Starting phenix.real_space_refine on Fri Dec 27 20:05:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wpb_32681/12_2024/7wpb_32681_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wpb_32681/12_2024/7wpb_32681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wpb_32681/12_2024/7wpb_32681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wpb_32681/12_2024/7wpb_32681.map" model { file = "/net/cci-nas-00/data/ceres_data/7wpb_32681/12_2024/7wpb_32681_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wpb_32681/12_2024/7wpb_32681_neut.cif" } resolution = 2.79 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= -0.001 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 Cl 1 4.86 5 C 4157 2.51 5 N 1076 2.21 5 O 1219 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6491 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1590 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.92, per 1000 atoms: 0.91 Number of scatterers: 6491 At special positions: 0 Unit cell: (98.056, 70.04, 119.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Cl 1 17.00 S 37 16.00 O 1219 8.00 N 1076 7.00 C 4157 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.04 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.02 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG D 901 " - " ASN D 322 " " NAG D 902 " - " ASN D 546 " " NAG D 903 " - " ASN D 90 " Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 935.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 905 " pdb="ZN ZN D 905 " - pdb=" NE2 HIS D 374 " 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1498 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 55.1% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 362 through 368 removed outlier: 3.767A pdb=" N LEU A 365 " --> pdb=" O TYR A 362 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR A 366 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 removed outlier: 3.817A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 381 through 385' Processing helix chain 'A' and resid 402 through 407 removed outlier: 4.669A pdb=" N ARG A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 removed outlier: 3.508A pdb=" N SER A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 53 removed outlier: 3.590A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 3.525A pdb=" N GLN D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.554A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 108 removed outlier: 4.046A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 removed outlier: 3.501A pdb=" N SER D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.522A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 176 removed outlier: 3.512A pdb=" N ARG D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 194 removed outlier: 3.709A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 205 through 208 Processing helix chain 'D' and resid 218 through 252 removed outlier: 3.765A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.621A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.607A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.849A pdb=" N ASP D 299 " --> pdb=" O ASP D 295 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 318 removed outlier: 3.739A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.882A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.574A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.615A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.701A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 removed outlier: 3.524A pdb=" N LYS D 419 " --> pdb=" O PRO D 415 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE D 421 " --> pdb=" O HIS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 446 removed outlier: 3.604A pdb=" N ILE D 436 " --> pdb=" O ASN D 432 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASN D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS D 441 " --> pdb=" O ASN D 437 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.579A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.608A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.890A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.515A pdb=" N ASN D 556 " --> pdb=" O GLN D 552 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AA2, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA3, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AA4, first strand: chain 'D' and resid 131 through 133 Processing sheet with id=AA5, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.046A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.130A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 277 hydrogen bonds defined for protein. 783 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: 1.73 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2061 1.34 - 1.46: 1592 1.46 - 1.58: 2962 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6673 Sorted by residual: bond pdb=" C1 NAG D 901 " pdb=" O5 NAG D 901 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.64e+00 bond pdb=" C1 NAG D 902 " pdb=" O5 NAG D 902 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.42e+00 bond pdb=" C1 NAG D 903 " pdb=" O5 NAG D 903 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.75e+00 bond pdb=" CB PRO D 500 " pdb=" CG PRO D 500 " ideal model delta sigma weight residual 1.492 1.419 0.073 5.00e-02 4.00e+02 2.11e+00 bond pdb=" CB PRO D 583 " pdb=" CG PRO D 583 " ideal model delta sigma weight residual 1.492 1.420 0.072 5.00e-02 4.00e+02 2.07e+00 ... (remaining 6668 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 8704 1.62 - 3.25: 300 3.25 - 4.87: 46 4.87 - 6.49: 14 6.49 - 8.11: 6 Bond angle restraints: 9070 Sorted by residual: angle pdb=" N ILE D 421 " pdb=" CA ILE D 421 " pdb=" C ILE D 421 " ideal model delta sigma weight residual 113.43 108.55 4.88 1.09e+00 8.42e-01 2.01e+01 angle pdb=" C ILE D 233 " pdb=" N LYS D 234 " pdb=" CA LYS D 234 " ideal model delta sigma weight residual 120.06 124.21 -4.15 1.19e+00 7.06e-01 1.21e+01 angle pdb=" CA TYR D 385 " pdb=" CB TYR D 385 " pdb=" CG TYR D 385 " ideal model delta sigma weight residual 113.90 120.02 -6.12 1.80e+00 3.09e-01 1.16e+01 angle pdb=" C PRO A 476 " pdb=" N CYS A 477 " pdb=" CA CYS A 477 " ideal model delta sigma weight residual 121.54 127.95 -6.41 1.91e+00 2.74e-01 1.13e+01 angle pdb=" C VAL A 364 " pdb=" CA VAL A 364 " pdb=" CB VAL A 364 " ideal model delta sigma weight residual 111.29 116.74 -5.45 1.64e+00 3.72e-01 1.11e+01 ... (remaining 9065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 3518 17.40 - 34.79: 354 34.79 - 52.19: 87 52.19 - 69.59: 13 69.59 - 86.98: 8 Dihedral angle restraints: 3980 sinusoidal: 1648 harmonic: 2332 Sorted by residual: dihedral pdb=" CA TYR D 83 " pdb=" C TYR D 83 " pdb=" N PRO D 84 " pdb=" CA PRO D 84 " ideal model delta harmonic sigma weight residual -180.00 -155.62 -24.38 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA ALA A 369 " pdb=" C ALA A 369 " pdb=" N PRO A 370 " pdb=" CA PRO A 370 " ideal model delta harmonic sigma weight residual 180.00 156.01 23.99 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA PHE A 371 " pdb=" C PHE A 371 " pdb=" N PHE A 372 " pdb=" CA PHE A 372 " ideal model delta harmonic sigma weight residual -180.00 -158.24 -21.76 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 3977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 596 0.040 - 0.081: 264 0.081 - 0.121: 80 0.121 - 0.162: 15 0.162 - 0.202: 2 Chirality restraints: 957 Sorted by residual: chirality pdb=" CB VAL D 581 " pdb=" CA VAL D 581 " pdb=" CG1 VAL D 581 " pdb=" CG2 VAL D 581 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB THR A 427 " pdb=" CA THR A 427 " pdb=" OG1 THR A 427 " pdb=" CG2 THR A 427 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.11e-01 chirality pdb=" CB VAL A 379 " pdb=" CA VAL A 379 " pdb=" CG1 VAL A 379 " pdb=" CG2 VAL A 379 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.14e-01 ... (remaining 954 not shown) Planarity restraints: 1175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 369 " 0.058 5.00e-02 4.00e+02 8.86e-02 1.25e+01 pdb=" N PRO A 370 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 517 " -0.041 5.00e-02 4.00e+02 6.18e-02 6.12e+00 pdb=" N PRO A 518 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 518 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 518 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 234 " 0.041 5.00e-02 4.00e+02 6.16e-02 6.07e+00 pdb=" N PRO D 235 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO D 235 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 235 " 0.035 5.00e-02 4.00e+02 ... (remaining 1172 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 93 2.66 - 3.22: 5481 3.22 - 3.78: 10416 3.78 - 4.34: 15330 4.34 - 4.90: 24216 Nonbonded interactions: 55536 Sorted by model distance: nonbonded pdb=" OE2 GLU D 402 " pdb="ZN ZN D 905 " model vdw 2.101 2.230 nonbonded pdb=" O ALA D 501 " pdb=" OG SER D 507 " model vdw 2.267 3.040 nonbonded pdb=" OH TYR D 183 " pdb=" OD1 ASP D 509 " model vdw 2.299 3.040 nonbonded pdb=" O LYS D 114 " pdb=" OG1 THR D 118 " model vdw 2.303 3.040 nonbonded pdb=" OE1 GLU A 403 " pdb=" OH TYR A 492 " model vdw 2.304 3.040 ... (remaining 55531 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.920 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.890 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:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 6673 Z= 0.337 Angle : 0.740 8.114 9070 Z= 0.414 Chirality : 0.049 0.202 957 Planarity : 0.007 0.089 1172 Dihedral : 15.214 86.982 2464 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.29 % Allowed : 3.86 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -4.67 (0.21), residues: 789 helix: -4.20 (0.11), residues: 382 sheet: 0.13 (0.70), residues: 53 loop : -2.13 (0.27), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 433 HIS 0.004 0.001 HIS D 417 PHE 0.014 0.002 PHE D 230 TYR 0.035 0.002 TYR D 381 ARG 0.003 0.001 ARG D 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 GLU cc_start: 0.7505 (pt0) cc_final: 0.7226 (pp20) REVERT: A 375 LYS cc_start: 0.7910 (mttp) cc_final: 0.7019 (tptp) REVERT: D 194 ASN cc_start: 0.8408 (m-40) cc_final: 0.8169 (m110) REVERT: D 295 ASP cc_start: 0.7274 (t70) cc_final: 0.7015 (t0) REVERT: D 470 LYS cc_start: 0.7862 (pttp) cc_final: 0.7130 (mttm) REVERT: D 494 ASP cc_start: 0.7403 (p0) cc_final: 0.7180 (p0) REVERT: D 578 ASN cc_start: 0.8306 (p0) cc_final: 0.7601 (t0) REVERT: D 582 ARG cc_start: 0.7710 (tpp-160) cc_final: 0.7441 (tpp-160) outliers start: 2 outliers final: 0 residues processed: 118 average time/residue: 1.3100 time to fit residues: 162.2566 Evaluate side-chains 86 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.0870 chunk 59 optimal weight: 0.4980 chunk 32 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.0970 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN A 471 GLN D 76 GLN D 98 GLN D 101 GLN D 194 ASN D 300 GLN D 378 HIS D 505 HIS D 531 GLN D 556 ASN D 586 ASN D 599 ASN D 601 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6673 Z= 0.163 Angle : 0.540 7.788 9070 Z= 0.285 Chirality : 0.042 0.202 957 Planarity : 0.006 0.063 1172 Dihedral : 5.577 56.193 926 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.00 % Allowed : 10.59 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.26 (0.26), residues: 789 helix: -1.67 (0.23), residues: 391 sheet: 0.55 (0.74), residues: 48 loop : -1.43 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 566 HIS 0.003 0.001 HIS D 241 PHE 0.012 0.001 PHE D 315 TYR 0.013 0.001 TYR D 385 ARG 0.007 0.000 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 GLU cc_start: 0.7535 (pt0) cc_final: 0.7146 (pp20) REVERT: A 353 LYS cc_start: 0.8094 (tttp) cc_final: 0.7875 (tttm) REVERT: D 201 ASP cc_start: 0.8760 (t0) cc_final: 0.8520 (t0) REVERT: D 295 ASP cc_start: 0.6980 (t70) cc_final: 0.6615 (t0) REVERT: D 470 LYS cc_start: 0.7959 (pttp) cc_final: 0.7398 (mttm) REVERT: D 582 ARG cc_start: 0.7641 (tpp-160) cc_final: 0.7142 (tpm170) REVERT: D 597 ASP cc_start: 0.7799 (t70) cc_final: 0.7082 (m-30) outliers start: 7 outliers final: 1 residues processed: 99 average time/residue: 1.3821 time to fit residues: 143.3354 Evaluate side-chains 78 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 194 ASN D 401 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6673 Z= 0.216 Angle : 0.543 6.583 9070 Z= 0.284 Chirality : 0.044 0.211 957 Planarity : 0.005 0.055 1172 Dihedral : 5.426 57.114 926 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.43 % Allowed : 11.16 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.19 (0.29), residues: 789 helix: -0.57 (0.26), residues: 393 sheet: 0.45 (0.74), residues: 48 loop : -1.10 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 478 HIS 0.003 0.001 HIS D 535 PHE 0.012 0.001 PHE D 32 TYR 0.016 0.001 TYR D 385 ARG 0.007 0.001 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 GLU cc_start: 0.7590 (pt0) cc_final: 0.7246 (pp20) REVERT: D 22 GLU cc_start: 0.7891 (tt0) cc_final: 0.7633 (tt0) REVERT: D 118 THR cc_start: 0.8430 (p) cc_final: 0.7980 (t) REVERT: D 295 ASP cc_start: 0.7015 (t70) cc_final: 0.6542 (t0) REVERT: D 470 LYS cc_start: 0.8102 (pttp) cc_final: 0.7396 (mttm) REVERT: D 582 ARG cc_start: 0.7605 (tpp-160) cc_final: 0.7085 (tpm170) REVERT: D 597 ASP cc_start: 0.7885 (t70) cc_final: 0.7118 (m-30) outliers start: 17 outliers final: 5 residues processed: 99 average time/residue: 1.2951 time to fit residues: 134.8809 Evaluate side-chains 85 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain D residue 298 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 0.0470 chunk 20 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN D 154 ASN D 401 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6673 Z= 0.220 Angle : 0.535 6.854 9070 Z= 0.281 Chirality : 0.044 0.230 957 Planarity : 0.005 0.078 1172 Dihedral : 5.367 57.409 926 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.29 % Allowed : 12.30 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.73 (0.29), residues: 789 helix: -0.12 (0.26), residues: 393 sheet: 0.50 (0.75), residues: 48 loop : -0.95 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 478 HIS 0.003 0.001 HIS D 535 PHE 0.011 0.001 PHE D 32 TYR 0.016 0.001 TYR D 385 ARG 0.008 0.000 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 GLU cc_start: 0.7564 (pt0) cc_final: 0.7214 (pp20) REVERT: D 22 GLU cc_start: 0.7879 (tt0) cc_final: 0.7631 (tt0) REVERT: D 118 THR cc_start: 0.8407 (p) cc_final: 0.8006 (t) REVERT: D 295 ASP cc_start: 0.7099 (t70) cc_final: 0.6607 (t0) REVERT: D 470 LYS cc_start: 0.8088 (pttp) cc_final: 0.7375 (mttm) REVERT: D 474 MET cc_start: 0.8311 (mmp) cc_final: 0.7958 (mmp) REVERT: D 582 ARG cc_start: 0.7634 (tpp-160) cc_final: 0.7103 (tpm170) outliers start: 16 outliers final: 9 residues processed: 91 average time/residue: 1.3090 time to fit residues: 125.3633 Evaluate side-chains 89 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.0870 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 401 HIS D 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 6673 Z= 0.256 Angle : 0.567 13.807 9070 Z= 0.295 Chirality : 0.045 0.322 957 Planarity : 0.005 0.066 1172 Dihedral : 5.457 58.223 926 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.86 % Allowed : 12.30 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.56 (0.29), residues: 789 helix: 0.04 (0.26), residues: 394 sheet: -0.06 (0.72), residues: 57 loop : -0.80 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 478 HIS 0.003 0.001 HIS D 241 PHE 0.012 0.001 PHE D 32 TYR 0.017 0.001 TYR D 385 ARG 0.008 0.001 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 GLU cc_start: 0.7601 (pt0) cc_final: 0.7230 (pp20) REVERT: A 375 LYS cc_start: 0.7883 (mttm) cc_final: 0.6950 (tptp) REVERT: A 525 LYS cc_start: 0.6426 (mtmp) cc_final: 0.6015 (pmtt) REVERT: D 22 GLU cc_start: 0.7889 (tt0) cc_final: 0.7650 (tt0) REVERT: D 23 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6972 (mt-10) REVERT: D 118 THR cc_start: 0.8351 (p) cc_final: 0.7976 (t) REVERT: D 295 ASP cc_start: 0.7082 (t70) cc_final: 0.6568 (t0) REVERT: D 470 LYS cc_start: 0.8087 (pttp) cc_final: 0.7373 (mttm) REVERT: D 474 MET cc_start: 0.8302 (mmp) cc_final: 0.7976 (mmp) REVERT: D 582 ARG cc_start: 0.7625 (tpp-160) cc_final: 0.7093 (tpm170) outliers start: 20 outliers final: 12 residues processed: 97 average time/residue: 1.2422 time to fit residues: 126.8187 Evaluate side-chains 93 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 ASN D 401 HIS D 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 6673 Z= 0.413 Angle : 0.644 11.412 9070 Z= 0.337 Chirality : 0.050 0.297 957 Planarity : 0.005 0.064 1172 Dihedral : 5.971 59.732 926 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.29 % Allowed : 13.30 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.78 (0.29), residues: 789 helix: -0.15 (0.26), residues: 395 sheet: -0.07 (0.73), residues: 57 loop : -0.91 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 478 HIS 0.004 0.001 HIS D 241 PHE 0.016 0.002 PHE D 308 TYR 0.021 0.002 TYR D 385 ARG 0.008 0.001 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 GLU cc_start: 0.7617 (pt0) cc_final: 0.7342 (pp20) REVERT: D 22 GLU cc_start: 0.8048 (tt0) cc_final: 0.7815 (tt0) REVERT: D 118 THR cc_start: 0.8309 (p) cc_final: 0.7949 (t) REVERT: D 192 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7342 (mtt90) REVERT: D 295 ASP cc_start: 0.7123 (t70) cc_final: 0.6623 (t0) REVERT: D 470 LYS cc_start: 0.8159 (pttp) cc_final: 0.7298 (mttm) REVERT: D 474 MET cc_start: 0.8350 (mmp) cc_final: 0.7911 (mmp) REVERT: D 582 ARG cc_start: 0.7662 (tpp-160) cc_final: 0.7107 (tpm170) outliers start: 23 outliers final: 11 residues processed: 92 average time/residue: 1.1663 time to fit residues: 113.4539 Evaluate side-chains 88 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 75 optimal weight: 0.4980 chunk 47 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN D 401 HIS D 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 6673 Z= 0.198 Angle : 0.548 14.439 9070 Z= 0.286 Chirality : 0.044 0.286 957 Planarity : 0.004 0.054 1172 Dihedral : 5.406 56.272 926 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.15 % Allowed : 14.88 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.41 (0.30), residues: 789 helix: 0.16 (0.27), residues: 398 sheet: 0.01 (0.74), residues: 57 loop : -0.73 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 566 HIS 0.003 0.001 HIS D 241 PHE 0.011 0.001 PHE D 315 TYR 0.013 0.001 TYR D 385 ARG 0.009 0.000 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: A 337 GLU cc_start: 0.7597 (pt0) cc_final: 0.7211 (pp20) REVERT: A 375 LYS cc_start: 0.7810 (mttm) cc_final: 0.6958 (tptp) REVERT: D 22 GLU cc_start: 0.7773 (tt0) cc_final: 0.7531 (tt0) REVERT: D 23 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6944 (mt-10) REVERT: D 118 THR cc_start: 0.8318 (p) cc_final: 0.7960 (t) REVERT: D 121 ASN cc_start: 0.7754 (m-40) cc_final: 0.7355 (m-40) REVERT: D 295 ASP cc_start: 0.6883 (t70) cc_final: 0.6410 (t0) REVERT: D 470 LYS cc_start: 0.8093 (pttp) cc_final: 0.7303 (mttm) REVERT: D 582 ARG cc_start: 0.7621 (tpp-160) cc_final: 0.7090 (tpm170) outliers start: 15 outliers final: 8 residues processed: 96 average time/residue: 1.2258 time to fit residues: 124.2121 Evaluate side-chains 92 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.0060 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 0.1980 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 42 optimal weight: 0.0040 overall best weight: 0.3008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 391 ASN D 154 ASN D 194 ASN D 531 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 6673 Z= 0.155 Angle : 0.512 13.515 9070 Z= 0.266 Chirality : 0.042 0.257 957 Planarity : 0.004 0.050 1172 Dihedral : 4.957 55.263 926 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.29 % Allowed : 15.31 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.01 (0.30), residues: 789 helix: 0.49 (0.27), residues: 396 sheet: 0.99 (0.79), residues: 47 loop : -0.64 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 566 HIS 0.003 0.001 HIS D 241 PHE 0.010 0.001 PHE D 315 TYR 0.011 0.001 TYR D 183 ARG 0.010 0.000 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: A 337 GLU cc_start: 0.7563 (pt0) cc_final: 0.7172 (pp20) REVERT: A 375 LYS cc_start: 0.7654 (mttm) cc_final: 0.6954 (tptp) REVERT: A 525 LYS cc_start: 0.6450 (mtmp) cc_final: 0.5836 (pmtt) REVERT: D 118 THR cc_start: 0.8309 (p) cc_final: 0.7938 (t) REVERT: D 295 ASP cc_start: 0.6759 (t70) cc_final: 0.6257 (t0) REVERT: D 470 LYS cc_start: 0.7960 (pttp) cc_final: 0.7358 (mttm) REVERT: D 582 ARG cc_start: 0.7558 (tpp-160) cc_final: 0.7055 (tpm170) REVERT: D 597 ASP cc_start: 0.7867 (t70) cc_final: 0.7052 (m-30) outliers start: 16 outliers final: 7 residues processed: 101 average time/residue: 1.2521 time to fit residues: 133.2500 Evaluate side-chains 91 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.0030 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 0.1980 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 0.0000 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN D 401 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 6673 Z= 0.155 Angle : 0.515 13.190 9070 Z= 0.268 Chirality : 0.042 0.252 957 Planarity : 0.004 0.049 1172 Dihedral : 4.812 54.947 926 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.29 % Allowed : 16.02 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.17 (0.30), residues: 789 helix: 0.65 (0.27), residues: 397 sheet: 1.04 (0.79), residues: 47 loop : -0.56 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 433 HIS 0.002 0.001 HIS D 374 PHE 0.011 0.001 PHE D 315 TYR 0.011 0.001 TYR D 183 ARG 0.007 0.000 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: A 337 GLU cc_start: 0.7556 (pt0) cc_final: 0.7130 (pp20) REVERT: A 375 LYS cc_start: 0.7611 (mttm) cc_final: 0.6916 (tptp) REVERT: A 525 LYS cc_start: 0.6407 (mtmp) cc_final: 0.5740 (pmtt) REVERT: D 118 THR cc_start: 0.8245 (p) cc_final: 0.7887 (t) REVERT: D 295 ASP cc_start: 0.6755 (t70) cc_final: 0.6249 (t0) REVERT: D 470 LYS cc_start: 0.7929 (pttp) cc_final: 0.7364 (mttm) REVERT: D 582 ARG cc_start: 0.7568 (tpp-160) cc_final: 0.7066 (tpm170) REVERT: D 597 ASP cc_start: 0.7855 (t70) cc_final: 0.7050 (m-30) outliers start: 9 outliers final: 6 residues processed: 101 average time/residue: 1.2156 time to fit residues: 129.5999 Evaluate side-chains 90 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 49 optimal weight: 0.0050 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 0.0060 chunk 9 optimal weight: 0.6980 overall best weight: 0.4010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 391 ASN D 154 ASN D 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6673 Z= 0.166 Angle : 0.527 13.094 9070 Z= 0.273 Chirality : 0.043 0.252 957 Planarity : 0.004 0.048 1172 Dihedral : 4.861 55.717 926 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.72 % Allowed : 16.88 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.19 (0.30), residues: 789 helix: 0.66 (0.27), residues: 394 sheet: 1.01 (0.79), residues: 47 loop : -0.54 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 433 HIS 0.003 0.001 HIS D 241 PHE 0.011 0.001 PHE D 315 TYR 0.011 0.001 TYR D 183 ARG 0.007 0.000 ARG A 354 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 337 GLU cc_start: 0.7569 (pt0) cc_final: 0.7145 (pp20) REVERT: A 375 LYS cc_start: 0.7612 (mttm) cc_final: 0.6914 (tptp) REVERT: A 525 LYS cc_start: 0.6436 (mtmp) cc_final: 0.5757 (pmtt) REVERT: D 118 THR cc_start: 0.8243 (p) cc_final: 0.7912 (t) REVERT: D 295 ASP cc_start: 0.6773 (t70) cc_final: 0.6265 (t0) REVERT: D 470 LYS cc_start: 0.7938 (pttp) cc_final: 0.7388 (mttm) REVERT: D 582 ARG cc_start: 0.7585 (tpp-160) cc_final: 0.7082 (tpm170) REVERT: D 597 ASP cc_start: 0.7870 (t70) cc_final: 0.7060 (m-30) outliers start: 12 outliers final: 8 residues processed: 92 average time/residue: 1.2325 time to fit residues: 119.6769 Evaluate side-chains 90 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 531 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN D 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.140051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.111001 restraints weight = 7627.780| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.68 r_work: 0.3078 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 6673 Z= 0.274 Angle : 0.600 13.894 9070 Z= 0.312 Chirality : 0.046 0.275 957 Planarity : 0.004 0.051 1172 Dihedral : 5.460 58.652 926 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.72 % Allowed : 16.88 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.09 (0.30), residues: 789 helix: 0.40 (0.26), residues: 398 sheet: 0.07 (0.75), residues: 57 loop : -0.51 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 349 HIS 0.004 0.001 HIS D 535 PHE 0.013 0.001 PHE D 308 TYR 0.016 0.002 TYR D 385 ARG 0.009 0.001 ARG A 354 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2950.19 seconds wall clock time: 54 minutes 8.77 seconds (3248.77 seconds total)