Starting phenix.real_space_refine on Sun May 3 03:40:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ryf_54378/05_2026/9ryf_54378.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ryf_54378/05_2026/9ryf_54378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ryf_54378/05_2026/9ryf_54378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ryf_54378/05_2026/9ryf_54378.map" model { file = "/net/cci-nas-00/data/ceres_data/9ryf_54378/05_2026/9ryf_54378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ryf_54378/05_2026/9ryf_54378.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 25 5.16 5 C 6558 2.51 5 N 1791 2.21 5 O 1788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10168 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4701 Classifications: {'peptide': 587} Link IDs: {'PTRANS': 24, 'TRANS': 562} Chain: "B" Number of atoms: 4508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4508 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 18, 'TRANS': 552} Chain: "C" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 897 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.43, per 1000 atoms: 0.24 Number of scatterers: 10168 At special positions: 0 Unit cell: (69.35, 89.3, 160.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 25 16.00 P 6 15.00 O 1788 8.00 N 1791 7.00 C 6558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 108 " distance=2.03 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: 0.95 Conformation dependent library (CDL) restraints added in 381.4 milliseconds 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2340 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 8 sheets defined 66.5% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 Processing helix chain 'A' and resid 25 through 44 removed outlier: 3.588A pdb=" N LEU A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 56 removed outlier: 4.177A pdb=" N PHE A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 120 removed outlier: 3.549A pdb=" N GLU A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 69 " --> pdb=" O PRO A 65 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N PHE A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU A 74 " --> pdb=" O PHE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 128 removed outlier: 4.001A pdb=" N TYR A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP A 126 " --> pdb=" O PRO A 122 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 127 " --> pdb=" O GLY A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 150 removed outlier: 4.093A pdb=" N ASP A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL A 141 " --> pdb=" O VAL A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 173 removed outlier: 3.942A pdb=" N PHE A 160 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 182 Processing helix chain 'A' and resid 183 through 222 removed outlier: 4.181A pdb=" N SER A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 229 Processing helix chain 'A' and resid 231 through 286 removed outlier: 3.612A pdb=" N LEU A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TRP A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 260 " --> pdb=" O TRP A 256 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE A 261 " --> pdb=" O PHE A 257 " (cutoff:3.500A) Proline residue: A 262 - end of helix removed outlier: 4.073A pdb=" N GLY A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 313 Proline residue: A 306 - end of helix removed outlier: 3.559A pdb=" N LYS A 313 " --> pdb=" O ASP A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 333 Processing helix chain 'A' and resid 399 through 408 removed outlier: 3.683A pdb=" N VAL A 403 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 428 through 435 Processing helix chain 'A' and resid 450 through 456 Processing helix chain 'A' and resid 462 through 474 removed outlier: 3.541A pdb=" N VAL A 466 " --> pdb=" O PRO A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 Processing helix chain 'A' and resid 484 through 487 removed outlier: 3.620A pdb=" N GLN A 487 " --> pdb=" O LYS A 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 484 through 487' Processing helix chain 'A' and resid 491 through 495 Processing helix chain 'A' and resid 498 through 512 Processing helix chain 'A' and resid 529 through 544 removed outlier: 3.885A pdb=" N ALA A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 560 removed outlier: 3.793A pdb=" N ARG A 560 " --> pdb=" O SER A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 587 through 597 Processing helix chain 'B' and resid 6 through 19 removed outlier: 3.633A pdb=" N LEU B 10 " --> pdb=" O ALA B 6 " (cutoff:3.500A) Proline residue: B 15 - end of helix Processing helix chain 'B' and resid 20 through 39 Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 59 through 103 removed outlier: 3.632A pdb=" N LEU B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 113 removed outlier: 3.774A pdb=" N TYR B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 134 removed outlier: 4.012A pdb=" N ASP B 125 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 158 Processing helix chain 'B' and resid 159 through 167 Processing helix chain 'B' and resid 168 through 207 removed outlier: 3.713A pdb=" N ILE B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA B 175 " --> pdb=" O GLY B 171 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ARG B 177 " --> pdb=" O PHE B 173 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU B 192 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 193 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 removed outlier: 3.672A pdb=" N VAL B 211 " --> pdb=" O GLY B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 243 removed outlier: 3.564A pdb=" N LEU B 227 " --> pdb=" O TRP B 223 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 270 removed outlier: 3.883A pdb=" N ALA B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 317 removed outlier: 4.386A pdb=" N TRP B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Proline residue: B 291 - end of helix removed outlier: 4.229A pdb=" N GLY B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TRP B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 335 Processing helix chain 'B' and resid 376 through 383 Processing helix chain 'B' and resid 406 through 413 removed outlier: 3.541A pdb=" N ALA B 413 " --> pdb=" O VAL B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 433 Processing helix chain 'B' and resid 440 through 451 Processing helix chain 'B' and resid 453 through 459 Processing helix chain 'B' and resid 462 through 466 removed outlier: 3.576A pdb=" N GLU B 465 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 473 Processing helix chain 'B' and resid 476 through 490 Processing helix chain 'B' and resid 506 through 518 Processing helix chain 'B' and resid 519 through 521 No H-bonds generated for 'chain 'B' and resid 519 through 521' Processing helix chain 'B' and resid 532 through 537 Processing helix chain 'B' and resid 555 through 561 Processing helix chain 'B' and resid 563 through 575 removed outlier: 3.835A pdb=" N ALA B 567 " --> pdb=" O GLY B 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.954A pdb=" N THR C 91 " --> pdb=" O PRO C 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 356 Processing sheet with id=AA2, first strand: chain 'A' and resid 358 through 361 removed outlier: 6.302A pdb=" N VAL A 358 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS A 377 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU A 360 " --> pdb=" O VAL A 375 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 436 through 439 removed outlier: 6.520A pdb=" N LEU A 519 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ILE A 552 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU A 521 " --> pdb=" O ILE A 552 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LEU A 566 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ALA A 390 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N PHE A 568 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A 392 " --> pdb=" O PHE A 568 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 575 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 448 through 449 Processing sheet with id=AA5, first strand: chain 'B' and resid 351 through 361 removed outlier: 6.393A pdb=" N LEU B 353 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LYS B 347 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ARG B 355 " --> pdb=" O GLY B 345 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLY B 345 " --> pdb=" O ARG B 355 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LEU B 357 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY B 343 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL B 344 " --> pdb=" O GLU B 392 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLU B 392 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N HIS B 400 " --> pdb=" O VAL B 397 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 414 through 417 removed outlier: 6.429A pdb=" N GLY B 415 " --> pdb=" O ILE B 497 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ASP B 499 " --> pdb=" O GLY B 415 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA B 417 " --> pdb=" O ASP B 499 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR B 366 " --> pdb=" O TRP B 541 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ILE B 543 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLY B 368 " --> pdb=" O ILE B 543 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU B 545 " --> pdb=" O GLY B 368 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR B 370 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE B 542 " --> pdb=" O GLU B 553 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU B 553 " --> pdb=" O ILE B 542 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL B 544 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA C 101 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'C' and resid 11 through 12 removed outlier: 5.811A pdb=" N ARG C 38 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLY C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) 650 hydrogen bonds defined for protein. 1881 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: 1.37 Time building geometry restraints manager: 1.22 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: 3337 1.34 - 1.46: 2266 1.46 - 1.58: 4729 1.58 - 1.70: 6 1.70 - 1.82: 45 Bond restraints: 10383 Sorted by residual: bond pdb=" C1' ATP B 601 " pdb=" O4' ATP B 601 " ideal model delta sigma weight residual 1.416 1.399 0.017 1.30e-02 5.92e+03 1.69e+00 bond pdb=" C1' ATP A 701 " pdb=" O4' ATP A 701 " ideal model delta sigma weight residual 1.416 1.402 0.014 1.30e-02 5.92e+03 1.22e+00 bond pdb=" C4' ATP A 701 " pdb=" O4' ATP A 701 " ideal model delta sigma weight residual 1.444 1.432 0.012 1.10e-02 8.26e+03 1.19e+00 bond pdb=" CD1 TYR A 202 " pdb=" CE1 TYR A 202 " ideal model delta sigma weight residual 1.382 1.349 0.033 3.00e-02 1.11e+03 1.19e+00 bond pdb=" CD LYS B 347 " pdb=" CE LYS B 347 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.53e-01 ... (remaining 10378 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 13757 1.59 - 3.19: 272 3.19 - 4.78: 50 4.78 - 6.38: 7 6.38 - 7.97: 3 Bond angle restraints: 14089 Sorted by residual: angle pdb=" CG1 ILE A 253 " pdb=" CB ILE A 253 " pdb=" CG2 ILE A 253 " ideal model delta sigma weight residual 110.70 118.67 -7.97 3.00e+00 1.11e-01 7.06e+00 angle pdb=" C1' ATP B 601 " pdb=" O4' ATP B 601 " pdb=" C4' ATP B 601 " ideal model delta sigma weight residual 109.40 105.23 4.17 1.61e+00 3.87e-01 6.75e+00 angle pdb=" C1' ATP A 701 " pdb=" C2' ATP A 701 " pdb=" O2' ATP A 701 " ideal model delta sigma weight residual 110.58 103.51 7.07 2.79e+00 1.28e-01 6.41e+00 angle pdb=" C2' ATP B 601 " pdb=" C1' ATP B 601 " pdb=" O4' ATP B 601 " ideal model delta sigma weight residual 106.53 103.57 2.96 1.18e+00 7.24e-01 6.36e+00 angle pdb=" C3' ATP B 601 " pdb=" C4' ATP B 601 " pdb=" C5' ATP B 601 " ideal model delta sigma weight residual 115.19 110.79 4.40 1.76e+00 3.23e-01 6.24e+00 ... (remaining 14084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 5627 17.10 - 34.20: 467 34.20 - 51.30: 74 51.30 - 68.40: 16 68.40 - 85.51: 14 Dihedral angle restraints: 6198 sinusoidal: 2542 harmonic: 3656 Sorted by residual: dihedral pdb=" CA LEU C 103 " pdb=" C LEU C 103 " pdb=" N LEU C 104 " pdb=" CA LEU C 104 " ideal model delta harmonic sigma weight residual 180.00 -157.79 -22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA GLU A 335 " pdb=" C GLU A 335 " pdb=" N GLU A 336 " pdb=" CA GLU A 336 " ideal model delta harmonic sigma weight residual -180.00 -161.18 -18.82 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ARG B 386 " pdb=" C ARG B 386 " pdb=" N LEU B 387 " pdb=" CA LEU B 387 " ideal model delta harmonic sigma weight residual 180.00 162.11 17.89 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 6195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1406 0.057 - 0.114: 167 0.114 - 0.172: 25 0.172 - 0.229: 0 0.229 - 0.286: 7 Chirality restraints: 1605 Sorted by residual: chirality pdb=" C2' ATP B 601 " pdb=" C1' ATP B 601 " pdb=" C3' ATP B 601 " pdb=" O2' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C3' ATP A 701 " pdb=" C2' ATP A 701 " pdb=" C4' ATP A 701 " pdb=" O3' ATP A 701 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB ILE A 253 " pdb=" CA ILE A 253 " pdb=" CG1 ILE A 253 " pdb=" CG2 ILE A 253 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 1602 not shown) Planarity restraints: 1780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 493 " -0.178 9.50e-02 1.11e+02 8.01e-02 4.20e+00 pdb=" NE ARG A 493 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 493 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 493 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 493 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 172 " 0.008 2.00e-02 2.50e+03 1.50e-02 2.25e+00 pdb=" C ILE B 172 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE B 172 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE B 173 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 118 " -0.024 5.00e-02 4.00e+02 3.56e-02 2.02e+00 pdb=" N PRO C 119 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO C 119 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 119 " -0.020 5.00e-02 4.00e+02 ... (remaining 1777 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2967 2.82 - 3.34: 10411 3.34 - 3.86: 16949 3.86 - 4.38: 20579 4.38 - 4.90: 35023 Nonbonded interactions: 85929 Sorted by model distance: nonbonded pdb=" O2' ATP B 601 " pdb=" O3' ATP B 601 " model vdw 2.303 2.432 nonbonded pdb=" O2' ATP A 701 " pdb=" O3' ATP A 701 " model vdw 2.323 2.432 nonbonded pdb=" O ASP A 411 " pdb=" OD1 ASP A 411 " model vdw 2.324 3.040 nonbonded pdb=" O LEU B 102 " pdb=" OH TYR B 110 " model vdw 2.421 3.040 nonbonded pdb=" OD1 ASP B 440 " pdb=" OE1 GLU B 442 " model vdw 2.430 3.040 ... (remaining 85924 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: 2.080 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.230 Find NCS groups from input model: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 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 : 0.004 0.035 10385 Z= 0.174 Angle : 0.586 7.973 14093 Z= 0.313 Chirality : 0.043 0.286 1605 Planarity : 0.005 0.080 1780 Dihedral : 13.137 85.505 3852 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.23), residues: 1273 helix: 0.84 (0.18), residues: 775 sheet: -0.99 (0.44), residues: 115 loop : -1.32 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 493 TYR 0.012 0.001 TYR A 202 PHE 0.016 0.001 PHE A 296 TRP 0.015 0.001 TRP A 256 HIS 0.006 0.001 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00384 (10383) covalent geometry : angle 0.58620 (14089) SS BOND : bond 0.00369 ( 2) SS BOND : angle 1.05594 ( 4) hydrogen bonds : bond 0.11070 ( 650) hydrogen bonds : angle 5.30388 ( 1881) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.411 Fit side-chains REVERT: A 26 ARG cc_start: 0.6832 (tpp80) cc_final: 0.5508 (ptt-90) REVERT: A 199 ARG cc_start: 0.7425 (tpt-90) cc_final: 0.6608 (ttm-80) REVERT: A 218 GLU cc_start: 0.7828 (tp30) cc_final: 0.7535 (tt0) REVERT: A 309 ASP cc_start: 0.7830 (t0) cc_final: 0.7138 (m-30) REVERT: A 464 GLU cc_start: 0.7852 (pp20) cc_final: 0.7159 (mp0) REVERT: A 477 GLU cc_start: 0.7959 (tt0) cc_final: 0.7577 (pt0) REVERT: A 534 LYS cc_start: 0.7454 (tttt) cc_final: 0.7093 (ttpp) REVERT: B 185 ARG cc_start: 0.7116 (ttp-110) cc_final: 0.6688 (ttp80) REVERT: B 319 LYS cc_start: 0.8436 (mmmm) cc_final: 0.7880 (mttt) REVERT: B 347 LYS cc_start: 0.8464 (ttmt) cc_final: 0.7957 (ttmm) REVERT: B 462 LYS cc_start: 0.8063 (mtpp) cc_final: 0.7520 (mtpt) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1353 time to fit residues: 31.3050 Evaluate side-chains 146 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS A 99 GLN A 217 GLN B 287 GLN B 524 GLN C 74 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.174207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.145398 restraints weight = 11865.383| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.68 r_work: 0.3537 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10385 Z= 0.154 Angle : 0.584 9.567 14093 Z= 0.293 Chirality : 0.041 0.149 1605 Planarity : 0.004 0.041 1780 Dihedral : 6.485 65.550 1501 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.86 % Allowed : 6.59 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.23), residues: 1273 helix: 1.04 (0.18), residues: 801 sheet: -0.49 (0.46), residues: 122 loop : -1.25 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 127 TYR 0.026 0.001 TYR A 202 PHE 0.020 0.002 PHE A 296 TRP 0.017 0.001 TRP B 541 HIS 0.004 0.001 HIS B 531 Details of bonding type rmsd covalent geometry : bond 0.00355 (10383) covalent geometry : angle 0.58390 (14089) SS BOND : bond 0.00186 ( 2) SS BOND : angle 0.64598 ( 4) hydrogen bonds : bond 0.04123 ( 650) hydrogen bonds : angle 4.40236 ( 1881) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 0.390 Fit side-chains REVERT: A 26 ARG cc_start: 0.6925 (tpp80) cc_final: 0.5507 (ptt-90) REVERT: A 199 ARG cc_start: 0.7457 (tpt-90) cc_final: 0.6669 (ttm-80) REVERT: A 309 ASP cc_start: 0.7878 (t0) cc_final: 0.7304 (m-30) REVERT: A 464 GLU cc_start: 0.7748 (pp20) cc_final: 0.7206 (mp0) REVERT: A 534 LYS cc_start: 0.7372 (tttt) cc_final: 0.7105 (ttpp) REVERT: A 536 LEU cc_start: 0.8382 (pp) cc_final: 0.7898 (tt) REVERT: B 14 TRP cc_start: 0.6655 (t-100) cc_final: 0.6314 (t-100) REVERT: B 58 PHE cc_start: 0.6985 (p90) cc_final: 0.6664 (p90) REVERT: B 185 ARG cc_start: 0.7328 (ttp-110) cc_final: 0.7012 (ttp80) REVERT: B 251 PHE cc_start: 0.6687 (t80) cc_final: 0.6483 (t80) REVERT: B 319 LYS cc_start: 0.8557 (mmmm) cc_final: 0.8095 (mttt) REVERT: B 347 LYS cc_start: 0.8732 (ttmt) cc_final: 0.8500 (ttmm) REVERT: B 462 LYS cc_start: 0.8116 (mtpp) cc_final: 0.7687 (mtpt) outliers start: 9 outliers final: 5 residues processed: 165 average time/residue: 0.1430 time to fit residues: 30.9937 Evaluate side-chains 154 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 149 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 473 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 81 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 40 optimal weight: 0.0970 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 89 optimal weight: 0.0970 chunk 100 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 HIS ** B 303 GLN ** 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 = 0.3955 r_free = 0.3955 target = 0.174407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.145975 restraints weight = 11901.548| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.63 r_work: 0.3545 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10385 Z= 0.138 Angle : 0.550 9.731 14093 Z= 0.274 Chirality : 0.039 0.137 1605 Planarity : 0.004 0.037 1780 Dihedral : 6.353 66.593 1501 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.62 % Allowed : 8.21 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.23), residues: 1273 helix: 1.22 (0.18), residues: 801 sheet: -0.11 (0.46), residues: 123 loop : -1.21 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 127 TYR 0.018 0.001 TYR A 202 PHE 0.016 0.001 PHE B 38 TRP 0.015 0.001 TRP B 541 HIS 0.006 0.001 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00315 (10383) covalent geometry : angle 0.55016 (14089) SS BOND : bond 0.00183 ( 2) SS BOND : angle 0.41849 ( 4) hydrogen bonds : bond 0.03856 ( 650) hydrogen bonds : angle 4.23791 ( 1881) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.426 Fit side-chains REVERT: A 26 ARG cc_start: 0.6861 (tpp80) cc_final: 0.5494 (ptt-90) REVERT: A 199 ARG cc_start: 0.7354 (tpt-90) cc_final: 0.6601 (ttm-80) REVERT: A 309 ASP cc_start: 0.7820 (t0) cc_final: 0.7336 (m-30) REVERT: A 425 ARG cc_start: 0.7218 (mpp-170) cc_final: 0.6807 (mpp-170) REVERT: A 464 GLU cc_start: 0.7806 (pp20) cc_final: 0.7288 (mp0) REVERT: A 534 LYS cc_start: 0.7271 (tttt) cc_final: 0.7025 (ttpp) REVERT: A 536 LEU cc_start: 0.8342 (pp) cc_final: 0.7790 (tt) REVERT: B 14 TRP cc_start: 0.6648 (t-100) cc_final: 0.6375 (t-100) REVERT: B 58 PHE cc_start: 0.7128 (p90) cc_final: 0.6907 (p90) REVERT: B 306 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7507 (mp) REVERT: B 319 LYS cc_start: 0.8534 (mmmm) cc_final: 0.8091 (mttt) REVERT: B 462 LYS cc_start: 0.8128 (mtpp) cc_final: 0.7854 (mtmt) REVERT: B 470 GLU cc_start: 0.8499 (mt-10) cc_final: 0.7489 (mp0) outliers start: 17 outliers final: 11 residues processed: 164 average time/residue: 0.1378 time to fit residues: 29.9169 Evaluate side-chains 161 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 569 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 123 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 89 optimal weight: 0.2980 chunk 34 optimal weight: 3.9990 chunk 96 optimal weight: 0.0870 chunk 71 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.174480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.147260 restraints weight = 12115.244| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.78 r_work: 0.3550 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10385 Z= 0.138 Angle : 0.537 9.615 14093 Z= 0.267 Chirality : 0.039 0.140 1605 Planarity : 0.004 0.040 1780 Dihedral : 6.330 69.068 1501 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.72 % Allowed : 9.74 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.23), residues: 1273 helix: 1.30 (0.18), residues: 798 sheet: -0.22 (0.45), residues: 116 loop : -1.13 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 482 TYR 0.017 0.001 TYR A 202 PHE 0.016 0.001 PHE B 38 TRP 0.016 0.001 TRP B 541 HIS 0.006 0.001 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00318 (10383) covalent geometry : angle 0.53677 (14089) SS BOND : bond 0.00137 ( 2) SS BOND : angle 0.40110 ( 4) hydrogen bonds : bond 0.03736 ( 650) hydrogen bonds : angle 4.12844 ( 1881) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.430 Fit side-chains REVERT: A 26 ARG cc_start: 0.7165 (tpp80) cc_final: 0.5818 (ptt-90) REVERT: A 199 ARG cc_start: 0.7493 (tpt-90) cc_final: 0.6870 (ttm-80) REVERT: A 309 ASP cc_start: 0.7955 (t0) cc_final: 0.7625 (m-30) REVERT: A 464 GLU cc_start: 0.7816 (pp20) cc_final: 0.7590 (mp0) REVERT: B 58 PHE cc_start: 0.6736 (p90) cc_final: 0.6505 (p90) REVERT: B 306 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7804 (mp) REVERT: B 319 LYS cc_start: 0.8485 (mmmm) cc_final: 0.8090 (mttt) REVERT: B 347 LYS cc_start: 0.8749 (ttmt) cc_final: 0.8419 (tttm) REVERT: B 470 GLU cc_start: 0.8572 (mt-10) cc_final: 0.7717 (mp0) REVERT: B 537 ARG cc_start: 0.8234 (mtm-85) cc_final: 0.7996 (mtm-85) REVERT: B 552 GLU cc_start: 0.8664 (tt0) cc_final: 0.8427 (tt0) outliers start: 18 outliers final: 14 residues processed: 168 average time/residue: 0.1437 time to fit residues: 31.8111 Evaluate side-chains 166 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain C residue 71 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 29 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 102 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN A 302 GLN B 53 GLN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.170691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.144014 restraints weight = 12088.635| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.58 r_work: 0.3505 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 10385 Z= 0.257 Angle : 0.658 9.776 14093 Z= 0.326 Chirality : 0.043 0.173 1605 Planarity : 0.005 0.039 1780 Dihedral : 6.803 61.211 1501 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.10 % Allowed : 10.89 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.23), residues: 1273 helix: 0.88 (0.18), residues: 796 sheet: -0.42 (0.45), residues: 116 loop : -1.29 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 127 TYR 0.026 0.002 TYR A 202 PHE 0.020 0.002 PHE A 296 TRP 0.025 0.002 TRP B 541 HIS 0.008 0.001 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00616 (10383) covalent geometry : angle 0.65830 (14089) SS BOND : bond 0.00309 ( 2) SS BOND : angle 0.58251 ( 4) hydrogen bonds : bond 0.04479 ( 650) hydrogen bonds : angle 4.42174 ( 1881) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.380 Fit side-chains REVERT: A 26 ARG cc_start: 0.7089 (tpp80) cc_final: 0.5829 (ptt-90) REVERT: A 199 ARG cc_start: 0.7579 (tpt-90) cc_final: 0.6833 (ttm-80) REVERT: A 309 ASP cc_start: 0.7924 (t0) cc_final: 0.7638 (m-30) REVERT: A 464 GLU cc_start: 0.7807 (pp20) cc_final: 0.7477 (mp0) REVERT: B 185 ARG cc_start: 0.7646 (ttp-110) cc_final: 0.7371 (ttp80) REVERT: B 306 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8041 (mp) REVERT: B 347 LYS cc_start: 0.8730 (ttmt) cc_final: 0.8331 (tttm) REVERT: B 470 GLU cc_start: 0.8571 (mt-10) cc_final: 0.7416 (mp0) outliers start: 22 outliers final: 17 residues processed: 165 average time/residue: 0.1268 time to fit residues: 28.1682 Evaluate side-chains 169 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 569 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 6 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 89 optimal weight: 0.4980 chunk 97 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 302 GLN B 53 GLN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.173262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.145768 restraints weight = 12064.632| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.55 r_work: 0.3530 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10385 Z= 0.138 Angle : 0.552 10.474 14093 Z= 0.273 Chirality : 0.039 0.135 1605 Planarity : 0.004 0.035 1780 Dihedral : 6.491 67.483 1501 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.39 % Allowed : 11.65 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.23), residues: 1273 helix: 1.17 (0.18), residues: 799 sheet: -0.36 (0.45), residues: 116 loop : -1.19 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 482 TYR 0.016 0.001 TYR A 202 PHE 0.015 0.001 PHE A 296 TRP 0.013 0.001 TRP A 193 HIS 0.003 0.001 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00315 (10383) covalent geometry : angle 0.55212 (14089) SS BOND : bond 0.00121 ( 2) SS BOND : angle 0.36083 ( 4) hydrogen bonds : bond 0.03751 ( 650) hydrogen bonds : angle 4.18602 ( 1881) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.7108 (tpp80) cc_final: 0.5845 (ptt-90) REVERT: A 199 ARG cc_start: 0.7556 (tpt-90) cc_final: 0.6822 (ttm-80) REVERT: A 309 ASP cc_start: 0.7866 (t0) cc_final: 0.7576 (m-30) REVERT: A 414 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7255 (ptt180) REVERT: A 464 GLU cc_start: 0.7793 (pp20) cc_final: 0.7524 (mp0) REVERT: A 536 LEU cc_start: 0.8374 (pp) cc_final: 0.7854 (tt) REVERT: B 306 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7840 (mp) REVERT: B 347 LYS cc_start: 0.8745 (ttmt) cc_final: 0.8401 (tttm) outliers start: 25 outliers final: 18 residues processed: 174 average time/residue: 0.1297 time to fit residues: 29.9977 Evaluate side-chains 176 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 123 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 115 optimal weight: 0.3980 chunk 118 optimal weight: 3.9990 chunk 41 optimal weight: 0.0370 chunk 64 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN ** B 303 GLN ** 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 = 0.3952 r_free = 0.3952 target = 0.174185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.145720 restraints weight = 11856.328| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.84 r_work: 0.3540 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10385 Z= 0.122 Angle : 0.525 9.637 14093 Z= 0.261 Chirality : 0.038 0.136 1605 Planarity : 0.004 0.034 1780 Dihedral : 6.321 73.408 1501 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.39 % Allowed : 12.70 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.24), residues: 1273 helix: 1.36 (0.18), residues: 799 sheet: -0.32 (0.45), residues: 116 loop : -1.03 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 482 TYR 0.015 0.001 TYR A 202 PHE 0.015 0.001 PHE B 38 TRP 0.013 0.001 TRP B 446 HIS 0.003 0.001 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00274 (10383) covalent geometry : angle 0.52464 (14089) SS BOND : bond 0.00128 ( 2) SS BOND : angle 0.33533 ( 4) hydrogen bonds : bond 0.03557 ( 650) hydrogen bonds : angle 4.08352 ( 1881) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6822 (tpp80) cc_final: 0.5484 (ptt-90) REVERT: A 199 ARG cc_start: 0.7352 (tpt-90) cc_final: 0.6459 (ttm-80) REVERT: A 309 ASP cc_start: 0.7770 (t0) cc_final: 0.7265 (m-30) REVERT: A 414 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.7036 (ptt180) REVERT: A 464 GLU cc_start: 0.7755 (pp20) cc_final: 0.7242 (mp0) REVERT: A 536 LEU cc_start: 0.8270 (pp) cc_final: 0.7790 (tt) REVERT: B 185 ARG cc_start: 0.7167 (ttp-110) cc_final: 0.6945 (ttp80) REVERT: B 306 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7424 (mp) REVERT: B 347 LYS cc_start: 0.8840 (ttmt) cc_final: 0.8325 (tttm) outliers start: 25 outliers final: 17 residues processed: 172 average time/residue: 0.1199 time to fit residues: 27.5188 Evaluate side-chains 173 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain C residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 17 optimal weight: 0.0270 chunk 113 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN B 123 ASN ** B 303 GLN ** 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 = 0.3961 r_free = 0.3961 target = 0.175172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.145814 restraints weight = 11807.086| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.98 r_work: 0.3534 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10385 Z= 0.116 Angle : 0.517 9.255 14093 Z= 0.256 Chirality : 0.038 0.136 1605 Planarity : 0.003 0.033 1780 Dihedral : 6.265 79.439 1501 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.10 % Allowed : 13.85 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.24), residues: 1273 helix: 1.46 (0.18), residues: 799 sheet: -0.27 (0.44), residues: 116 loop : -0.93 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 482 TYR 0.013 0.001 TYR A 202 PHE 0.015 0.001 PHE B 38 TRP 0.013 0.001 TRP B 446 HIS 0.003 0.001 HIS B 538 Details of bonding type rmsd covalent geometry : bond 0.00258 (10383) covalent geometry : angle 0.51732 (14089) SS BOND : bond 0.00124 ( 2) SS BOND : angle 0.38504 ( 4) hydrogen bonds : bond 0.03487 ( 650) hydrogen bonds : angle 4.03922 ( 1881) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6761 (tpp80) cc_final: 0.5391 (ptt-90) REVERT: A 199 ARG cc_start: 0.7276 (tpt-90) cc_final: 0.6370 (ttm-80) REVERT: A 309 ASP cc_start: 0.7670 (t0) cc_final: 0.7134 (m-30) REVERT: A 414 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.6997 (ptt180) REVERT: A 464 GLU cc_start: 0.7743 (pp20) cc_final: 0.7177 (mp0) REVERT: B 117 ASP cc_start: 0.7409 (t0) cc_final: 0.7191 (t0) REVERT: B 306 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7424 (mp) REVERT: B 347 LYS cc_start: 0.8843 (ttmt) cc_final: 0.8307 (tttm) REVERT: B 569 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.6872 (ptp) outliers start: 22 outliers final: 16 residues processed: 173 average time/residue: 0.1340 time to fit residues: 30.8076 Evaluate side-chains 172 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 28 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 90 optimal weight: 0.4980 chunk 111 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN ** B 303 GLN ** 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 = 0.3942 r_free = 0.3942 target = 0.173484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.144348 restraints weight = 11837.452| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.96 r_work: 0.3528 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10385 Z= 0.132 Angle : 0.534 9.193 14093 Z= 0.263 Chirality : 0.039 0.136 1605 Planarity : 0.004 0.033 1780 Dihedral : 6.325 82.415 1501 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.10 % Allowed : 13.66 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.24), residues: 1273 helix: 1.48 (0.18), residues: 793 sheet: -0.32 (0.44), residues: 116 loop : -0.94 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 482 TYR 0.014 0.001 TYR A 202 PHE 0.014 0.001 PHE B 38 TRP 0.012 0.001 TRP A 193 HIS 0.003 0.001 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00303 (10383) covalent geometry : angle 0.53375 (14089) SS BOND : bond 0.00166 ( 2) SS BOND : angle 0.44724 ( 4) hydrogen bonds : bond 0.03573 ( 650) hydrogen bonds : angle 4.07389 ( 1881) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6758 (tpp80) cc_final: 0.5395 (ptt-90) REVERT: A 199 ARG cc_start: 0.7245 (tpt-90) cc_final: 0.6360 (ttm-80) REVERT: A 309 ASP cc_start: 0.7682 (t0) cc_final: 0.7162 (m-30) REVERT: A 414 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.6965 (ptt180) REVERT: A 464 GLU cc_start: 0.7713 (pp20) cc_final: 0.7154 (mp0) REVERT: A 536 LEU cc_start: 0.8247 (pp) cc_final: 0.7774 (tt) REVERT: B 117 ASP cc_start: 0.7415 (t0) cc_final: 0.7198 (t0) REVERT: B 253 MET cc_start: 0.6950 (ttm) cc_final: 0.6626 (ttp) REVERT: B 306 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7480 (mp) REVERT: B 347 LYS cc_start: 0.8846 (ttmt) cc_final: 0.8299 (tttm) outliers start: 22 outliers final: 19 residues processed: 165 average time/residue: 0.1181 time to fit residues: 26.4090 Evaluate side-chains 173 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 44 optimal weight: 0.6980 chunk 17 optimal weight: 0.0980 chunk 117 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 0.0870 chunk 15 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN ** B 303 GLN ** 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 = 0.3963 r_free = 0.3963 target = 0.175673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.145983 restraints weight = 11673.840| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.90 r_work: 0.3547 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10385 Z= 0.117 Angle : 0.521 9.346 14093 Z= 0.257 Chirality : 0.038 0.136 1605 Planarity : 0.003 0.033 1780 Dihedral : 6.285 88.375 1501 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.10 % Allowed : 13.94 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.24), residues: 1273 helix: 1.57 (0.18), residues: 793 sheet: -0.31 (0.44), residues: 116 loop : -0.90 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 482 TYR 0.013 0.001 TYR A 202 PHE 0.015 0.001 PHE B 38 TRP 0.013 0.001 TRP A 193 HIS 0.003 0.001 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00260 (10383) covalent geometry : angle 0.52067 (14089) SS BOND : bond 0.00136 ( 2) SS BOND : angle 0.37447 ( 4) hydrogen bonds : bond 0.03452 ( 650) hydrogen bonds : angle 4.02945 ( 1881) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6646 (tpp80) cc_final: 0.5290 (ptt-90) REVERT: A 199 ARG cc_start: 0.7162 (tpt-90) cc_final: 0.6247 (ttm-80) REVERT: A 309 ASP cc_start: 0.7564 (t0) cc_final: 0.7016 (m-30) REVERT: A 414 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.6859 (ptt180) REVERT: A 464 GLU cc_start: 0.7646 (pp20) cc_final: 0.7036 (mp0) REVERT: A 533 GLU cc_start: 0.7488 (mm-30) cc_final: 0.6887 (mm-30) REVERT: A 536 LEU cc_start: 0.8142 (pp) cc_final: 0.7786 (tp) REVERT: B 23 ARG cc_start: 0.7307 (mtp85) cc_final: 0.6974 (mtm-85) REVERT: B 117 ASP cc_start: 0.7363 (t0) cc_final: 0.7132 (t0) REVERT: B 306 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7246 (mp) REVERT: B 347 LYS cc_start: 0.8816 (ttmt) cc_final: 0.8225 (tttm) REVERT: B 569 MET cc_start: 0.6919 (OUTLIER) cc_final: 0.6697 (ptp) outliers start: 22 outliers final: 19 residues processed: 165 average time/residue: 0.1336 time to fit residues: 29.2990 Evaluate side-chains 173 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 49 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 28 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 102 optimal weight: 0.0970 chunk 44 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.175172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.144900 restraints weight = 11796.571| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.16 r_work: 0.3521 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10385 Z= 0.135 Angle : 0.544 10.298 14093 Z= 0.268 Chirality : 0.039 0.173 1605 Planarity : 0.004 0.036 1780 Dihedral : 6.342 88.974 1501 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.20 % Allowed : 14.04 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.23), residues: 1273 helix: 1.49 (0.18), residues: 793 sheet: -0.31 (0.44), residues: 116 loop : -0.94 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 301 TYR 0.014 0.001 TYR A 202 PHE 0.017 0.001 PHE B 38 TRP 0.013 0.001 TRP A 193 HIS 0.003 0.001 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00312 (10383) covalent geometry : angle 0.54433 (14089) SS BOND : bond 0.00172 ( 2) SS BOND : angle 0.45741 ( 4) hydrogen bonds : bond 0.03583 ( 650) hydrogen bonds : angle 4.05743 ( 1881) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2810.24 seconds wall clock time: 48 minutes 45.14 seconds (2925.14 seconds total)