Starting phenix.real_space_refine on Wed Mar 4 08:42:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7soy_25363/03_2026/7soy_25363.cif Found real_map, /net/cci-nas-00/data/ceres_data/7soy_25363/03_2026/7soy_25363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7soy_25363/03_2026/7soy_25363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7soy_25363/03_2026/7soy_25363.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7soy_25363/03_2026/7soy_25363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7soy_25363/03_2026/7soy_25363.map" } resolution = 3.4 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= 0.008 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 7799 2.51 5 N 2053 2.21 5 O 2256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12180 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4543 Classifications: {'peptide': 583} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 556} Chain: "B" Number of atoms: 2963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2963 Classifications: {'peptide': 355} Link IDs: {'PTRANS': 22, 'TRANS': 332} Chain breaks: 1 Chain: "C" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2322 Classifications: {'peptide': 288} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 276} Chain: "P" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2352 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 15, 'TRANS': 287} Chain breaks: 2 Time building chain proxies: 2.63, per 1000 atoms: 0.22 Number of scatterers: 12180 At special positions: 0 Unit cell: (113.95, 112.36, 108.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 2256 8.00 N 2053 7.00 C 7799 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: 1.02 Conformation dependent library (CDL) restraints added in 677.9 milliseconds 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2916 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 6 sheets defined 73.7% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 Processing helix chain 'A' and resid 24 through 34 Processing helix chain 'A' and resid 34 through 42 Processing helix chain 'A' and resid 43 through 50 Processing helix chain 'A' and resid 50 through 59 removed outlier: 3.636A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 76 Processing helix chain 'A' and resid 81 through 84 removed outlier: 4.142A pdb=" N GLU A 84 " --> pdb=" O GLY A 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 81 through 84' Processing helix chain 'A' and resid 85 through 99 removed outlier: 3.789A pdb=" N LEU A 89 " --> pdb=" O TYR A 85 " (cutoff:3.500A) Proline residue: A 91 - end of helix removed outlier: 3.764A pdb=" N LEU A 96 " --> pdb=" O PRO A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 119 removed outlier: 3.770A pdb=" N ARG A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N HIS A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 127 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 140 through 155 removed outlier: 3.830A pdb=" N ARG A 144 " --> pdb=" O TRP A 140 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY A 149 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SER A 152 " --> pdb=" O CYS A 148 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 175 Processing helix chain 'A' and resid 178 through 196 removed outlier: 4.427A pdb=" N GLY A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLU A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 214 removed outlier: 4.292A pdb=" N ILE A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Proline residue: A 207 - end of helix Processing helix chain 'A' and resid 217 through 235 removed outlier: 3.850A pdb=" N VAL A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 241 removed outlier: 4.324A pdb=" N GLU A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 253 Processing helix chain 'A' and resid 256 through 266 removed outlier: 3.633A pdb=" N ARG A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 275 Processing helix chain 'A' and resid 275 through 282 Processing helix chain 'A' and resid 282 through 292 removed outlier: 3.573A pdb=" N ALA A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 305 Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 317 through 325 Processing helix chain 'A' and resid 325 through 335 removed outlier: 3.922A pdb=" N CYS A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 350 removed outlier: 4.414A pdb=" N MET A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 357 removed outlier: 3.909A pdb=" N ILE A 355 " --> pdb=" O GLY A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 364 Processing helix chain 'A' and resid 364 through 374 Processing helix chain 'A' and resid 377 through 387 removed outlier: 3.762A pdb=" N ARG A 381 " --> pdb=" O CYS A 377 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 395 Processing helix chain 'A' and resid 396 through 413 removed outlier: 3.795A pdb=" N LEU A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) Proline residue: A 406 - end of helix Processing helix chain 'A' and resid 416 through 435 removed outlier: 3.664A pdb=" N ARG A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Proline residue: A 428 - end of helix Processing helix chain 'A' and resid 435 through 442 removed outlier: 3.544A pdb=" N LYS A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 452 removed outlier: 3.923A pdb=" N LEU A 446 " --> pdb=" O LYS A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 474 Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.916A pdb=" N ALA A 478 " --> pdb=" O GLY A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 490 removed outlier: 3.681A pdb=" N LYS A 485 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A 490 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 513 removed outlier: 3.670A pdb=" N THR A 501 " --> pdb=" O HIS A 497 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 520 removed outlier: 3.513A pdb=" N HIS A 520 " --> pdb=" O ILE A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 529 removed outlier: 3.866A pdb=" N THR A 524 " --> pdb=" O HIS A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 548 Processing helix chain 'A' and resid 552 through 559 Processing helix chain 'A' and resid 559 through 569 Processing helix chain 'A' and resid 572 through 586 Processing helix chain 'B' and resid 35 through 51 Processing helix chain 'B' and resid 62 through 83 Processing helix chain 'B' and resid 90 through 104 removed outlier: 4.338A pdb=" N GLU B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 147 Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 160 through 170 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 175 through 193 Processing helix chain 'B' and resid 196 through 214 Processing helix chain 'B' and resid 220 through 234 removed outlier: 3.866A pdb=" N GLY B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 250 Processing helix chain 'B' and resid 250 through 257 removed outlier: 3.672A pdb=" N HIS B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 257 " --> pdb=" O PRO B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 278 removed outlier: 4.522A pdb=" N TYR B 263 " --> pdb=" O SER B 259 " (cutoff:3.500A) Proline residue: B 265 - end of helix Processing helix chain 'B' and resid 281 through 292 removed outlier: 3.613A pdb=" N MET B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 315 Processing helix chain 'B' and resid 316 through 336 removed outlier: 3.718A pdb=" N LYS B 322 " --> pdb=" O SER B 318 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLU B 325 " --> pdb=" O VAL B 321 " (cutoff:3.500A) Proline residue: B 326 - end of helix Processing helix chain 'B' and resid 339 through 352 removed outlier: 3.783A pdb=" N TRP B 350 " --> pdb=" O ALA B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 362 removed outlier: 3.536A pdb=" N ASN B 362 " --> pdb=" O LEU B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 380 removed outlier: 3.995A pdb=" N ILE B 366 " --> pdb=" O ASN B 362 " (cutoff:3.500A) Proline residue: B 368 - end of helix Proline residue: B 372 - end of helix Processing helix chain 'B' and resid 383 through 401 Processing helix chain 'C' and resid 7 through 19 Processing helix chain 'C' and resid 24 through 40 Processing helix chain 'C' and resid 61 through 73 Processing helix chain 'C' and resid 92 through 107 Processing helix chain 'C' and resid 120 through 127 Processing helix chain 'C' and resid 128 through 138 Processing helix chain 'C' and resid 140 through 153 removed outlier: 3.604A pdb=" N TYR C 152 " --> pdb=" O ASP C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 183 removed outlier: 3.858A pdb=" N ILE C 180 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 201 removed outlier: 4.038A pdb=" N CYS C 196 " --> pdb=" O GLU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 233 Processing helix chain 'C' and resid 264 through 268 removed outlier: 3.562A pdb=" N ARG C 268 " --> pdb=" O TYR C 265 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 50 removed outlier: 4.542A pdb=" N TYR P 49 " --> pdb=" O PRO P 45 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 91 Processing helix chain 'P' and resid 92 through 103 Processing helix chain 'P' and resid 127 through 143 Processing helix chain 'P' and resid 156 through 169 removed outlier: 3.524A pdb=" N ALA P 160 " --> pdb=" O ALA P 156 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 190 Processing helix chain 'P' and resid 190 through 200 removed outlier: 3.610A pdb=" N MET P 194 " --> pdb=" O ALA P 190 " (cutoff:3.500A) Processing helix chain 'P' and resid 207 through 219 Processing helix chain 'P' and resid 223 through 234 removed outlier: 3.911A pdb=" N VAL P 232 " --> pdb=" O ARG P 228 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLY P 233 " --> pdb=" O VAL P 229 " (cutoff:3.500A) Processing helix chain 'P' and resid 290 through 302 removed outlier: 3.575A pdb=" N THR P 294 " --> pdb=" O GLU P 290 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASP P 299 " --> pdb=" O GLU P 295 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N GLY P 300 " --> pdb=" O LYS P 296 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TRP P 301 " --> pdb=" O TYR P 297 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE P 302 " --> pdb=" O TRP P 298 " (cutoff:3.500A) Processing helix chain 'P' and resid 304 through 312 Processing helix chain 'P' and resid 327 through 336 Processing helix chain 'P' and resid 350 through 355 removed outlier: 4.076A pdb=" N ALA P 355 " --> pdb=" O VAL P 351 " (cutoff:3.500A) Processing helix chain 'P' and resid 355 through 370 Processing sheet with id=AA1, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.424A pdb=" N PHE C 164 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL C 237 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ILE C 259 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ARG C 239 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 111 through 113 removed outlier: 6.102A pdb=" N TYR C 80 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N THR C 53 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N MET C 83 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N CYS C 55 " --> pdb=" O MET C 83 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLY C 56 " --> pdb=" O ALA C 274 " (cutoff:3.500A) removed outlier: 9.271A pdb=" N ALA C 274 " --> pdb=" O GLY C 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 210 through 211 Processing sheet with id=AA4, first strand: chain 'P' and resid 52 through 54 removed outlier: 6.098A pdb=" N VAL P 78 " --> pdb=" O MET P 151 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE P 153 " --> pdb=" O VAL P 78 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU P 80 " --> pdb=" O ILE P 153 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N HIS P 155 " --> pdb=" O LEU P 80 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU P 82 " --> pdb=" O HIS P 155 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU P 177 " --> pdb=" O LEU P 317 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N LEU P 319 " --> pdb=" O LEU P 177 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N MET P 179 " --> pdb=" O LEU P 319 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN P 340 " --> pdb=" O LYS P 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 57 through 59 Processing sheet with id=AA6, first strand: chain 'P' and resid 235 through 237 719 hydrogen bonds defined for protein. 2127 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: 2.14 Time building geometry restraints manager: 1.42 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: 3856 1.34 - 1.46: 1618 1.46 - 1.58: 6859 1.58 - 1.70: 0 1.70 - 1.82: 111 Bond restraints: 12444 Sorted by residual: bond pdb=" N VAL P 183 " pdb=" CA VAL P 183 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.19e-02 7.06e+03 8.36e+00 bond pdb=" N VAL P 120 " pdb=" CA VAL P 120 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.17e-02 7.31e+03 8.05e+00 bond pdb=" N ILE A 355 " pdb=" CA ILE A 355 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 7.94e+00 bond pdb=" N ILE C 71 " pdb=" CA ILE C 71 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.23e-02 6.61e+03 7.91e+00 bond pdb=" N CYS A 317 " pdb=" CA CYS A 317 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.33e-02 5.65e+03 7.57e+00 ... (remaining 12439 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 16105 1.32 - 2.65: 597 2.65 - 3.97: 128 3.97 - 5.30: 39 5.30 - 6.62: 6 Bond angle restraints: 16875 Sorted by residual: angle pdb=" N LEU B 305 " pdb=" CA LEU B 305 " pdb=" C LEU B 305 " ideal model delta sigma weight residual 111.02 105.91 5.11 1.22e+00 6.72e-01 1.75e+01 angle pdb=" N LEU A 522 " pdb=" CA LEU A 522 " pdb=" C LEU A 522 " ideal model delta sigma weight residual 112.75 107.30 5.45 1.36e+00 5.41e-01 1.60e+01 angle pdb=" N LEU B 46 " pdb=" CA LEU B 46 " pdb=" C LEU B 46 " ideal model delta sigma weight residual 111.07 107.24 3.83 1.07e+00 8.73e-01 1.28e+01 angle pdb=" CA GLU A 197 " pdb=" C GLU A 197 " pdb=" O GLU A 197 " ideal model delta sigma weight residual 121.94 117.92 4.02 1.15e+00 7.56e-01 1.22e+01 angle pdb=" N LYS B 300 " pdb=" CA LYS B 300 " pdb=" C LYS B 300 " ideal model delta sigma weight residual 111.28 107.73 3.55 1.09e+00 8.42e-01 1.06e+01 ... (remaining 16870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 6884 16.96 - 33.92: 551 33.92 - 50.88: 87 50.88 - 67.84: 18 67.84 - 84.80: 9 Dihedral angle restraints: 7549 sinusoidal: 3065 harmonic: 4484 Sorted by residual: dihedral pdb=" CA TYR A 155 " pdb=" C TYR A 155 " pdb=" N PRO A 156 " pdb=" CA PRO A 156 " ideal model delta harmonic sigma weight residual -180.00 -157.58 -22.42 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA MET B 324 " pdb=" C MET B 324 " pdb=" N GLU B 325 " pdb=" CA GLU B 325 " ideal model delta harmonic sigma weight residual 180.00 -161.75 -18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ASP A 57 " pdb=" C ASP A 57 " pdb=" N THR A 58 " pdb=" CA THR A 58 " ideal model delta harmonic sigma weight residual 180.00 -161.77 -18.23 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 7546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1497 0.047 - 0.094: 324 0.094 - 0.142: 81 0.142 - 0.189: 10 0.189 - 0.236: 4 Chirality restraints: 1916 Sorted by residual: chirality pdb=" CA LEU B 305 " pdb=" N LEU B 305 " pdb=" C LEU B 305 " pdb=" CB LEU B 305 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ILE A 13 " pdb=" N ILE A 13 " pdb=" C ILE A 13 " pdb=" CB ILE A 13 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA LEU B 46 " pdb=" N LEU B 46 " pdb=" C LEU B 46 " pdb=" CB LEU B 46 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.94e-01 ... (remaining 1913 not shown) Planarity restraints: 2163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 349 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C ILE A 349 " -0.036 2.00e-02 2.50e+03 pdb=" O ILE A 349 " 0.013 2.00e-02 2.50e+03 pdb=" N MET A 350 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU P 344 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO P 345 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO P 345 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO P 345 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS P 119 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.68e+00 pdb=" C LYS P 119 " 0.028 2.00e-02 2.50e+03 pdb=" O LYS P 119 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL P 120 " -0.009 2.00e-02 2.50e+03 ... (remaining 2160 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2199 2.76 - 3.30: 13422 3.30 - 3.83: 21774 3.83 - 4.37: 25935 4.37 - 4.90: 42156 Nonbonded interactions: 105486 Sorted by model distance: nonbonded pdb=" O LEU B 254 " pdb=" OH TYR B 263 " model vdw 2.231 3.040 nonbonded pdb=" O LEU C 23 " pdb=" OH TYR C 137 " model vdw 2.306 3.040 nonbonded pdb=" N VAL P 78 " pdb=" O PRO P 149 " model vdw 2.317 3.120 nonbonded pdb=" O LEU B 305 " pdb=" OH TYR B 349 " model vdw 2.318 3.040 nonbonded pdb=" O CYS P 312 " pdb=" NZ LYS P 316 " model vdw 2.326 3.120 ... (remaining 105481 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.230 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: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.430 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12444 Z= 0.219 Angle : 0.627 6.621 16875 Z= 0.387 Chirality : 0.043 0.236 1916 Planarity : 0.004 0.048 2163 Dihedral : 12.631 84.797 4633 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.37 % Allowed : 0.37 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.32 (0.22), residues: 1515 helix: 1.41 (0.16), residues: 1009 sheet: -0.46 (0.64), residues: 72 loop : 0.04 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 89 TYR 0.015 0.001 TYR A 426 PHE 0.019 0.001 PHE A 128 TRP 0.014 0.001 TRP P 214 HIS 0.006 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00338 (12444) covalent geometry : angle 0.62688 (16875) hydrogen bonds : bond 0.14607 ( 719) hydrogen bonds : angle 5.78274 ( 2127) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.9651 (m-30) cc_final: 0.9238 (p0) REVERT: A 426 TYR cc_start: 0.8978 (m-80) cc_final: 0.8374 (m-80) REVERT: A 489 MET cc_start: 0.9392 (tmm) cc_final: 0.9095 (tmm) REVERT: B 356 MET cc_start: 0.9386 (mmp) cc_final: 0.9131 (mmt) REVERT: C 267 TYR cc_start: 0.8938 (m-80) cc_final: 0.8624 (m-80) REVERT: P 131 MET cc_start: 0.9451 (mmt) cc_final: 0.9058 (mmm) REVERT: P 142 MET cc_start: 0.9750 (tpp) cc_final: 0.9342 (tpp) REVERT: P 285 TYR cc_start: 0.9392 (m-80) cc_final: 0.9111 (m-80) REVERT: P 297 TYR cc_start: 0.7340 (m-80) cc_final: 0.6577 (t80) outliers start: 5 outliers final: 1 residues processed: 119 average time/residue: 0.1059 time to fit residues: 18.7654 Evaluate side-chains 78 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 172 ASN B 330 GLN ** P 223 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 = 0.3487 r_free = 0.3487 target = 0.050963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.035472 restraints weight = 84144.138| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 5.37 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12444 Z= 0.163 Angle : 0.584 6.982 16875 Z= 0.305 Chirality : 0.040 0.148 1916 Planarity : 0.004 0.037 2163 Dihedral : 4.516 29.822 1644 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.52 % Allowed : 5.85 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.45 (0.22), residues: 1515 helix: 1.51 (0.16), residues: 1028 sheet: -0.71 (0.62), residues: 73 loop : 0.07 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 303 TYR 0.013 0.001 TYR B 138 PHE 0.015 0.001 PHE P 95 TRP 0.037 0.002 TRP P 301 HIS 0.004 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00346 (12444) covalent geometry : angle 0.58384 (16875) hydrogen bonds : bond 0.04377 ( 719) hydrogen bonds : angle 4.88768 ( 2127) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 TYR cc_start: 0.9260 (m-80) cc_final: 0.8974 (m-80) REVERT: A 389 ASP cc_start: 0.9680 (m-30) cc_final: 0.9290 (p0) REVERT: B 98 MET cc_start: 0.8723 (tpp) cc_final: 0.8455 (tpp) REVERT: B 356 MET cc_start: 0.9274 (mmp) cc_final: 0.9035 (mmp) REVERT: C 267 TYR cc_start: 0.8945 (m-80) cc_final: 0.8641 (m-80) REVERT: P 131 MET cc_start: 0.9411 (mmt) cc_final: 0.9089 (mmm) REVERT: P 297 TYR cc_start: 0.7654 (m-80) cc_final: 0.7214 (t80) REVERT: P 301 TRP cc_start: 0.7788 (m-90) cc_final: 0.7395 (m-90) outliers start: 7 outliers final: 3 residues processed: 89 average time/residue: 0.0914 time to fit residues: 12.8194 Evaluate side-chains 75 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 177 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 24 optimal weight: 0.0970 chunk 103 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 140 optimal weight: 40.0000 chunk 118 optimal weight: 5.9990 chunk 47 optimal weight: 0.0770 chunk 94 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 overall best weight: 1.6342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 GLN B 401 ASN ** P 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.051275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.035676 restraints weight = 83061.067| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 5.66 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12444 Z= 0.131 Angle : 0.546 8.524 16875 Z= 0.280 Chirality : 0.039 0.161 1916 Planarity : 0.004 0.035 2163 Dihedral : 4.349 25.530 1641 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.44 % Allowed : 8.00 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.22), residues: 1515 helix: 1.54 (0.16), residues: 1028 sheet: -0.79 (0.62), residues: 73 loop : 0.13 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 143 TYR 0.012 0.001 TYR B 138 PHE 0.021 0.001 PHE A 76 TRP 0.014 0.001 TRP P 214 HIS 0.003 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00274 (12444) covalent geometry : angle 0.54616 (16875) hydrogen bonds : bond 0.03901 ( 719) hydrogen bonds : angle 4.66657 ( 2127) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 PHE cc_start: 0.9332 (m-10) cc_final: 0.9108 (m-10) REVERT: A 85 TYR cc_start: 0.9297 (m-80) cc_final: 0.8996 (m-80) REVERT: A 389 ASP cc_start: 0.9695 (m-30) cc_final: 0.9256 (p0) REVERT: B 98 MET cc_start: 0.8851 (tpp) cc_final: 0.8639 (tpp) REVERT: C 66 MET cc_start: 0.9079 (tpt) cc_final: 0.8799 (tpp) REVERT: C 267 TYR cc_start: 0.9003 (m-80) cc_final: 0.8681 (m-80) REVERT: P 131 MET cc_start: 0.9375 (mmt) cc_final: 0.9055 (mmm) REVERT: P 297 TYR cc_start: 0.7477 (m-80) cc_final: 0.7038 (t80) REVERT: P 301 TRP cc_start: 0.7708 (m-90) cc_final: 0.7089 (m-90) outliers start: 6 outliers final: 3 residues processed: 89 average time/residue: 0.0929 time to fit residues: 13.2218 Evaluate side-chains 77 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 177 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 66 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 51 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 5 optimal weight: 0.4980 chunk 130 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN B 82 HIS ** P 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.051170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.035496 restraints weight = 81955.111| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 5.53 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12444 Z= 0.116 Angle : 0.534 6.360 16875 Z= 0.273 Chirality : 0.039 0.206 1916 Planarity : 0.004 0.061 2163 Dihedral : 4.301 25.190 1641 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.52 % Allowed : 9.56 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.54 (0.22), residues: 1515 helix: 1.58 (0.16), residues: 1027 sheet: -0.78 (0.63), residues: 73 loop : 0.11 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 143 TYR 0.009 0.001 TYR A 426 PHE 0.009 0.001 PHE A 538 TRP 0.012 0.001 TRP P 214 HIS 0.005 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00247 (12444) covalent geometry : angle 0.53396 (16875) hydrogen bonds : bond 0.03630 ( 719) hydrogen bonds : angle 4.53239 ( 2127) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 TYR cc_start: 0.9198 (m-80) cc_final: 0.8876 (m-80) REVERT: A 389 ASP cc_start: 0.9638 (m-30) cc_final: 0.9274 (p0) REVERT: B 98 MET cc_start: 0.8901 (tpp) cc_final: 0.8633 (tpp) REVERT: B 287 MET cc_start: 0.9109 (mtm) cc_final: 0.8900 (mpp) REVERT: B 324 MET cc_start: 0.8885 (mtt) cc_final: 0.8402 (mmm) REVERT: B 356 MET cc_start: 0.9474 (mmp) cc_final: 0.9036 (mmt) REVERT: C 66 MET cc_start: 0.9037 (tpt) cc_final: 0.8673 (tpp) REVERT: C 267 TYR cc_start: 0.9027 (m-80) cc_final: 0.8720 (m-80) REVERT: P 131 MET cc_start: 0.9381 (mmt) cc_final: 0.9058 (mmm) REVERT: P 297 TYR cc_start: 0.7387 (m-80) cc_final: 0.6927 (t80) REVERT: P 301 TRP cc_start: 0.7584 (m-90) cc_final: 0.6888 (m-90) REVERT: P 307 ASN cc_start: 0.9270 (t0) cc_final: 0.9043 (p0) outliers start: 7 outliers final: 6 residues processed: 83 average time/residue: 0.0882 time to fit residues: 11.7871 Evaluate side-chains 77 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain P residue 69 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN ** P 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.051438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.035769 restraints weight = 80924.756| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 5.54 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12444 Z= 0.105 Angle : 0.538 11.919 16875 Z= 0.270 Chirality : 0.039 0.172 1916 Planarity : 0.004 0.046 2163 Dihedral : 4.213 25.126 1641 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.59 % Allowed : 10.89 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.61 (0.22), residues: 1515 helix: 1.61 (0.16), residues: 1033 sheet: -0.75 (0.64), residues: 73 loop : 0.20 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 143 TYR 0.011 0.001 TYR A 426 PHE 0.017 0.001 PHE B 141 TRP 0.011 0.001 TRP P 214 HIS 0.006 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00222 (12444) covalent geometry : angle 0.53752 (16875) hydrogen bonds : bond 0.03475 ( 719) hydrogen bonds : angle 4.42530 ( 2127) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 PHE cc_start: 0.9165 (m-80) cc_final: 0.8918 (m-80) REVERT: A 85 TYR cc_start: 0.9162 (m-80) cc_final: 0.8848 (m-80) REVERT: A 389 ASP cc_start: 0.9612 (m-30) cc_final: 0.9156 (p0) REVERT: B 98 MET cc_start: 0.8770 (tpp) cc_final: 0.8499 (tpp) REVERT: B 324 MET cc_start: 0.8797 (mtt) cc_final: 0.8448 (mtt) REVERT: B 356 MET cc_start: 0.9479 (mmp) cc_final: 0.9037 (mmt) REVERT: C 66 MET cc_start: 0.8929 (tpt) cc_final: 0.8593 (tpp) REVERT: C 267 TYR cc_start: 0.9000 (m-80) cc_final: 0.8679 (m-80) REVERT: P 131 MET cc_start: 0.9407 (mmt) cc_final: 0.9093 (mmm) REVERT: P 150 ILE cc_start: 0.9090 (mt) cc_final: 0.8847 (mm) REVERT: P 297 TYR cc_start: 0.7281 (m-80) cc_final: 0.6793 (t80) REVERT: P 301 TRP cc_start: 0.7594 (m-90) cc_final: 0.6860 (m-90) REVERT: P 307 ASN cc_start: 0.9268 (t0) cc_final: 0.9023 (p0) outliers start: 8 outliers final: 5 residues processed: 89 average time/residue: 0.0849 time to fit residues: 12.1395 Evaluate side-chains 81 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain P residue 69 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 146 optimal weight: 20.0000 chunk 82 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 60 optimal weight: 40.0000 chunk 19 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 139 optimal weight: 30.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.049685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.034074 restraints weight = 86171.370| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 5.39 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12444 Z= 0.216 Angle : 0.598 7.667 16875 Z= 0.307 Chirality : 0.040 0.174 1916 Planarity : 0.004 0.054 2163 Dihedral : 4.385 25.275 1641 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.89 % Allowed : 12.07 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.44 (0.22), residues: 1515 helix: 1.53 (0.16), residues: 1022 sheet: -1.20 (0.59), residues: 78 loop : 0.15 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 143 TYR 0.011 0.001 TYR A 426 PHE 0.014 0.001 PHE A 578 TRP 0.014 0.001 TRP P 214 HIS 0.006 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00453 (12444) covalent geometry : angle 0.59799 (16875) hydrogen bonds : bond 0.03889 ( 719) hydrogen bonds : angle 4.70495 ( 2127) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.9710 (tpm170) cc_final: 0.9496 (tpp-160) REVERT: A 76 PHE cc_start: 0.9118 (m-10) cc_final: 0.8915 (m-80) REVERT: A 85 TYR cc_start: 0.9170 (m-80) cc_final: 0.8814 (m-80) REVERT: A 389 ASP cc_start: 0.9609 (m-30) cc_final: 0.9158 (p0) REVERT: A 520 HIS cc_start: 0.9223 (OUTLIER) cc_final: 0.8483 (m90) REVERT: B 356 MET cc_start: 0.9496 (mmp) cc_final: 0.9054 (mmt) REVERT: C 66 MET cc_start: 0.8834 (tpt) cc_final: 0.8468 (tpp) REVERT: C 267 TYR cc_start: 0.9036 (m-80) cc_final: 0.8671 (m-80) REVERT: C 276 MET cc_start: 0.9107 (ttp) cc_final: 0.8723 (ttm) REVERT: P 131 MET cc_start: 0.9389 (mmt) cc_final: 0.9098 (mmm) REVERT: P 297 TYR cc_start: 0.7197 (m-80) cc_final: 0.6686 (t80) REVERT: P 301 TRP cc_start: 0.7564 (m-90) cc_final: 0.6832 (m-90) outliers start: 12 outliers final: 8 residues processed: 84 average time/residue: 0.0939 time to fit residues: 12.4861 Evaluate side-chains 80 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 520 HIS Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain P residue 69 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 73 optimal weight: 0.9980 chunk 50 optimal weight: 0.0970 chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.051057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.035481 restraints weight = 80917.056| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 5.49 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12444 Z= 0.107 Angle : 0.586 14.194 16875 Z= 0.287 Chirality : 0.039 0.197 1916 Planarity : 0.004 0.043 2163 Dihedral : 4.295 25.432 1641 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.74 % Allowed : 12.52 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.57 (0.22), residues: 1515 helix: 1.60 (0.16), residues: 1034 sheet: -0.91 (0.63), residues: 73 loop : 0.13 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 143 TYR 0.008 0.001 TYR A 426 PHE 0.012 0.001 PHE B 141 TRP 0.011 0.001 TRP P 214 HIS 0.005 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00224 (12444) covalent geometry : angle 0.58562 (16875) hydrogen bonds : bond 0.03498 ( 719) hydrogen bonds : angle 4.47682 ( 2127) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 PHE cc_start: 0.9100 (m-10) cc_final: 0.8869 (m-80) REVERT: A 85 TYR cc_start: 0.9224 (m-80) cc_final: 0.8854 (m-80) REVERT: A 389 ASP cc_start: 0.9636 (m-30) cc_final: 0.9197 (p0) REVERT: A 520 HIS cc_start: 0.9275 (OUTLIER) cc_final: 0.8538 (m90) REVERT: A 538 PHE cc_start: 0.9441 (OUTLIER) cc_final: 0.9094 (p90) REVERT: B 98 MET cc_start: 0.8799 (tpp) cc_final: 0.8582 (tpp) REVERT: B 138 TYR cc_start: 0.9074 (m-80) cc_final: 0.8778 (m-80) REVERT: B 324 MET cc_start: 0.8895 (mtt) cc_final: 0.8366 (mmm) REVERT: B 350 TRP cc_start: 0.9116 (m100) cc_final: 0.8676 (m100) REVERT: B 356 MET cc_start: 0.9500 (mmp) cc_final: 0.9013 (mmt) REVERT: C 66 MET cc_start: 0.8990 (tpt) cc_final: 0.8589 (tpp) REVERT: C 245 MET cc_start: 0.8978 (mmm) cc_final: 0.8737 (mmm) REVERT: C 267 TYR cc_start: 0.9055 (m-80) cc_final: 0.8663 (m-80) REVERT: P 131 MET cc_start: 0.9359 (mmt) cc_final: 0.9066 (mmm) REVERT: P 297 TYR cc_start: 0.7169 (m-80) cc_final: 0.6652 (t80) REVERT: P 301 TRP cc_start: 0.7526 (m-90) cc_final: 0.6803 (m-90) outliers start: 10 outliers final: 7 residues processed: 87 average time/residue: 0.0821 time to fit residues: 11.4831 Evaluate side-chains 80 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 520 HIS Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain P residue 69 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 144 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 129 optimal weight: 20.0000 chunk 117 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 0 optimal weight: 50.0000 chunk 73 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.049862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.034246 restraints weight = 85355.551| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 5.41 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12444 Z= 0.170 Angle : 0.600 8.718 16875 Z= 0.300 Chirality : 0.040 0.265 1916 Planarity : 0.004 0.046 2163 Dihedral : 4.359 25.378 1641 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.89 % Allowed : 13.11 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.49 (0.22), residues: 1515 helix: 1.57 (0.16), residues: 1024 sheet: -1.22 (0.59), residues: 78 loop : 0.15 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 143 TYR 0.008 0.001 TYR B 158 PHE 0.013 0.001 PHE B 141 TRP 0.015 0.001 TRP P 214 HIS 0.004 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00363 (12444) covalent geometry : angle 0.59953 (16875) hydrogen bonds : bond 0.03653 ( 719) hydrogen bonds : angle 4.62724 ( 2127) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 TYR cc_start: 0.9178 (m-80) cc_final: 0.8800 (m-80) REVERT: A 350 MET cc_start: 0.8669 (ptt) cc_final: 0.8078 (ptt) REVERT: A 389 ASP cc_start: 0.9606 (m-30) cc_final: 0.9186 (p0) REVERT: A 520 HIS cc_start: 0.9204 (OUTLIER) cc_final: 0.8442 (m90) REVERT: A 538 PHE cc_start: 0.9385 (OUTLIER) cc_final: 0.9114 (p90) REVERT: B 98 MET cc_start: 0.8684 (tpp) cc_final: 0.8303 (tpp) REVERT: B 324 MET cc_start: 0.8802 (mtt) cc_final: 0.8319 (mmm) REVERT: B 350 TRP cc_start: 0.9127 (m100) cc_final: 0.8501 (m100) REVERT: B 356 MET cc_start: 0.9438 (mmp) cc_final: 0.8912 (mmt) REVERT: C 66 MET cc_start: 0.8798 (tpt) cc_final: 0.8424 (tpp) REVERT: C 267 TYR cc_start: 0.9027 (m-80) cc_final: 0.8633 (m-80) REVERT: P 131 MET cc_start: 0.9390 (mmt) cc_final: 0.9091 (mmm) REVERT: P 297 TYR cc_start: 0.7159 (m-80) cc_final: 0.6627 (t80) REVERT: P 301 TRP cc_start: 0.7494 (m-90) cc_final: 0.6785 (m-90) outliers start: 12 outliers final: 7 residues processed: 79 average time/residue: 0.0860 time to fit residues: 10.8878 Evaluate side-chains 76 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 520 HIS Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain P residue 69 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 50 optimal weight: 0.0870 chunk 3 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.050941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.035548 restraints weight = 82566.823| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 5.53 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12444 Z= 0.107 Angle : 0.605 14.238 16875 Z= 0.292 Chirality : 0.039 0.242 1916 Planarity : 0.004 0.047 2163 Dihedral : 4.271 25.298 1641 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.74 % Allowed : 13.11 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.57 (0.22), residues: 1515 helix: 1.60 (0.16), residues: 1027 sheet: -0.98 (0.61), residues: 77 loop : 0.19 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 143 TYR 0.008 0.001 TYR B 79 PHE 0.011 0.001 PHE B 141 TRP 0.014 0.001 TRP P 214 HIS 0.004 0.000 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00229 (12444) covalent geometry : angle 0.60460 (16875) hydrogen bonds : bond 0.03408 ( 719) hydrogen bonds : angle 4.47706 ( 2127) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 PHE cc_start: 0.8990 (m-80) cc_final: 0.8701 (m-80) REVERT: A 85 TYR cc_start: 0.9242 (m-80) cc_final: 0.8859 (m-80) REVERT: A 350 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8351 (ptt) REVERT: A 389 ASP cc_start: 0.9637 (m-30) cc_final: 0.9226 (p0) REVERT: A 520 HIS cc_start: 0.9294 (OUTLIER) cc_final: 0.8542 (m90) REVERT: A 538 PHE cc_start: 0.9438 (OUTLIER) cc_final: 0.9129 (p90) REVERT: B 98 MET cc_start: 0.8837 (tpp) cc_final: 0.8418 (tpp) REVERT: B 324 MET cc_start: 0.8902 (mtt) cc_final: 0.8350 (mmm) REVERT: B 350 TRP cc_start: 0.9100 (m100) cc_final: 0.8640 (m100) REVERT: B 356 MET cc_start: 0.9412 (mmp) cc_final: 0.9011 (mmm) REVERT: C 66 MET cc_start: 0.8948 (tpt) cc_final: 0.8554 (tpp) REVERT: C 245 MET cc_start: 0.8929 (mmm) cc_final: 0.8652 (mmm) REVERT: C 267 TYR cc_start: 0.9022 (m-80) cc_final: 0.8613 (m-80) REVERT: C 276 MET cc_start: 0.9187 (ttp) cc_final: 0.8876 (ttt) REVERT: P 131 MET cc_start: 0.9353 (mmt) cc_final: 0.9058 (mmm) REVERT: P 297 TYR cc_start: 0.7092 (m-80) cc_final: 0.6564 (t80) REVERT: P 301 TRP cc_start: 0.7459 (m-90) cc_final: 0.6781 (m-90) outliers start: 10 outliers final: 7 residues processed: 80 average time/residue: 0.0882 time to fit residues: 11.3143 Evaluate side-chains 81 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 520 HIS Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain P residue 69 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 72 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 129 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 38 optimal weight: 0.0470 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.050306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.034734 restraints weight = 84313.240| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 5.45 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12444 Z= 0.133 Angle : 0.614 14.502 16875 Z= 0.301 Chirality : 0.040 0.264 1916 Planarity : 0.004 0.047 2163 Dihedral : 4.260 25.188 1641 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.89 % Allowed : 13.19 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.57 (0.22), residues: 1515 helix: 1.61 (0.16), residues: 1028 sheet: -0.97 (0.61), residues: 77 loop : 0.16 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 143 TYR 0.007 0.001 TYR B 92 PHE 0.015 0.001 PHE B 99 TRP 0.015 0.001 TRP P 214 HIS 0.004 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00288 (12444) covalent geometry : angle 0.61355 (16875) hydrogen bonds : bond 0.03477 ( 719) hydrogen bonds : angle 4.53941 ( 2127) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 PHE cc_start: 0.8948 (m-80) cc_final: 0.8697 (m-80) REVERT: A 85 TYR cc_start: 0.9159 (m-80) cc_final: 0.8764 (m-80) REVERT: A 350 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8296 (ppp) REVERT: A 389 ASP cc_start: 0.9582 (m-30) cc_final: 0.9148 (p0) REVERT: A 520 HIS cc_start: 0.9152 (OUTLIER) cc_final: 0.8407 (m90) REVERT: A 538 PHE cc_start: 0.9364 (OUTLIER) cc_final: 0.9098 (p90) REVERT: B 98 MET cc_start: 0.8711 (tpp) cc_final: 0.8339 (tpp) REVERT: B 324 MET cc_start: 0.8798 (mtt) cc_final: 0.8295 (mmm) REVERT: B 350 TRP cc_start: 0.9093 (m100) cc_final: 0.8534 (m100) REVERT: B 356 MET cc_start: 0.9370 (mmp) cc_final: 0.8954 (mmm) REVERT: C 66 MET cc_start: 0.8760 (tpt) cc_final: 0.8394 (tpp) REVERT: C 245 MET cc_start: 0.8753 (mmm) cc_final: 0.8491 (mmm) REVERT: C 267 TYR cc_start: 0.9015 (m-80) cc_final: 0.8599 (m-80) REVERT: C 276 MET cc_start: 0.9063 (ttp) cc_final: 0.8793 (ttt) REVERT: P 131 MET cc_start: 0.9387 (mmt) cc_final: 0.9077 (mmm) REVERT: P 297 TYR cc_start: 0.7125 (m-80) cc_final: 0.6567 (t80) REVERT: P 301 TRP cc_start: 0.7480 (m-90) cc_final: 0.6741 (m-90) outliers start: 12 outliers final: 8 residues processed: 80 average time/residue: 0.0809 time to fit residues: 10.3435 Evaluate side-chains 80 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 520 HIS Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain P residue 69 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 117 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 97 optimal weight: 0.0370 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 383 ASN ** P 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.049844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.034407 restraints weight = 85736.817| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 5.45 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12444 Z= 0.161 Angle : 0.625 13.793 16875 Z= 0.309 Chirality : 0.040 0.244 1916 Planarity : 0.004 0.046 2163 Dihedral : 4.325 25.220 1641 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.96 % Allowed : 13.04 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.51 (0.22), residues: 1515 helix: 1.56 (0.16), residues: 1029 sheet: -0.99 (0.62), residues: 77 loop : 0.17 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 143 TYR 0.008 0.001 TYR B 158 PHE 0.012 0.001 PHE A 76 TRP 0.014 0.001 TRP P 214 HIS 0.003 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00346 (12444) covalent geometry : angle 0.62466 (16875) hydrogen bonds : bond 0.03607 ( 719) hydrogen bonds : angle 4.60980 ( 2127) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2463.74 seconds wall clock time: 43 minutes 12.06 seconds (2592.06 seconds total)