Starting phenix.real_space_refine on Tue Mar 11 19:44:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wpb_32681/03_2025/7wpb_32681_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wpb_32681/03_2025/7wpb_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_32681/03_2025/7wpb_32681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wpb_32681/03_2025/7wpb_32681.map" model { file = "/net/cci-nas-00/data/ceres_data/7wpb_32681/03_2025/7wpb_32681_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wpb_32681/03_2025/7wpb_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 7.53, per 1000 atoms: 1.16 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: 1.37 Conformation dependent library (CDL) restraints added in 883.1 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: 0.81 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: 1.95 Time building geometry restraints manager: 1.71 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: 5.180 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 23.430 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 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:13.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.680 ------------------------------------------------------------------------------- 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 : 0.758 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: 1.2668 time to fit residues: 156.9189 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 : 0.712 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.144028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.114190 restraints weight = 7670.407| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.71 r_work: 0.3131 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 GLU cc_start: 0.8039 (pt0) cc_final: 0.7551 (pp20) REVERT: D 201 ASP cc_start: 0.9030 (t0) cc_final: 0.8823 (t0) REVERT: D 295 ASP cc_start: 0.7248 (t70) cc_final: 0.6832 (t0) REVERT: D 430 GLU cc_start: 0.7451 (pm20) cc_final: 0.7239 (pm20) REVERT: D 470 LYS cc_start: 0.8101 (pttp) cc_final: 0.7433 (mttm) REVERT: D 582 ARG cc_start: 0.8075 (tpp-160) cc_final: 0.7457 (tpm170) REVERT: D 597 ASP cc_start: 0.8233 (t70) cc_final: 0.7387 (m-30) outliers start: 7 outliers final: 1 residues processed: 99 average time/residue: 1.3829 time to fit residues: 143.4629 Evaluate side-chains 79 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 73 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 5 optimal weight: 0.0470 chunk 26 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 ASN D 64 ASN D 194 ASN D 401 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.139194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.109070 restraints weight = 7760.374| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.69 r_work: 0.3076 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6673 Z= 0.328 Angle : 0.602 7.744 9070 Z= 0.315 Chirality : 0.047 0.231 957 Planarity : 0.005 0.056 1172 Dihedral : 5.809 59.030 926 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.58 % Allowed : 11.30 % Favored : 86.12 % 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: -1.34 (0.28), residues: 789 helix: -0.68 (0.25), residues: 393 sheet: -0.25 (0.70), residues: 58 loop : -1.10 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 478 HIS 0.004 0.001 HIS D 401 PHE 0.015 0.002 PHE D 32 TYR 0.020 0.002 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 106 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: A 337 GLU cc_start: 0.8110 (pt0) cc_final: 0.7685 (pp20) REVERT: A 439 ASP cc_start: 0.8573 (m-30) cc_final: 0.8325 (m-30) REVERT: D 22 GLU cc_start: 0.8419 (tt0) cc_final: 0.8186 (tt0) REVERT: D 118 THR cc_start: 0.8361 (p) cc_final: 0.7936 (t) REVERT: D 295 ASP cc_start: 0.7390 (t70) cc_final: 0.6824 (t0) REVERT: D 470 LYS cc_start: 0.8293 (pttp) cc_final: 0.7362 (mttm) REVERT: D 582 ARG cc_start: 0.8110 (tpp-160) cc_final: 0.7491 (tpm170) outliers start: 18 outliers final: 8 residues processed: 96 average time/residue: 1.3334 time to fit residues: 134.5249 Evaluate side-chains 87 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 424 ASP 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 42 optimal weight: 8.9990 chunk 29 optimal weight: 0.3980 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 0.0570 chunk 62 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.141739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.113283 restraints weight = 7735.597| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.71 r_work: 0.3132 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6673 Z= 0.185 Angle : 0.519 6.717 9070 Z= 0.272 Chirality : 0.043 0.230 957 Planarity : 0.004 0.052 1172 Dihedral : 5.283 56.153 926 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.43 % Allowed : 11.87 % Favored : 85.69 % 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: -0.70 (0.29), residues: 789 helix: -0.10 (0.26), residues: 394 sheet: 0.51 (0.76), residues: 48 loop : -0.93 (0.32), residues: 347 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 0.011 0.001 PHE D 315 TYR 0.014 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 103 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 337 GLU cc_start: 0.8044 (pt0) cc_final: 0.7619 (pp20) REVERT: A 439 ASP cc_start: 0.8328 (m-30) cc_final: 0.8089 (m-30) REVERT: D 22 GLU cc_start: 0.8238 (tt0) cc_final: 0.8016 (tt0) REVERT: D 118 THR cc_start: 0.8379 (p) cc_final: 0.7991 (t) REVERT: D 295 ASP cc_start: 0.7398 (t70) cc_final: 0.6858 (t0) REVERT: D 470 LYS cc_start: 0.8219 (pttp) cc_final: 0.7428 (mttm) REVERT: D 474 MET cc_start: 0.8414 (mmp) cc_final: 0.8196 (mmp) REVERT: D 582 ARG cc_start: 0.8070 (tpp-160) cc_final: 0.7460 (tpm170) REVERT: D 597 ASP cc_start: 0.8285 (t70) cc_final: 0.7373 (m-30) outliers start: 17 outliers final: 7 residues processed: 98 average time/residue: 1.2919 time to fit residues: 133.4336 Evaluate side-chains 86 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 522 CYS Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 298 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.0170 chunk 50 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 401 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.141692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.113252 restraints weight = 7705.889| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.71 r_work: 0.3127 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 6673 Z= 0.198 Angle : 0.536 13.597 9070 Z= 0.280 Chirality : 0.044 0.312 957 Planarity : 0.005 0.081 1172 Dihedral : 5.242 56.960 926 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.72 % Allowed : 13.16 % Favored : 84.12 % 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: -0.45 (0.30), residues: 789 helix: 0.14 (0.26), residues: 397 sheet: 0.70 (0.77), residues: 47 loop : -0.86 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 478 HIS 0.003 0.001 HIS D 241 PHE 0.010 0.001 PHE D 315 TYR 0.014 0.001 TYR D 385 ARG 0.008 0.000 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 109 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 337 GLU cc_start: 0.8057 (pt0) cc_final: 0.7620 (pp20) REVERT: A 375 LYS cc_start: 0.8050 (mttm) cc_final: 0.7104 (tptp) REVERT: A 439 ASP cc_start: 0.8328 (m-30) cc_final: 0.8086 (m-30) REVERT: A 525 LYS cc_start: 0.6314 (mtmm) cc_final: 0.5985 (pmtt) REVERT: D 23 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7355 (mt-10) REVERT: D 118 THR cc_start: 0.8371 (p) cc_final: 0.8008 (t) REVERT: D 295 ASP cc_start: 0.7385 (t70) cc_final: 0.6852 (t0) REVERT: D 470 LYS cc_start: 0.8167 (pttp) cc_final: 0.7427 (mttm) REVERT: D 582 ARG cc_start: 0.8057 (tpp-160) cc_final: 0.7443 (tpm170) outliers start: 19 outliers final: 10 residues processed: 100 average time/residue: 1.3018 time to fit residues: 136.8987 Evaluate side-chains 94 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 480 VAL 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 23 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 0.0020 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 401 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.142193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.113929 restraints weight = 7633.378| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.64 r_work: 0.3129 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6673 Z= 0.187 Angle : 0.525 11.158 9070 Z= 0.275 Chirality : 0.043 0.271 957 Planarity : 0.004 0.068 1172 Dihedral : 5.138 56.557 926 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.72 % Allowed : 13.73 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.24 (0.30), residues: 789 helix: 0.31 (0.27), residues: 396 sheet: 0.66 (0.77), residues: 47 loop : -0.74 (0.33), residues: 346 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 0.010 0.001 PHE D 315 TYR 0.014 0.001 TYR D 385 ARG 0.009 0.000 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 107 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 GLU cc_start: 0.8011 (pt0) cc_final: 0.7572 (pp20) REVERT: A 375 LYS cc_start: 0.7995 (mttm) cc_final: 0.7035 (tptp) REVERT: A 439 ASP cc_start: 0.8355 (m-30) cc_final: 0.8120 (m-30) REVERT: A 525 LYS cc_start: 0.6405 (mtmm) cc_final: 0.5996 (pmtt) REVERT: D 23 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7338 (mt-10) REVERT: D 118 THR cc_start: 0.8307 (p) cc_final: 0.7972 (t) REVERT: D 295 ASP cc_start: 0.7324 (t70) cc_final: 0.6793 (t0) REVERT: D 470 LYS cc_start: 0.8127 (pttp) cc_final: 0.7397 (mttm) REVERT: D 582 ARG cc_start: 0.8019 (tpp-160) cc_final: 0.7419 (tpm170) REVERT: D 597 ASP cc_start: 0.8261 (t70) cc_final: 0.7332 (m-30) outliers start: 19 outliers final: 10 residues processed: 100 average time/residue: 1.2411 time to fit residues: 130.9041 Evaluate side-chains 93 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 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 440 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 0.0980 chunk 23 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 44 optimal weight: 4.9990 chunk 45 optimal weight: 0.0030 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN D 117 ASN D 175 GLN D 194 ASN D 401 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.144073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.115667 restraints weight = 7646.244| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.72 r_work: 0.3152 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 6673 Z= 0.159 Angle : 0.516 14.226 9070 Z= 0.269 Chirality : 0.043 0.278 957 Planarity : 0.004 0.059 1172 Dihedral : 4.926 55.646 926 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.00 % Allowed : 14.74 % Favored : 83.26 % 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: -0.02 (0.30), residues: 789 helix: 0.49 (0.27), residues: 393 sheet: 0.87 (0.80), residues: 47 loop : -0.63 (0.33), residues: 349 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 0.010 0.001 PHE D 315 TYR 0.012 0.001 TYR D 50 ARG 0.007 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 103 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 337 GLU cc_start: 0.8032 (pt0) cc_final: 0.7605 (pp20) REVERT: A 375 LYS cc_start: 0.7917 (mttm) cc_final: 0.7113 (tptp) REVERT: A 439 ASP cc_start: 0.8321 (m-30) cc_final: 0.8048 (m-30) REVERT: A 525 LYS cc_start: 0.6382 (mtmm) cc_final: 0.5924 (pmtt) REVERT: D 23 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7348 (mt-10) REVERT: D 118 THR cc_start: 0.8345 (p) cc_final: 0.7992 (t) REVERT: D 295 ASP cc_start: 0.7144 (t70) cc_final: 0.6603 (t0) REVERT: D 470 LYS cc_start: 0.8103 (pttp) cc_final: 0.7432 (mttm) REVERT: D 582 ARG cc_start: 0.8013 (tpp-160) cc_final: 0.7444 (tpm170) REVERT: D 597 ASP cc_start: 0.8277 (t70) cc_final: 0.7345 (m-30) outliers start: 14 outliers final: 7 residues processed: 99 average time/residue: 1.2117 time to fit residues: 126.3448 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 : 0.795 ------------------------------------------------------------------------------- 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 23 GLU Chi-restraints excluded: chain D residue 183 TYR 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 41 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 36 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 67 optimal weight: 0.4980 chunk 58 optimal weight: 0.0980 chunk 50 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 0.0970 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN D 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.144569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.116085 restraints weight = 7656.333| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.73 r_work: 0.3158 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 6673 Z= 0.155 Angle : 0.510 13.378 9070 Z= 0.265 Chirality : 0.042 0.261 957 Planarity : 0.004 0.055 1172 Dihedral : 4.835 55.703 926 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.29 % Allowed : 15.16 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.13 (0.30), residues: 789 helix: 0.62 (0.27), residues: 393 sheet: 0.84 (0.79), residues: 47 loop : -0.54 (0.33), residues: 349 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 0.010 0.001 PHE D 315 TYR 0.011 0.001 TYR D 183 ARG 0.008 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 : 1.321 Fit side-chains revert: symmetry clash REVERT: A 337 GLU cc_start: 0.8001 (pt0) cc_final: 0.7545 (pp20) REVERT: A 375 LYS cc_start: 0.7822 (mttm) cc_final: 0.7045 (tptp) REVERT: A 525 LYS cc_start: 0.6400 (mtmm) cc_final: 0.5913 (pmtt) REVERT: D 118 THR cc_start: 0.8295 (p) cc_final: 0.7965 (t) REVERT: D 295 ASP cc_start: 0.7139 (t70) cc_final: 0.6604 (t0) REVERT: D 383 MET cc_start: 0.9235 (mtp) cc_final: 0.8939 (mtp) REVERT: D 470 LYS cc_start: 0.8073 (pttp) cc_final: 0.7455 (mttm) REVERT: D 582 ARG cc_start: 0.8003 (tpp-160) cc_final: 0.7441 (tpm170) REVERT: D 597 ASP cc_start: 0.8266 (t70) cc_final: 0.7344 (m-30) outliers start: 16 outliers final: 7 residues processed: 99 average time/residue: 1.2143 time to fit residues: 127.1603 Evaluate side-chains 90 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 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 440 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN D 154 ASN D 194 ASN D 401 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.140065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.111071 restraints weight = 7770.816| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.77 r_work: 0.3098 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 6673 Z= 0.275 Angle : 0.592 14.032 9070 Z= 0.308 Chirality : 0.046 0.282 957 Planarity : 0.004 0.057 1172 Dihedral : 5.413 58.742 926 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.86 % Allowed : 15.45 % 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: -0.11 (0.30), residues: 789 helix: 0.40 (0.26), residues: 398 sheet: 0.05 (0.76), residues: 57 loop : -0.54 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 349 HIS 0.004 0.001 HIS D 535 PHE 0.013 0.002 PHE D 308 TYR 0.018 0.002 TYR D 385 ARG 0.008 0.001 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 96 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 GLU cc_start: 0.8069 (pt0) cc_final: 0.7615 (pp20) REVERT: A 375 LYS cc_start: 0.8002 (mttm) cc_final: 0.7140 (tptp) REVERT: A 525 LYS cc_start: 0.6394 (mtmm) cc_final: 0.6001 (pmtt) REVERT: D 118 THR cc_start: 0.8284 (p) cc_final: 0.7977 (t) REVERT: D 121 ASN cc_start: 0.7758 (m-40) cc_final: 0.7425 (m-40) REVERT: D 295 ASP cc_start: 0.7290 (t70) cc_final: 0.6745 (t0) REVERT: D 383 MET cc_start: 0.9269 (mtp) cc_final: 0.9007 (mtp) REVERT: D 470 LYS cc_start: 0.8150 (pttp) cc_final: 0.7452 (mttm) REVERT: D 582 ARG cc_start: 0.8057 (tpp-160) cc_final: 0.7441 (tpm170) outliers start: 13 outliers final: 9 residues processed: 93 average time/residue: 1.2249 time to fit residues: 120.2311 Evaluate side-chains 90 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 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 440 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN D 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.140432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.111387 restraints weight = 7741.947| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.65 r_work: 0.3108 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 6673 Z= 0.250 Angle : 0.579 13.723 9070 Z= 0.301 Chirality : 0.045 0.278 957 Planarity : 0.004 0.058 1172 Dihedral : 5.393 57.623 926 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.72 % Allowed : 15.88 % 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: -0.15 (0.30), residues: 789 helix: 0.37 (0.26), residues: 398 sheet: -0.01 (0.75), residues: 57 loop : -0.55 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 478 HIS 0.003 0.001 HIS D 241 PHE 0.012 0.001 PHE D 32 TYR 0.016 0.001 TYR D 385 ARG 0.008 0.001 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 91 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 GLU cc_start: 0.8095 (pt0) cc_final: 0.7643 (pp20) REVERT: A 375 LYS cc_start: 0.7999 (mttm) cc_final: 0.7140 (tptp) REVERT: D 118 THR cc_start: 0.8337 (p) cc_final: 0.8016 (t) REVERT: D 121 ASN cc_start: 0.7722 (m-40) cc_final: 0.7383 (m-40) REVERT: D 295 ASP cc_start: 0.7179 (t70) cc_final: 0.6637 (t0) REVERT: D 383 MET cc_start: 0.9270 (mtp) cc_final: 0.8992 (mtp) REVERT: D 470 LYS cc_start: 0.8149 (pttp) cc_final: 0.7466 (mttm) REVERT: D 582 ARG cc_start: 0.8040 (tpp-160) cc_final: 0.7447 (tpm170) outliers start: 12 outliers final: 9 residues processed: 88 average time/residue: 1.1874 time to fit residues: 110.6234 Evaluate side-chains 87 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 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 440 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 23 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN D 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.138571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.109966 restraints weight = 7872.069| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.58 r_work: 0.3069 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 6673 Z= 0.346 Angle : 0.633 14.146 9070 Z= 0.330 Chirality : 0.048 0.293 957 Planarity : 0.005 0.061 1172 Dihedral : 5.802 58.792 926 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.57 % Allowed : 15.88 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.34 (0.30), residues: 789 helix: 0.19 (0.26), residues: 401 sheet: -0.04 (0.76), residues: 57 loop : -0.64 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 349 HIS 0.004 0.001 HIS D 493 PHE 0.015 0.002 PHE D 32 TYR 0.019 0.002 TYR D 385 ARG 0.008 0.001 ARG A 354 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5074.47 seconds wall clock time: 87 minutes 15.23 seconds (5235.23 seconds total)