272 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.19), residues: 2045 helix: 0.27 (0.16), residues: 1065 sheet: -1.85 (0.34), residues: 240 loop : -1.13 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 35 TYR 0.039 0.002 TYR M 111 PHE 0.029 0.002 PHE M 120 TRP 0.043 0.002 TRP G 417 HIS 0.005 0.001 HIS G 100 Details of bonding type rmsd covalent geometry : bond 0.00421 (16873) covalent geometry : angle 0.71200 (22827) hydrogen bonds : bond 0.03603 ( 776) hydrogen bonds : angle 4.77382 ( 2256) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 0.481 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: B 31 LYS cc_start: 0.9175 (tptt) cc_final: 0.8884 (tptm) REVERT: B 126 LEU cc_start: 0.8983 (tt) cc_final: 0.8387 (tp) REVERT: B 155 LEU cc_start: 0.9104 (tp) cc_final: 0.8668 (tp) REVERT: B 165 LEU cc_start: 0.9085 (tp) cc_final: 0.8871 (tp) REVERT: B 283 LYS cc_start: 0.8975 (mttt) cc_final: 0.8560 (mttm) REVERT: B 323 VAL cc_start: 0.8837 (m) cc_final: 0.8622 (p) REVERT: B 449 ILE cc_start: 0.8508 (mm) cc_final: 0.8187 (mm) REVERT: C 66 TRP cc_start: 0.8025 (m100) cc_final: 0.7498 (m100) REVERT: C 124 PHE cc_start: 0.8624 (m-10) cc_final: 0.8409 (m-80) REVERT: C 156 GLN cc_start: 0.8000 (tp-100) cc_final: 0.7020 (tm-30) REVERT: C 175 ASN cc_start: 0.8264 (m110) cc_final: 0.8036 (m110) REVERT: G 25 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6877 (mt-10) REVERT: G 250 LEU cc_start: 0.9596 (mm) cc_final: 0.9340 (mm) REVERT: G 303 SER cc_start: 0.8763 (m) cc_final: 0.8348 (p) REVERT: G 320 ASN cc_start: 0.8123 (m-40) cc_final: 0.7370 (p0) REVERT: G 366 MET cc_start: 0.8414 (ptt) cc_final: 0.8128 (ptt) REVERT: G 381 MET cc_start: 0.7884 (ptm) cc_final: 0.7444 (ptt) REVERT: G 395 GLU cc_start: 0.7994 (pt0) cc_final: 0.7525 (mp0) REVERT: M 45 MET cc_start: 0.7887 (mmm) cc_final: 0.7622 (mmp) REVERT: M 74 ASN cc_start: 0.8370 (t0) cc_final: 0.7606 (t0) REVERT: M 207 MET cc_start: 0.8364 (mmp) cc_final: 0.8097 (mmp) REVERT: M 294 MET cc_start: 0.7314 (tmm) cc_final: 0.6895 (tmm) REVERT: M 311 GLU cc_start: 0.8319 (tt0) cc_final: 0.7610 (tt0) REVERT: M 368 GLU cc_start: 0.6897 (tt0) cc_final: 0.6574 (mt-10) REVERT: S 1 MET cc_start: 0.8393 (tpt) cc_final: 0.7595 (tpt) REVERT: S 7 LEU cc_start: 0.8497 (mm) cc_final: 0.7973 (mm) REVERT: S 32 THR cc_start: 0.9309 (p) cc_final: 0.9071 (p) REVERT: S 61 ARG cc_start: 0.8033 (ttt-90) cc_final: 0.7421 (ptm-80) REVERT: S 93 LYS cc_start: 0.8610 (tttp) cc_final: 0.8273 (tppt) REVERT: S 109 LYS cc_start: 0.8315 (mmtp) cc_final: 0.8052 (mttm) REVERT: S 133 LYS cc_start: 0.9171 (mtmt) cc_final: 0.8712 (mtmm) outliers start: 0 outliers final: 0 residues processed: 360 average time/residue: 0.1274 time to fit residues: 69.9204 Evaluate side-chains 265 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 64 optimal weight: 10.0000 chunk 119 optimal weight: 0.0270 chunk 96 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 167 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 ASN B 173 ASN B 319 HIS ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 HIS ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 HIS ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.094000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.081574 restraints weight = 54310.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.083278 restraints weight = 34419.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.085098 restraints weight = 22605.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.085728 restraints weight = 15116.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.086004 restraints weight = 12670.038| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16873 Z= 0.128 Angle : 0.689 15.716 22827 Z= 0.335 Chirality : 0.045 0.192 2634 Planarity : 0.004 0.054 2890 Dihedral : 8.683 174.453 2272 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.19), residues: 2045 helix: 0.40 (0.16), residues: 1057 sheet: -1.79 (0.34), residues: 236 loop : -1.09 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 96 TYR 0.040 0.002 TYR M 111 PHE 0.027 0.002 PHE B 91 TRP 0.040 0.002 TRP G 417 HIS 0.005 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00298 (16873) covalent geometry : angle 0.68858 (22827) hydrogen bonds : bond 0.03356 ( 776) hydrogen bonds : angle 4.63002 ( 2256) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2853.97 seconds wall clock time: 50 minutes 12.01 seconds (3012.01 seconds total)