Starting phenix.real_space_refine on Fri Dec 27 18:57:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wk6_32560/12_2024/7wk6_32560.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wk6_32560/12_2024/7wk6_32560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wk6_32560/12_2024/7wk6_32560.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wk6_32560/12_2024/7wk6_32560.map" model { file = "/net/cci-nas-00/data/ceres_data/7wk6_32560/12_2024/7wk6_32560.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wk6_32560/12_2024/7wk6_32560.cif" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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 37 5.16 5 C 4119 2.51 5 N 1069 2.21 5 O 1203 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6428 Number of models: 1 Model: "" Number of chains: 2 Chain: "E" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Time building chain proxies: 4.52, per 1000 atoms: 0.70 Number of scatterers: 6428 At special positions: 0 Unit cell: (76.51, 99.463, 113.672, 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 37 16.00 O 1203 8.00 N 1069 7.00 C 4119 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.06 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.01 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.02 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: 1.31 Conformation dependent library (CDL) restraints added in 880.7 milliseconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 47.7% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'E' and resid 349 through 353 removed outlier: 4.154A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 372 removed outlier: 4.096A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'A' and resid 20 through 49 removed outlier: 3.770A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 removed outlier: 4.025A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP A 67 " --> pdb=" O ASN A 63 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS A 68 " --> pdb=" O ASN A 64 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TRP A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 90 through 98 Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.680A pdb=" N ARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 167 removed outlier: 3.662A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 176 through 192 removed outlier: 3.707A pdb=" N GLU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 219 through 231 removed outlier: 4.243A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 248 removed outlier: 3.508A pdb=" N ARG A 245 " --> pdb=" O HIS A 241 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.577A pdb=" N VAL A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 316 removed outlier: 3.961A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.637A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 383 removed outlier: 3.956A pdb=" N THR A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.463A pdb=" N ALA A 387 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 400 through 412 removed outlier: 3.549A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 412 " --> pdb=" O MET A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 434 through 447 removed outlier: 3.532A pdb=" N PHE A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 465 removed outlier: 4.211A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS A 465 " --> pdb=" O TRP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 473 Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.627A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 removed outlier: 3.817A pdb=" N SER A 502 " --> pdb=" O ASP A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.707A pdb=" N ASN A 508 " --> pdb=" O PHE A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 523 removed outlier: 3.831A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 533 Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.755A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.615A pdb=" N GLN A 552 " --> pdb=" O THR A 548 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 removed outlier: 3.574A pdb=" N GLU A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.514A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.810A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL E 433 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS E 378 " --> pdb=" O VAL E 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.158A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 352 removed outlier: 5.396A pdb=" N ALA A 348 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU A 359 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASP A 350 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG A 357 " --> pdb=" O ASP A 350 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 352 " --> pdb=" O ASP A 355 " (cutoff:3.500A) 200 hydrogen bonds defined for protein. 555 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: 1.74 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1106 1.32 - 1.45: 1931 1.45 - 1.58: 3516 1.58 - 1.71: 0 1.71 - 1.84: 58 Bond restraints: 6611 Sorted by residual: bond pdb=" CA SER E 366 " pdb=" C SER E 366 " ideal model delta sigma weight residual 1.523 1.436 0.087 1.30e-02 5.92e+03 4.52e+01 bond pdb=" CA LYS A 31 " pdb=" C LYS A 31 " ideal model delta sigma weight residual 1.524 1.454 0.070 1.26e-02 6.30e+03 3.09e+01 bond pdb=" CA TYR E 365 " pdb=" C TYR E 365 " ideal model delta sigma weight residual 1.522 1.449 0.073 1.41e-02 5.03e+03 2.67e+01 bond pdb=" CA ASN A 33 " pdb=" C ASN A 33 " ideal model delta sigma weight residual 1.524 1.460 0.064 1.27e-02 6.20e+03 2.51e+01 bond pdb=" CA GLU A 35 " pdb=" CB GLU A 35 " ideal model delta sigma weight residual 1.528 1.452 0.077 1.59e-02 3.96e+03 2.33e+01 ... (remaining 6606 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 8820 3.26 - 6.52: 139 6.52 - 9.78: 20 9.78 - 13.05: 4 13.05 - 16.31: 3 Bond angle restraints: 8986 Sorted by residual: angle pdb=" N CYS A 141 " pdb=" CA CYS A 141 " pdb=" C CYS A 141 " ideal model delta sigma weight residual 109.29 122.96 -13.67 1.41e+00 5.03e-01 9.40e+01 angle pdb=" N CYS E 488 " pdb=" CA CYS E 488 " pdb=" C CYS E 488 " ideal model delta sigma weight residual 107.20 90.89 16.31 1.70e+00 3.46e-01 9.20e+01 angle pdb=" N LEU A 142 " pdb=" CA LEU A 142 " pdb=" C LEU A 142 " ideal model delta sigma weight residual 109.50 124.40 -14.90 1.58e+00 4.01e-01 8.89e+01 angle pdb=" N LEU E 371 " pdb=" CA LEU E 371 " pdb=" C LEU E 371 " ideal model delta sigma weight residual 113.20 103.39 9.81 1.21e+00 6.83e-01 6.57e+01 angle pdb=" N PRO E 373 " pdb=" CA PRO E 373 " pdb=" C PRO E 373 " ideal model delta sigma weight residual 113.53 102.47 11.06 1.39e+00 5.18e-01 6.33e+01 ... (remaining 8981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.99: 3458 18.99 - 37.99: 372 37.99 - 56.98: 59 56.98 - 75.97: 12 75.97 - 94.97: 4 Dihedral angle restraints: 3905 sinusoidal: 1579 harmonic: 2326 Sorted by residual: dihedral pdb=" CA GLU A 145 " pdb=" C GLU A 145 " pdb=" N PRO A 146 " pdb=" CA PRO A 146 " ideal model delta harmonic sigma weight residual -180.00 -85.03 -94.97 0 5.00e+00 4.00e-02 3.61e+02 dihedral pdb=" CB CYS E 391 " pdb=" SG CYS E 391 " pdb=" SG CYS E 525 " pdb=" CB CYS E 525 " ideal model delta sinusoidal sigma weight residual 93.00 17.56 75.44 1 1.00e+01 1.00e-02 7.19e+01 dihedral pdb=" CA CYS A 344 " pdb=" C CYS A 344 " pdb=" N HIS A 345 " pdb=" CA HIS A 345 " ideal model delta harmonic sigma weight residual 180.00 153.20 26.80 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 3902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 846 0.099 - 0.198: 75 0.198 - 0.297: 11 0.297 - 0.395: 3 0.395 - 0.494: 4 Chirality restraints: 939 Sorted by residual: chirality pdb=" CA LYS A 353 " pdb=" N LYS A 353 " pdb=" C LYS A 353 " pdb=" CB LYS A 353 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" CA PHE E 375 " pdb=" N PHE E 375 " pdb=" C PHE E 375 " pdb=" CB PHE E 375 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" CA ALA E 372 " pdb=" N ALA E 372 " pdb=" C ALA E 372 " pdb=" CB ALA E 372 " both_signs ideal model delta sigma weight residual False 2.48 2.02 0.47 2.00e-01 2.50e+01 5.45e+00 ... (remaining 936 not shown) Planarity restraints: 1166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 368 " -0.023 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C LEU E 368 " 0.077 2.00e-02 2.50e+03 pdb=" O LEU E 368 " -0.029 2.00e-02 2.50e+03 pdb=" N TYR E 369 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 500 " 0.021 2.00e-02 2.50e+03 4.21e-02 1.77e+01 pdb=" C THR E 500 " -0.073 2.00e-02 2.50e+03 pdb=" O THR E 500 " 0.027 2.00e-02 2.50e+03 pdb=" N TYR E 501 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 367 " 0.019 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C VAL E 367 " -0.064 2.00e-02 2.50e+03 pdb=" O VAL E 367 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU E 368 " 0.022 2.00e-02 2.50e+03 ... (remaining 1163 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2240 2.84 - 3.36: 5639 3.36 - 3.87: 10703 3.87 - 4.39: 12421 4.39 - 4.90: 20478 Nonbonded interactions: 51481 Sorted by model distance: nonbonded pdb=" O THR A 449 " pdb=" OG1 THR A 453 " model vdw 2.328 3.040 nonbonded pdb=" O SER A 254 " pdb=" OG SER A 254 " model vdw 2.333 3.040 nonbonded pdb=" OD1 ASP A 431 " pdb=" OG1 THR A 434 " model vdw 2.337 3.040 nonbonded pdb=" O ASN A 121 " pdb=" OG1 THR A 125 " model vdw 2.351 3.040 nonbonded pdb=" OG1 THR E 500 " pdb=" OH TYR A 41 " model vdw 2.371 3.040 ... (remaining 51476 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.640 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.150 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 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 : 0.008 0.087 6611 Z= 0.485 Angle : 1.068 16.306 8986 Z= 0.647 Chirality : 0.071 0.494 939 Planarity : 0.007 0.062 1166 Dihedral : 15.403 94.965 2390 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.70 % Favored : 94.92 % Rotamer: Outliers : 0.57 % Allowed : 7.90 % Favored : 91.52 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.05 (0.22), residues: 787 helix: -4.47 (0.12), residues: 325 sheet: -2.25 (0.93), residues: 35 loop : -2.50 (0.25), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 478 HIS 0.018 0.002 HIS A 34 PHE 0.020 0.002 PHE A 32 TYR 0.016 0.002 TYR A 183 ARG 0.006 0.001 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 250 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 358 ILE cc_start: 0.8796 (mt) cc_final: 0.8589 (mt) REVERT: E 422 ASN cc_start: 0.8156 (m110) cc_final: 0.7906 (m110) REVERT: E 442 ASP cc_start: 0.8719 (t70) cc_final: 0.8280 (t0) REVERT: E 461 LEU cc_start: 0.8407 (mt) cc_final: 0.8194 (mp) REVERT: E 467 ASP cc_start: 0.7953 (p0) cc_final: 0.7526 (p0) REVERT: E 468 ILE cc_start: 0.9020 (pt) cc_final: 0.8803 (pt) REVERT: E 471 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7783 (tp30) REVERT: E 474 GLN cc_start: 0.7884 (tt0) cc_final: 0.7632 (tt0) REVERT: E 492 LEU cc_start: 0.8677 (mt) cc_final: 0.8358 (mt) REVERT: E 494 SER cc_start: 0.9040 (m) cc_final: 0.8690 (p) REVERT: A 22 GLU cc_start: 0.7459 (tp30) cc_final: 0.7256 (tp30) REVERT: A 26 LYS cc_start: 0.8012 (mttt) cc_final: 0.7757 (mmmm) REVERT: A 47 SER cc_start: 0.8583 (t) cc_final: 0.8333 (t) REVERT: A 55 THR cc_start: 0.7870 (m) cc_final: 0.7165 (p) REVERT: A 64 ASN cc_start: 0.8703 (t0) cc_final: 0.8503 (t0) REVERT: A 101 GLN cc_start: 0.8013 (tt0) cc_final: 0.7701 (mt0) REVERT: A 144 LEU cc_start: 0.7666 (tp) cc_final: 0.7360 (tp) REVERT: A 157 ASP cc_start: 0.7950 (m-30) cc_final: 0.7695 (t70) REVERT: A 161 ARG cc_start: 0.8378 (mtp180) cc_final: 0.8063 (mmm-85) REVERT: A 163 TRP cc_start: 0.7499 (t60) cc_final: 0.7196 (t60) REVERT: A 168 TRP cc_start: 0.8242 (t-100) cc_final: 0.7753 (t-100) REVERT: A 181 GLU cc_start: 0.7868 (tp30) cc_final: 0.7609 (tp30) REVERT: A 215 TYR cc_start: 0.8248 (m-80) cc_final: 0.7927 (m-80) REVERT: A 219 ARG cc_start: 0.7908 (mtm-85) cc_final: 0.7514 (mtm-85) REVERT: A 227 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7521 (mm-30) REVERT: A 265 HIS cc_start: 0.8826 (p-80) cc_final: 0.7984 (p-80) REVERT: A 271 TRP cc_start: 0.4633 (t60) cc_final: 0.4293 (t60) REVERT: A 277 ASN cc_start: 0.8575 (m-40) cc_final: 0.8284 (m-40) REVERT: A 302 TRP cc_start: 0.8349 (m-10) cc_final: 0.7970 (m-10) REVERT: A 310 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7629 (mm-30) REVERT: A 313 LYS cc_start: 0.8259 (mttt) cc_final: 0.7521 (mtpt) REVERT: A 323 MET cc_start: 0.8182 (mmm) cc_final: 0.7902 (mmm) REVERT: A 332 MET cc_start: 0.7968 (ttp) cc_final: 0.7329 (tmm) REVERT: A 341 LYS cc_start: 0.7902 (tptt) cc_final: 0.7603 (tptt) REVERT: A 363 LYS cc_start: 0.8480 (mtmm) cc_final: 0.7947 (mppt) REVERT: A 408 MET cc_start: 0.7901 (mmt) cc_final: 0.7489 (mmp) REVERT: A 419 LYS cc_start: 0.8243 (tptp) cc_final: 0.8021 (mttt) REVERT: A 423 LEU cc_start: 0.8754 (mt) cc_final: 0.8226 (mt) REVERT: A 437 ASN cc_start: 0.7487 (m-40) cc_final: 0.7194 (m-40) REVERT: A 459 TRP cc_start: 0.8262 (t60) cc_final: 0.7979 (t60) REVERT: A 462 MET cc_start: 0.7529 (mtm) cc_final: 0.7267 (mtp) REVERT: A 465 LYS cc_start: 0.8708 (mttt) cc_final: 0.8355 (ttmt) REVERT: A 473 TRP cc_start: 0.7532 (t-100) cc_final: 0.6665 (t-100) REVERT: A 475 LYS cc_start: 0.8865 (tppt) cc_final: 0.8636 (tptp) REVERT: A 499 ASP cc_start: 0.7772 (m-30) cc_final: 0.6844 (t0) REVERT: A 500 PRO cc_start: 0.8465 (Cg_endo) cc_final: 0.7806 (Cg_exo) REVERT: A 534 LYS cc_start: 0.8638 (mmtp) cc_final: 0.8341 (mmmm) REVERT: A 579 MET cc_start: 0.8615 (ttp) cc_final: 0.8391 (ttm) REVERT: A 582 ARG cc_start: 0.7412 (tpp80) cc_final: 0.6851 (tpp80) REVERT: A 603 PHE cc_start: 0.7057 (t80) cc_final: 0.6647 (t80) outliers start: 4 outliers final: 3 residues processed: 252 average time/residue: 0.2481 time to fit residues: 77.5408 Evaluate side-chains 227 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 224 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 432 CYS Chi-restraints excluded: chain E residue 483 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.8980 chunk 59 optimal weight: 0.0000 chunk 32 optimal weight: 0.0670 chunk 20 optimal weight: 0.2980 chunk 39 optimal weight: 0.4980 chunk 31 optimal weight: 0.4980 chunk 61 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 overall best weight: 0.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 417 ASN E 477 ASN ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN A 330 ASN A 373 HIS A 417 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6611 Z= 0.198 Angle : 0.622 8.893 8986 Z= 0.324 Chirality : 0.044 0.124 939 Planarity : 0.005 0.036 1166 Dihedral : 5.368 65.531 864 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.05 % Favored : 96.82 % Rotamer: Outliers : 2.44 % Allowed : 16.67 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.26), residues: 787 helix: -3.20 (0.20), residues: 353 sheet: -1.43 (0.93), residues: 33 loop : -1.60 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 478 HIS 0.003 0.001 HIS E 505 PHE 0.011 0.001 PHE E 490 TYR 0.016 0.001 TYR A 158 ARG 0.004 0.000 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 224 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 422 ASN cc_start: 0.8081 (m110) cc_final: 0.7695 (m-40) REVERT: E 442 ASP cc_start: 0.8794 (t70) cc_final: 0.8315 (t0) REVERT: E 465 GLU cc_start: 0.7960 (tt0) cc_final: 0.7737 (tt0) REVERT: E 467 ASP cc_start: 0.7767 (p0) cc_final: 0.7432 (p0) REVERT: E 494 SER cc_start: 0.8841 (m) cc_final: 0.8378 (p) REVERT: A 23 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7324 (mp0) REVERT: A 26 LYS cc_start: 0.8152 (mttt) cc_final: 0.7829 (mmmm) REVERT: A 40 PHE cc_start: 0.8616 (t80) cc_final: 0.8234 (t80) REVERT: A 42 GLN cc_start: 0.8262 (tt0) cc_final: 0.8015 (tt0) REVERT: A 47 SER cc_start: 0.8677 (t) cc_final: 0.8382 (t) REVERT: A 55 THR cc_start: 0.7747 (m) cc_final: 0.7042 (p) REVERT: A 62 MET cc_start: 0.7971 (tmm) cc_final: 0.7182 (tmm) REVERT: A 101 GLN cc_start: 0.7931 (tt0) cc_final: 0.7703 (mt0) REVERT: A 102 GLN cc_start: 0.7954 (pp30) cc_final: 0.7702 (pp30) REVERT: A 126 ILE cc_start: 0.8945 (tp) cc_final: 0.8648 (tt) REVERT: A 142 LEU cc_start: 0.7746 (mt) cc_final: 0.7545 (mt) REVERT: A 144 LEU cc_start: 0.8337 (tp) cc_final: 0.7838 (tp) REVERT: A 157 ASP cc_start: 0.7892 (m-30) cc_final: 0.7642 (t70) REVERT: A 158 TYR cc_start: 0.7390 (t80) cc_final: 0.6892 (t80) REVERT: A 168 TRP cc_start: 0.8247 (t-100) cc_final: 0.7824 (t-100) REVERT: A 182 GLU cc_start: 0.7304 (tm-30) cc_final: 0.6736 (tm-30) REVERT: A 186 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8013 (mp) REVERT: A 209 VAL cc_start: 0.8634 (t) cc_final: 0.8373 (m) REVERT: A 219 ARG cc_start: 0.8140 (mtm-85) cc_final: 0.7817 (mtm-85) REVERT: A 227 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7737 (tp30) REVERT: A 267 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8355 (mm) REVERT: A 271 TRP cc_start: 0.4993 (t60) cc_final: 0.4434 (t60) REVERT: A 299 ASP cc_start: 0.8094 (t0) cc_final: 0.7865 (t0) REVERT: A 313 LYS cc_start: 0.8146 (mttt) cc_final: 0.7653 (mtpt) REVERT: A 325 GLN cc_start: 0.7968 (tp-100) cc_final: 0.7291 (tp-100) REVERT: A 332 MET cc_start: 0.8058 (ttp) cc_final: 0.7545 (tmm) REVERT: A 353 LYS cc_start: 0.8332 (mtpt) cc_final: 0.8128 (mmmt) REVERT: A 368 ASP cc_start: 0.8203 (t0) cc_final: 0.7321 (t0) REVERT: A 429 GLN cc_start: 0.7374 (tp40) cc_final: 0.7062 (tp40) REVERT: A 465 LYS cc_start: 0.8666 (mttt) cc_final: 0.8342 (ttmt) REVERT: A 472 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7537 (mm-40) REVERT: A 475 LYS cc_start: 0.8325 (tppt) cc_final: 0.8085 (tmtt) REVERT: A 499 ASP cc_start: 0.7908 (m-30) cc_final: 0.7095 (t0) REVERT: A 500 PRO cc_start: 0.8584 (Cg_endo) cc_final: 0.8168 (Cg_exo) REVERT: A 504 PHE cc_start: 0.7948 (t80) cc_final: 0.7698 (t80) REVERT: A 574 VAL cc_start: 0.8981 (m) cc_final: 0.8743 (p) REVERT: A 582 ARG cc_start: 0.7453 (tpp80) cc_final: 0.6961 (mpp80) REVERT: A 603 PHE cc_start: 0.6950 (t80) cc_final: 0.6611 (t80) outliers start: 17 outliers final: 5 residues processed: 235 average time/residue: 0.2170 time to fit residues: 64.6203 Evaluate side-chains 222 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 215 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 491 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.2980 chunk 21 optimal weight: 0.2980 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 70 optimal weight: 0.0670 chunk 76 optimal weight: 0.1980 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.2518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6611 Z= 0.186 Angle : 0.617 9.660 8986 Z= 0.311 Chirality : 0.043 0.119 939 Planarity : 0.004 0.042 1166 Dihedral : 4.885 57.876 861 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.67 % Favored : 97.20 % Rotamer: Outliers : 2.30 % Allowed : 21.55 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.28), residues: 787 helix: -2.43 (0.23), residues: 361 sheet: -1.45 (0.88), residues: 34 loop : -1.14 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 478 HIS 0.003 0.001 HIS A 378 PHE 0.027 0.001 PHE A 428 TYR 0.014 0.001 TYR A 215 ARG 0.005 0.000 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 212 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 335 LEU cc_start: 0.8444 (tp) cc_final: 0.8215 (tp) REVERT: E 442 ASP cc_start: 0.8812 (t70) cc_final: 0.8367 (t0) REVERT: E 473 TYR cc_start: 0.7644 (t80) cc_final: 0.7324 (t80) REVERT: E 494 SER cc_start: 0.8803 (m) cc_final: 0.8300 (p) REVERT: A 23 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7412 (mp0) REVERT: A 26 LYS cc_start: 0.8232 (mttt) cc_final: 0.7916 (mmmm) REVERT: A 47 SER cc_start: 0.8696 (t) cc_final: 0.8283 (p) REVERT: A 55 THR cc_start: 0.7690 (m) cc_final: 0.6998 (p) REVERT: A 62 MET cc_start: 0.8017 (tmm) cc_final: 0.7239 (tmm) REVERT: A 101 GLN cc_start: 0.7864 (tt0) cc_final: 0.7655 (tt0) REVERT: A 102 GLN cc_start: 0.8080 (pp30) cc_final: 0.7865 (pp30) REVERT: A 105 SER cc_start: 0.8351 (p) cc_final: 0.7977 (t) REVERT: A 126 ILE cc_start: 0.8915 (tp) cc_final: 0.8644 (tt) REVERT: A 144 LEU cc_start: 0.8341 (tp) cc_final: 0.7832 (tp) REVERT: A 157 ASP cc_start: 0.7907 (m-30) cc_final: 0.7643 (t70) REVERT: A 158 TYR cc_start: 0.7553 (t80) cc_final: 0.6879 (t80) REVERT: A 166 GLU cc_start: 0.7367 (tp30) cc_final: 0.6792 (tp30) REVERT: A 168 TRP cc_start: 0.8217 (t-100) cc_final: 0.7779 (t-100) REVERT: A 182 GLU cc_start: 0.7434 (tm-30) cc_final: 0.7091 (tm-30) REVERT: A 204 ARG cc_start: 0.8456 (mtm-85) cc_final: 0.8176 (mtm180) REVERT: A 219 ARG cc_start: 0.8156 (mtm-85) cc_final: 0.7952 (mtm-85) REVERT: A 227 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7625 (tp30) REVERT: A 267 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8198 (mm) REVERT: A 271 TRP cc_start: 0.4970 (t60) cc_final: 0.4369 (t60) REVERT: A 299 ASP cc_start: 0.8145 (t0) cc_final: 0.7848 (t0) REVERT: A 313 LYS cc_start: 0.7996 (mttt) cc_final: 0.7714 (mtpt) REVERT: A 320 LEU cc_start: 0.8942 (mm) cc_final: 0.8732 (mt) REVERT: A 332 MET cc_start: 0.8058 (ttp) cc_final: 0.7604 (tmm) REVERT: A 353 LYS cc_start: 0.8262 (mtpt) cc_final: 0.8009 (mmmt) REVERT: A 363 LYS cc_start: 0.8752 (mppt) cc_final: 0.8368 (mppt) REVERT: A 368 ASP cc_start: 0.8085 (t0) cc_final: 0.7827 (t0) REVERT: A 406 GLU cc_start: 0.7803 (tp30) cc_final: 0.7479 (tp30) REVERT: A 429 GLN cc_start: 0.7361 (tp40) cc_final: 0.7042 (tp40) REVERT: A 465 LYS cc_start: 0.8812 (mttt) cc_final: 0.8458 (ttmt) REVERT: A 472 GLN cc_start: 0.7746 (mm-40) cc_final: 0.7456 (mm-40) REVERT: A 475 LYS cc_start: 0.8287 (tppt) cc_final: 0.7992 (tmtt) REVERT: A 504 PHE cc_start: 0.8072 (t80) cc_final: 0.7777 (t80) REVERT: A 559 ARG cc_start: 0.8144 (ptt180) cc_final: 0.7858 (ptm160) REVERT: A 574 VAL cc_start: 0.8972 (m) cc_final: 0.8767 (p) REVERT: A 603 PHE cc_start: 0.7003 (t80) cc_final: 0.6637 (t80) outliers start: 16 outliers final: 9 residues processed: 219 average time/residue: 0.2522 time to fit residues: 69.1874 Evaluate side-chains 211 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 201 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 495 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 6611 Z= 0.356 Angle : 0.723 10.032 8986 Z= 0.362 Chirality : 0.048 0.142 939 Planarity : 0.004 0.044 1166 Dihedral : 5.113 55.685 861 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.56 % Favored : 96.32 % Rotamer: Outliers : 3.74 % Allowed : 23.28 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.28), residues: 787 helix: -2.07 (0.24), residues: 365 sheet: -1.20 (0.89), residues: 34 loop : -0.92 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 436 HIS 0.004 0.001 HIS A 378 PHE 0.020 0.002 PHE A 400 TYR 0.025 0.002 TYR A 158 ARG 0.006 0.001 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: E 403 ARG cc_start: 0.8172 (ttp80) cc_final: 0.7436 (ptm-80) REVERT: E 422 ASN cc_start: 0.8237 (m110) cc_final: 0.7925 (m110) REVERT: E 442 ASP cc_start: 0.8759 (t70) cc_final: 0.8252 (t0) REVERT: E 494 SER cc_start: 0.8871 (m) cc_final: 0.8309 (p) REVERT: E 505 HIS cc_start: 0.8440 (m170) cc_final: 0.8187 (m170) REVERT: E 517 LEU cc_start: 0.8773 (mm) cc_final: 0.8428 (mp) REVERT: A 23 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7359 (mp0) REVERT: A 26 LYS cc_start: 0.8250 (mttt) cc_final: 0.7956 (mmtt) REVERT: A 40 PHE cc_start: 0.8701 (t80) cc_final: 0.8346 (t80) REVERT: A 47 SER cc_start: 0.8758 (t) cc_final: 0.8379 (p) REVERT: A 55 THR cc_start: 0.7780 (m) cc_final: 0.7115 (p) REVERT: A 62 MET cc_start: 0.8143 (tmm) cc_final: 0.7317 (tmm) REVERT: A 101 GLN cc_start: 0.7967 (tt0) cc_final: 0.7470 (tp40) REVERT: A 102 GLN cc_start: 0.8433 (pp30) cc_final: 0.8062 (pp30) REVERT: A 110 GLU cc_start: 0.7239 (tp30) cc_final: 0.6949 (tp30) REVERT: A 121 ASN cc_start: 0.8585 (m-40) cc_final: 0.8339 (m-40) REVERT: A 123 MET cc_start: 0.8358 (ttt) cc_final: 0.7828 (ttp) REVERT: A 126 ILE cc_start: 0.8891 (tp) cc_final: 0.8640 (tt) REVERT: A 144 LEU cc_start: 0.8392 (tp) cc_final: 0.7831 (tp) REVERT: A 157 ASP cc_start: 0.7860 (m-30) cc_final: 0.7654 (t0) REVERT: A 161 ARG cc_start: 0.8854 (mtp180) cc_final: 0.8137 (mmm-85) REVERT: A 166 GLU cc_start: 0.7442 (tp30) cc_final: 0.7231 (tp30) REVERT: A 168 TRP cc_start: 0.8308 (t-100) cc_final: 0.7776 (t-100) REVERT: A 204 ARG cc_start: 0.8616 (mtm-85) cc_final: 0.8052 (mtm180) REVERT: A 227 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7770 (tp30) REVERT: A 267 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8349 (mt) REVERT: A 271 TRP cc_start: 0.5164 (t60) cc_final: 0.4210 (t60) REVERT: A 299 ASP cc_start: 0.8326 (t0) cc_final: 0.8018 (t0) REVERT: A 313 LYS cc_start: 0.8072 (mttt) cc_final: 0.7803 (ttmm) REVERT: A 325 GLN cc_start: 0.8087 (tp-100) cc_final: 0.7716 (tm-30) REVERT: A 329 GLU cc_start: 0.7931 (mt-10) cc_final: 0.6110 (mt-10) REVERT: A 332 MET cc_start: 0.8027 (ttp) cc_final: 0.7567 (tmm) REVERT: A 353 LYS cc_start: 0.8348 (mtpt) cc_final: 0.8031 (mtpt) REVERT: A 368 ASP cc_start: 0.8174 (t0) cc_final: 0.7694 (t0) REVERT: A 375 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7579 (mm-30) REVERT: A 406 GLU cc_start: 0.7970 (tp30) cc_final: 0.7687 (tp30) REVERT: A 419 LYS cc_start: 0.8210 (tptp) cc_final: 0.7962 (mtpt) REVERT: A 429 GLN cc_start: 0.7505 (tp40) cc_final: 0.7109 (tp40) REVERT: A 465 LYS cc_start: 0.8878 (mttt) cc_final: 0.8419 (ttmt) REVERT: A 472 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7652 (mm-40) REVERT: A 475 LYS cc_start: 0.8420 (tppt) cc_final: 0.8194 (tmtt) REVERT: A 480 MET cc_start: 0.8767 (mmm) cc_final: 0.8280 (mmm) REVERT: A 484 ILE cc_start: 0.8689 (mt) cc_final: 0.8485 (mt) REVERT: A 504 PHE cc_start: 0.8177 (t80) cc_final: 0.7821 (t80) REVERT: A 557 MET cc_start: 0.7951 (tmm) cc_final: 0.7677 (tmm) REVERT: A 559 ARG cc_start: 0.8271 (ptt180) cc_final: 0.7931 (ptm160) REVERT: A 574 VAL cc_start: 0.9030 (m) cc_final: 0.8809 (p) REVERT: A 577 LYS cc_start: 0.8916 (ptpp) cc_final: 0.8660 (ptpp) REVERT: A 582 ARG cc_start: 0.7573 (tpp80) cc_final: 0.7127 (tpp80) REVERT: A 603 PHE cc_start: 0.7215 (t80) cc_final: 0.6793 (t80) outliers start: 26 outliers final: 17 residues processed: 225 average time/residue: 0.2315 time to fit residues: 64.7836 Evaluate side-chains 223 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 204 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 579 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.2980 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 52 optimal weight: 0.0970 chunk 0 optimal weight: 0.8980 chunk 38 optimal weight: 0.0970 chunk 67 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 HIS A 380 GLN A 540 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6611 Z= 0.226 Angle : 0.655 11.503 8986 Z= 0.324 Chirality : 0.045 0.135 939 Planarity : 0.004 0.032 1166 Dihedral : 4.920 53.501 861 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.67 % Favored : 97.20 % Rotamer: Outliers : 3.16 % Allowed : 26.01 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.28), residues: 787 helix: -1.69 (0.24), residues: 369 sheet: -1.28 (0.83), residues: 36 loop : -0.86 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 436 HIS 0.002 0.001 HIS A 378 PHE 0.015 0.001 PHE A 400 TYR 0.025 0.002 TYR A 158 ARG 0.004 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 215 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 347 PHE cc_start: 0.8798 (m-10) cc_final: 0.8445 (m-80) REVERT: E 355 ARG cc_start: 0.8342 (ttm170) cc_final: 0.7717 (ttm-80) REVERT: E 357 ARG cc_start: 0.7999 (mtp-110) cc_final: 0.7730 (mtp-110) REVERT: E 403 ARG cc_start: 0.8305 (ttp80) cc_final: 0.7540 (ptm-80) REVERT: E 422 ASN cc_start: 0.8171 (m110) cc_final: 0.7852 (m110) REVERT: E 442 ASP cc_start: 0.8706 (t70) cc_final: 0.8226 (t0) REVERT: E 473 TYR cc_start: 0.7754 (t80) cc_final: 0.7425 (t80) REVERT: E 494 SER cc_start: 0.8843 (m) cc_final: 0.8320 (p) REVERT: E 495 TYR cc_start: 0.8452 (m-10) cc_final: 0.8221 (m-80) REVERT: E 505 HIS cc_start: 0.8295 (m170) cc_final: 0.7987 (m170) REVERT: E 517 LEU cc_start: 0.8724 (mm) cc_final: 0.8448 (mp) REVERT: A 23 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7282 (mp0) REVERT: A 26 LYS cc_start: 0.8239 (mttt) cc_final: 0.7881 (mmtt) REVERT: A 31 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.6971 (tttt) REVERT: A 40 PHE cc_start: 0.8653 (t80) cc_final: 0.8328 (t80) REVERT: A 47 SER cc_start: 0.8764 (t) cc_final: 0.8393 (p) REVERT: A 55 THR cc_start: 0.7840 (m) cc_final: 0.7213 (p) REVERT: A 62 MET cc_start: 0.8134 (tmm) cc_final: 0.7291 (tmm) REVERT: A 87 GLU cc_start: 0.7101 (pm20) cc_final: 0.6901 (pm20) REVERT: A 101 GLN cc_start: 0.7920 (tt0) cc_final: 0.7352 (tp40) REVERT: A 102 GLN cc_start: 0.8467 (pp30) cc_final: 0.8135 (pp30) REVERT: A 110 GLU cc_start: 0.7160 (tp30) cc_final: 0.6764 (tp30) REVERT: A 121 ASN cc_start: 0.8672 (m-40) cc_final: 0.8432 (m-40) REVERT: A 123 MET cc_start: 0.8430 (ttt) cc_final: 0.7864 (ttp) REVERT: A 126 ILE cc_start: 0.8850 (tp) cc_final: 0.8630 (tt) REVERT: A 144 LEU cc_start: 0.8335 (tp) cc_final: 0.7724 (tp) REVERT: A 166 GLU cc_start: 0.7409 (tp30) cc_final: 0.7156 (tp30) REVERT: A 168 TRP cc_start: 0.8361 (t-100) cc_final: 0.7864 (t-100) REVERT: A 204 ARG cc_start: 0.8529 (mtm-85) cc_final: 0.8298 (mtm180) REVERT: A 227 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7708 (tp30) REVERT: A 249 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.6948 (tmm) REVERT: A 267 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8310 (mt) REVERT: A 271 TRP cc_start: 0.5035 (t60) cc_final: 0.4132 (t60) REVERT: A 299 ASP cc_start: 0.8328 (t0) cc_final: 0.8004 (t0) REVERT: A 325 GLN cc_start: 0.8035 (tp-100) cc_final: 0.7745 (tm-30) REVERT: A 329 GLU cc_start: 0.7877 (mt-10) cc_final: 0.5826 (mt-10) REVERT: A 332 MET cc_start: 0.7957 (ttp) cc_final: 0.7552 (tmm) REVERT: A 353 LYS cc_start: 0.8313 (mtpt) cc_final: 0.8028 (mmmt) REVERT: A 363 LYS cc_start: 0.8747 (mppt) cc_final: 0.8318 (mppt) REVERT: A 375 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7517 (mm-30) REVERT: A 406 GLU cc_start: 0.7961 (tp30) cc_final: 0.7706 (tp30) REVERT: A 419 LYS cc_start: 0.8183 (tptp) cc_final: 0.7961 (mtpt) REVERT: A 429 GLN cc_start: 0.7447 (tp40) cc_final: 0.6906 (tp40) REVERT: A 465 LYS cc_start: 0.8828 (mttt) cc_final: 0.8397 (ttmt) REVERT: A 472 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7265 (mm-40) REVERT: A 475 LYS cc_start: 0.8348 (tppt) cc_final: 0.8095 (tmtt) REVERT: A 476 LYS cc_start: 0.8072 (mtpt) cc_final: 0.7805 (mtpt) REVERT: A 480 MET cc_start: 0.8760 (mmm) cc_final: 0.8366 (mmm) REVERT: A 484 ILE cc_start: 0.8711 (mt) cc_final: 0.8327 (mm) REVERT: A 504 PHE cc_start: 0.8170 (t80) cc_final: 0.7794 (t80) REVERT: A 518 ARG cc_start: 0.7765 (ttp-170) cc_final: 0.7541 (tmm-80) REVERT: A 557 MET cc_start: 0.7897 (tmm) cc_final: 0.7595 (tmm) REVERT: A 559 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7847 (ptm160) REVERT: A 574 VAL cc_start: 0.9052 (m) cc_final: 0.8802 (p) REVERT: A 577 LYS cc_start: 0.8884 (ptpp) cc_final: 0.8627 (ptpp) REVERT: A 582 ARG cc_start: 0.7556 (tpp80) cc_final: 0.7100 (tpp80) REVERT: A 603 PHE cc_start: 0.7205 (t80) cc_final: 0.6801 (t80) outliers start: 22 outliers final: 12 residues processed: 223 average time/residue: 0.2444 time to fit residues: 67.5083 Evaluate side-chains 223 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 206 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 559 ARG Chi-restraints excluded: chain A residue 579 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 62 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 0.3980 chunk 39 optimal weight: 0.0030 chunk 72 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN A 540 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6611 Z= 0.248 Angle : 0.676 12.006 8986 Z= 0.332 Chirality : 0.046 0.130 939 Planarity : 0.004 0.042 1166 Dihedral : 4.901 51.812 861 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.92 % Favored : 96.95 % Rotamer: Outliers : 3.88 % Allowed : 26.72 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.29), residues: 787 helix: -1.32 (0.26), residues: 367 sheet: -1.24 (0.80), residues: 36 loop : -0.78 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 436 HIS 0.003 0.001 HIS A 401 PHE 0.016 0.001 PHE A 400 TYR 0.020 0.002 TYR A 158 ARG 0.004 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 210 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 347 PHE cc_start: 0.8783 (m-10) cc_final: 0.8405 (m-80) REVERT: E 403 ARG cc_start: 0.8357 (ttp80) cc_final: 0.7607 (ptm-80) REVERT: E 422 ASN cc_start: 0.8112 (m110) cc_final: 0.7804 (m110) REVERT: E 442 ASP cc_start: 0.8677 (t70) cc_final: 0.8193 (t0) REVERT: E 473 TYR cc_start: 0.7808 (t80) cc_final: 0.7328 (t80) REVERT: E 494 SER cc_start: 0.8841 (m) cc_final: 0.8314 (p) REVERT: E 495 TYR cc_start: 0.8460 (m-10) cc_final: 0.8196 (m-80) REVERT: E 505 HIS cc_start: 0.8308 (m170) cc_final: 0.8013 (m170) REVERT: A 23 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7269 (mp0) REVERT: A 26 LYS cc_start: 0.8273 (mttt) cc_final: 0.7925 (mmmm) REVERT: A 31 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.6959 (tttp) REVERT: A 40 PHE cc_start: 0.8643 (t80) cc_final: 0.8320 (t80) REVERT: A 47 SER cc_start: 0.8757 (t) cc_final: 0.8376 (p) REVERT: A 55 THR cc_start: 0.7863 (m) cc_final: 0.7274 (p) REVERT: A 62 MET cc_start: 0.8174 (tmm) cc_final: 0.7308 (tmm) REVERT: A 101 GLN cc_start: 0.7936 (tt0) cc_final: 0.7579 (tt0) REVERT: A 102 GLN cc_start: 0.8527 (pp30) cc_final: 0.8219 (pp30) REVERT: A 110 GLU cc_start: 0.7111 (tp30) cc_final: 0.6676 (tp30) REVERT: A 121 ASN cc_start: 0.8770 (m-40) cc_final: 0.8451 (m110) REVERT: A 123 MET cc_start: 0.8526 (ttt) cc_final: 0.8057 (ttt) REVERT: A 126 ILE cc_start: 0.8886 (tp) cc_final: 0.8675 (tt) REVERT: A 144 LEU cc_start: 0.8352 (tp) cc_final: 0.7762 (tp) REVERT: A 166 GLU cc_start: 0.7364 (tp30) cc_final: 0.6744 (tp30) REVERT: A 168 TRP cc_start: 0.8379 (t-100) cc_final: 0.7891 (t-100) REVERT: A 204 ARG cc_start: 0.8488 (mtm-85) cc_final: 0.8022 (mtm180) REVERT: A 227 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7721 (tp30) REVERT: A 249 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.7152 (tmm) REVERT: A 267 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8313 (mt) REVERT: A 271 TRP cc_start: 0.5071 (t60) cc_final: 0.4107 (t60) REVERT: A 299 ASP cc_start: 0.8330 (t0) cc_final: 0.8088 (t0) REVERT: A 313 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7903 (ttpp) REVERT: A 332 MET cc_start: 0.7887 (ttp) cc_final: 0.7510 (tmm) REVERT: A 353 LYS cc_start: 0.8310 (mtpt) cc_final: 0.8077 (mtpt) REVERT: A 367 ASP cc_start: 0.8027 (t0) cc_final: 0.7744 (t0) REVERT: A 375 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7598 (mm-30) REVERT: A 406 GLU cc_start: 0.8029 (tp30) cc_final: 0.7788 (tp30) REVERT: A 465 LYS cc_start: 0.8795 (mttt) cc_final: 0.8373 (ttmt) REVERT: A 472 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7221 (mm-40) REVERT: A 475 LYS cc_start: 0.8340 (tppt) cc_final: 0.8086 (tmtt) REVERT: A 480 MET cc_start: 0.8748 (mmm) cc_final: 0.8437 (mmm) REVERT: A 484 ILE cc_start: 0.8732 (mt) cc_final: 0.8396 (mm) REVERT: A 499 ASP cc_start: 0.8198 (m-30) cc_final: 0.7910 (t0) REVERT: A 518 ARG cc_start: 0.7823 (ttp-170) cc_final: 0.7575 (tmm-80) REVERT: A 557 MET cc_start: 0.7910 (tmm) cc_final: 0.7617 (tmm) REVERT: A 559 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7890 (ptm160) REVERT: A 574 VAL cc_start: 0.9061 (m) cc_final: 0.8800 (p) REVERT: A 577 LYS cc_start: 0.8906 (ptpp) cc_final: 0.8704 (ptpp) REVERT: A 582 ARG cc_start: 0.7526 (tpp80) cc_final: 0.7086 (tpp80) REVERT: A 603 PHE cc_start: 0.7231 (t80) cc_final: 0.6868 (t80) outliers start: 27 outliers final: 16 residues processed: 218 average time/residue: 0.2564 time to fit residues: 69.4841 Evaluate side-chains 228 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 559 ARG Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 75 optimal weight: 0.3980 chunk 47 optimal weight: 0.0010 chunk 45 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6611 Z= 0.265 Angle : 0.694 11.330 8986 Z= 0.342 Chirality : 0.046 0.137 939 Planarity : 0.004 0.035 1166 Dihedral : 4.881 50.626 861 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.92 % Favored : 96.95 % Rotamer: Outliers : 3.59 % Allowed : 26.58 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.30), residues: 787 helix: -1.10 (0.26), residues: 370 sheet: -0.94 (0.85), residues: 35 loop : -0.62 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 436 HIS 0.003 0.001 HIS A 401 PHE 0.026 0.002 PHE A 428 TYR 0.017 0.001 TYR A 180 ARG 0.014 0.001 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 364 ASP cc_start: 0.8355 (t70) cc_final: 0.8022 (t0) REVERT: E 403 ARG cc_start: 0.8414 (ttp80) cc_final: 0.7567 (ptm-80) REVERT: E 422 ASN cc_start: 0.8123 (m110) cc_final: 0.7786 (m110) REVERT: E 442 ASP cc_start: 0.8677 (t70) cc_final: 0.8124 (t0) REVERT: E 494 SER cc_start: 0.8842 (m) cc_final: 0.8341 (p) REVERT: E 505 HIS cc_start: 0.8346 (m170) cc_final: 0.7988 (m170) REVERT: A 23 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7205 (mp0) REVERT: A 26 LYS cc_start: 0.8292 (mttt) cc_final: 0.7974 (mmtt) REVERT: A 40 PHE cc_start: 0.8650 (t80) cc_final: 0.8338 (t80) REVERT: A 47 SER cc_start: 0.8758 (t) cc_final: 0.8391 (p) REVERT: A 55 THR cc_start: 0.7894 (m) cc_final: 0.7330 (p) REVERT: A 62 MET cc_start: 0.8164 (tmm) cc_final: 0.7264 (tmm) REVERT: A 81 GLN cc_start: 0.8097 (tp40) cc_final: 0.7857 (tp40) REVERT: A 88 ILE cc_start: 0.8844 (mp) cc_final: 0.8625 (mt) REVERT: A 101 GLN cc_start: 0.7944 (tt0) cc_final: 0.7593 (tp40) REVERT: A 102 GLN cc_start: 0.8601 (pp30) cc_final: 0.8330 (pp30) REVERT: A 121 ASN cc_start: 0.8876 (m-40) cc_final: 0.8532 (m-40) REVERT: A 123 MET cc_start: 0.8555 (ttt) cc_final: 0.8112 (ttt) REVERT: A 126 ILE cc_start: 0.8917 (tp) cc_final: 0.8693 (tt) REVERT: A 155 SER cc_start: 0.7459 (t) cc_final: 0.6956 (p) REVERT: A 166 GLU cc_start: 0.7459 (tp30) cc_final: 0.6829 (tp30) REVERT: A 204 ARG cc_start: 0.8451 (mtm-85) cc_final: 0.8139 (mtm180) REVERT: A 227 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7703 (tp30) REVERT: A 249 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.7175 (tmm) REVERT: A 267 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8297 (mt) REVERT: A 271 TRP cc_start: 0.5064 (t60) cc_final: 0.4069 (t60) REVERT: A 299 ASP cc_start: 0.8350 (t0) cc_final: 0.8113 (t0) REVERT: A 332 MET cc_start: 0.7933 (ttp) cc_final: 0.7518 (tmm) REVERT: A 353 LYS cc_start: 0.8296 (mtpt) cc_final: 0.8061 (mtpt) REVERT: A 375 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7434 (mm-30) REVERT: A 406 GLU cc_start: 0.8060 (tp30) cc_final: 0.7476 (tp30) REVERT: A 465 LYS cc_start: 0.8811 (mttt) cc_final: 0.8360 (ttmt) REVERT: A 472 GLN cc_start: 0.7964 (mm-40) cc_final: 0.7388 (mm-40) REVERT: A 475 LYS cc_start: 0.8313 (tppt) cc_final: 0.8079 (tmtt) REVERT: A 480 MET cc_start: 0.8686 (mmm) cc_final: 0.8300 (mmm) REVERT: A 484 ILE cc_start: 0.8702 (mt) cc_final: 0.8415 (mt) REVERT: A 499 ASP cc_start: 0.8195 (m-30) cc_final: 0.7935 (t0) REVERT: A 518 ARG cc_start: 0.7855 (ttp-170) cc_final: 0.7592 (tmm-80) REVERT: A 559 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7938 (ptm160) REVERT: A 574 VAL cc_start: 0.9062 (m) cc_final: 0.8781 (p) REVERT: A 582 ARG cc_start: 0.7512 (tpp80) cc_final: 0.7093 (tpp80) REVERT: A 603 PHE cc_start: 0.7256 (t80) cc_final: 0.6904 (t80) outliers start: 25 outliers final: 15 residues processed: 219 average time/residue: 0.2730 time to fit residues: 75.0749 Evaluate side-chains 218 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 559 ARG Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 59 optimal weight: 0.2980 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 42 optimal weight: 0.0470 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 6611 Z= 0.265 Angle : 0.725 11.119 8986 Z= 0.359 Chirality : 0.046 0.130 939 Planarity : 0.004 0.038 1166 Dihedral : 5.169 53.433 861 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.80 % Favored : 97.08 % Rotamer: Outliers : 3.59 % Allowed : 28.30 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.30), residues: 787 helix: -0.86 (0.27), residues: 368 sheet: -1.06 (0.80), residues: 35 loop : -0.72 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 436 HIS 0.004 0.001 HIS A 401 PHE 0.015 0.001 PHE A 400 TYR 0.016 0.001 TYR A 180 ARG 0.012 0.001 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 403 ARG cc_start: 0.8409 (ttp80) cc_final: 0.7944 (ttp80) REVERT: E 422 ASN cc_start: 0.8142 (m110) cc_final: 0.7716 (m110) REVERT: E 442 ASP cc_start: 0.8698 (t70) cc_final: 0.8172 (t0) REVERT: E 494 SER cc_start: 0.8841 (m) cc_final: 0.8319 (p) REVERT: E 505 HIS cc_start: 0.8338 (m170) cc_final: 0.7869 (m90) REVERT: A 22 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7265 (mm-30) REVERT: A 26 LYS cc_start: 0.8256 (mttt) cc_final: 0.7904 (mmmm) REVERT: A 31 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7114 (tttp) REVERT: A 40 PHE cc_start: 0.8622 (t80) cc_final: 0.8321 (t80) REVERT: A 47 SER cc_start: 0.8783 (t) cc_final: 0.8414 (p) REVERT: A 55 THR cc_start: 0.7919 (m) cc_final: 0.7367 (p) REVERT: A 62 MET cc_start: 0.8249 (tmm) cc_final: 0.7386 (tmm) REVERT: A 81 GLN cc_start: 0.8176 (tp40) cc_final: 0.7909 (tp40) REVERT: A 101 GLN cc_start: 0.7897 (tt0) cc_final: 0.7453 (tp40) REVERT: A 121 ASN cc_start: 0.8974 (m-40) cc_final: 0.8621 (m110) REVERT: A 123 MET cc_start: 0.8544 (ttt) cc_final: 0.8119 (mtt) REVERT: A 124 SER cc_start: 0.8552 (m) cc_final: 0.8281 (p) REVERT: A 126 ILE cc_start: 0.8911 (tp) cc_final: 0.8681 (tt) REVERT: A 155 SER cc_start: 0.7507 (t) cc_final: 0.7002 (p) REVERT: A 163 TRP cc_start: 0.7318 (t60) cc_final: 0.7044 (t60) REVERT: A 168 TRP cc_start: 0.8406 (t-100) cc_final: 0.7807 (t-100) REVERT: A 204 ARG cc_start: 0.8403 (mtm-85) cc_final: 0.7989 (mtm180) REVERT: A 227 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7703 (tp30) REVERT: A 249 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.7198 (tmm) REVERT: A 267 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8321 (mt) REVERT: A 271 TRP cc_start: 0.5046 (t60) cc_final: 0.4054 (t60) REVERT: A 299 ASP cc_start: 0.8366 (t0) cc_final: 0.8106 (t0) REVERT: A 327 PHE cc_start: 0.8806 (t80) cc_final: 0.8547 (t80) REVERT: A 353 LYS cc_start: 0.8248 (mtpt) cc_final: 0.7906 (mtpt) REVERT: A 375 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7453 (mm-30) REVERT: A 406 GLU cc_start: 0.7969 (tp30) cc_final: 0.7472 (tp30) REVERT: A 465 LYS cc_start: 0.8767 (mttt) cc_final: 0.8326 (ttmt) REVERT: A 472 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7397 (mm-40) REVERT: A 475 LYS cc_start: 0.8371 (tppt) cc_final: 0.8118 (tmtt) REVERT: A 476 LYS cc_start: 0.7969 (mtpt) cc_final: 0.7752 (mtpt) REVERT: A 480 MET cc_start: 0.8694 (mmm) cc_final: 0.8421 (mmm) REVERT: A 484 ILE cc_start: 0.8696 (mt) cc_final: 0.8404 (mt) REVERT: A 499 ASP cc_start: 0.8169 (m-30) cc_final: 0.7900 (t0) REVERT: A 518 ARG cc_start: 0.7843 (ttp-170) cc_final: 0.7548 (tmm-80) REVERT: A 534 LYS cc_start: 0.8596 (mmmm) cc_final: 0.8392 (mmmm) REVERT: A 559 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7929 (ptm160) REVERT: A 574 VAL cc_start: 0.9037 (m) cc_final: 0.8776 (p) REVERT: A 582 ARG cc_start: 0.7514 (tpp80) cc_final: 0.7072 (tpp80) REVERT: A 603 PHE cc_start: 0.7270 (t80) cc_final: 0.6925 (t80) outliers start: 25 outliers final: 16 residues processed: 220 average time/residue: 0.2489 time to fit residues: 67.9055 Evaluate side-chains 226 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 559 ARG Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 45 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 360 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 ASN ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 6611 Z= 0.322 Angle : 0.773 11.075 8986 Z= 0.376 Chirality : 0.048 0.132 939 Planarity : 0.004 0.040 1166 Dihedral : 5.244 52.006 861 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.18 % Favored : 96.70 % Rotamer: Outliers : 4.02 % Allowed : 28.45 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.30), residues: 787 helix: -0.83 (0.27), residues: 366 sheet: -1.66 (0.70), residues: 47 loop : -0.62 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 436 HIS 0.004 0.001 HIS A 401 PHE 0.030 0.002 PHE A 428 TYR 0.019 0.002 TYR A 180 ARG 0.011 0.001 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 211 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 403 ARG cc_start: 0.8343 (ttp80) cc_final: 0.7749 (ttp80) REVERT: E 422 ASN cc_start: 0.8171 (m110) cc_final: 0.7701 (m-40) REVERT: E 442 ASP cc_start: 0.8661 (t70) cc_final: 0.8124 (t0) REVERT: E 494 SER cc_start: 0.8847 (m) cc_final: 0.8285 (p) REVERT: E 505 HIS cc_start: 0.8384 (m170) cc_final: 0.7835 (m90) REVERT: A 23 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7111 (mp0) REVERT: A 26 LYS cc_start: 0.8281 (mttt) cc_final: 0.7978 (mmtt) REVERT: A 31 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7122 (tttp) REVERT: A 40 PHE cc_start: 0.8654 (t80) cc_final: 0.8351 (t80) REVERT: A 47 SER cc_start: 0.8763 (t) cc_final: 0.8425 (p) REVERT: A 55 THR cc_start: 0.8075 (m) cc_final: 0.7519 (p) REVERT: A 62 MET cc_start: 0.8289 (tmm) cc_final: 0.7412 (tmm) REVERT: A 101 GLN cc_start: 0.7868 (tt0) cc_final: 0.7325 (tp40) REVERT: A 123 MET cc_start: 0.8504 (ttt) cc_final: 0.8136 (ttp) REVERT: A 124 SER cc_start: 0.8660 (m) cc_final: 0.8406 (p) REVERT: A 126 ILE cc_start: 0.8955 (tp) cc_final: 0.8701 (tt) REVERT: A 155 SER cc_start: 0.7438 (t) cc_final: 0.6929 (p) REVERT: A 163 TRP cc_start: 0.7437 (t60) cc_final: 0.7141 (t60) REVERT: A 168 TRP cc_start: 0.8433 (t-100) cc_final: 0.7796 (t-100) REVERT: A 198 ASP cc_start: 0.8183 (m-30) cc_final: 0.7942 (m-30) REVERT: A 204 ARG cc_start: 0.8416 (mtm-85) cc_final: 0.7906 (mtm-85) REVERT: A 227 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7698 (tp30) REVERT: A 249 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7243 (tmm) REVERT: A 271 TRP cc_start: 0.5011 (t60) cc_final: 0.3903 (t60) REVERT: A 299 ASP cc_start: 0.8397 (t0) cc_final: 0.8143 (t0) REVERT: A 310 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7750 (mm-30) REVERT: A 327 PHE cc_start: 0.8729 (t80) cc_final: 0.8415 (t80) REVERT: A 353 LYS cc_start: 0.8201 (mtpt) cc_final: 0.7806 (mtpt) REVERT: A 375 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7431 (mm-30) REVERT: A 465 LYS cc_start: 0.8777 (mttt) cc_final: 0.8337 (ttmt) REVERT: A 472 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7392 (mm-40) REVERT: A 475 LYS cc_start: 0.8385 (tppt) cc_final: 0.8126 (tmtt) REVERT: A 484 ILE cc_start: 0.8712 (mt) cc_final: 0.8449 (mt) REVERT: A 534 LYS cc_start: 0.8614 (mmmm) cc_final: 0.8368 (mmmm) REVERT: A 559 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.8001 (ptm160) REVERT: A 574 VAL cc_start: 0.8998 (m) cc_final: 0.8750 (p) REVERT: A 582 ARG cc_start: 0.7560 (tpp80) cc_final: 0.7124 (tpp80) REVERT: A 603 PHE cc_start: 0.7310 (t80) cc_final: 0.6958 (t80) outliers start: 28 outliers final: 18 residues processed: 220 average time/residue: 0.2336 time to fit residues: 64.4227 Evaluate side-chains 226 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 559 ARG Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.2980 chunk 71 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.0980 chunk 49 optimal weight: 0.0980 chunk 65 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 chunk 57 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 overall best weight: 0.2380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 360 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6611 Z= 0.225 Angle : 0.758 11.819 8986 Z= 0.370 Chirality : 0.046 0.172 939 Planarity : 0.004 0.039 1166 Dihedral : 5.068 49.915 861 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.92 % Favored : 96.95 % Rotamer: Outliers : 3.02 % Allowed : 29.60 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.30), residues: 787 helix: -0.66 (0.27), residues: 366 sheet: -1.80 (0.64), residues: 51 loop : -0.45 (0.35), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 610 HIS 0.004 0.001 HIS A 34 PHE 0.027 0.002 PHE A 32 TYR 0.022 0.001 TYR E 473 ARG 0.010 0.001 ARG E 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 403 ARG cc_start: 0.8371 (ttp80) cc_final: 0.7927 (ttp80) REVERT: E 422 ASN cc_start: 0.8132 (m110) cc_final: 0.7757 (m-40) REVERT: E 442 ASP cc_start: 0.8622 (t70) cc_final: 0.8157 (t0) REVERT: E 494 SER cc_start: 0.8812 (m) cc_final: 0.8303 (p) REVERT: E 505 HIS cc_start: 0.8284 (m170) cc_final: 0.7805 (m90) REVERT: A 22 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7295 (mm-30) REVERT: A 26 LYS cc_start: 0.8236 (mttt) cc_final: 0.7854 (mmmm) REVERT: A 31 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7253 (tttp) REVERT: A 40 PHE cc_start: 0.8604 (t80) cc_final: 0.8300 (t80) REVERT: A 47 SER cc_start: 0.8790 (t) cc_final: 0.8382 (p) REVERT: A 55 THR cc_start: 0.7944 (m) cc_final: 0.7393 (p) REVERT: A 62 MET cc_start: 0.8287 (tmm) cc_final: 0.7462 (tmm) REVERT: A 81 GLN cc_start: 0.8242 (tp40) cc_final: 0.8024 (tp40) REVERT: A 82 MET cc_start: 0.7733 (tpp) cc_final: 0.7498 (tpt) REVERT: A 101 GLN cc_start: 0.7800 (tt0) cc_final: 0.7435 (tp40) REVERT: A 123 MET cc_start: 0.8459 (ttt) cc_final: 0.8081 (ttp) REVERT: A 124 SER cc_start: 0.8593 (m) cc_final: 0.8329 (p) REVERT: A 126 ILE cc_start: 0.8903 (tp) cc_final: 0.8662 (tt) REVERT: A 163 TRP cc_start: 0.7304 (t60) cc_final: 0.7006 (t60) REVERT: A 227 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7691 (tp30) REVERT: A 249 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7172 (tmm) REVERT: A 267 LEU cc_start: 0.8592 (mp) cc_final: 0.8326 (mm) REVERT: A 271 TRP cc_start: 0.5041 (t60) cc_final: 0.4075 (t60) REVERT: A 299 ASP cc_start: 0.8355 (t0) cc_final: 0.8098 (t0) REVERT: A 307 ILE cc_start: 0.8386 (tp) cc_final: 0.8128 (tt) REVERT: A 327 PHE cc_start: 0.8646 (t80) cc_final: 0.8340 (t80) REVERT: A 353 LYS cc_start: 0.8194 (mtpt) cc_final: 0.7651 (mmmt) REVERT: A 375 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7448 (mm-30) REVERT: A 446 ILE cc_start: 0.8740 (mm) cc_final: 0.8528 (mt) REVERT: A 465 LYS cc_start: 0.8710 (mttt) cc_final: 0.8186 (ttmt) REVERT: A 472 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7489 (mm-40) REVERT: A 475 LYS cc_start: 0.8306 (tppt) cc_final: 0.8082 (tmtt) REVERT: A 484 ILE cc_start: 0.8668 (mt) cc_final: 0.8416 (mt) REVERT: A 534 LYS cc_start: 0.8606 (mmmm) cc_final: 0.8346 (mmmm) REVERT: A 559 ARG cc_start: 0.8249 (ptt180) cc_final: 0.7986 (ptm160) REVERT: A 564 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7708 (mm-30) REVERT: A 574 VAL cc_start: 0.9010 (m) cc_final: 0.8780 (p) REVERT: A 582 ARG cc_start: 0.7496 (tpp80) cc_final: 0.7089 (tpp80) REVERT: A 603 PHE cc_start: 0.7263 (t80) cc_final: 0.6926 (t80) outliers start: 21 outliers final: 15 residues processed: 211 average time/residue: 0.2442 time to fit residues: 65.0845 Evaluate side-chains 223 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 0.0770 chunk 70 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 360 ASN E 394 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 ASN ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN A 598 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.109728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.094611 restraints weight = 12136.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.098084 restraints weight = 5690.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.100310 restraints weight = 3235.270| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6611 Z= 0.320 Angle : 0.784 11.654 8986 Z= 0.385 Chirality : 0.048 0.203 939 Planarity : 0.004 0.040 1166 Dihedral : 5.261 50.315 861 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.30 % Favored : 96.57 % Rotamer: Outliers : 2.87 % Allowed : 30.17 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.30), residues: 787 helix: -0.70 (0.27), residues: 369 sheet: -1.77 (0.64), residues: 51 loop : -0.47 (0.35), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 436 HIS 0.005 0.001 HIS A 401 PHE 0.025 0.002 PHE A 428 TYR 0.022 0.002 TYR E 473 ARG 0.008 0.001 ARG E 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2093.13 seconds wall clock time: 38 minutes 49.71 seconds (2329.71 seconds total)