Starting phenix.real_space_refine on Mon Mar 11 01:20:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpb_32681/03_2024/7wpb_32681_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpb_32681/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpb_32681/03_2024/7wpb_32681.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpb_32681/03_2024/7wpb_32681.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpb_32681/03_2024/7wpb_32681_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpb_32681/03_2024/7wpb_32681_neut.pdb" } 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 Residue "A GLU 337": "OE1" <-> "OE2" Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A ARG 490": "NH1" <-> "NH2" Residue "A ARG 495": "NH1" <-> "NH2" Residue "A GLU 513": "OE1" <-> "OE2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D GLU 208": "OE1" <-> "OE2" Residue "D GLU 238": "OE1" <-> "OE2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "D GLU 406": "OE1" <-> "OE2" Residue "D GLU 467": "OE1" <-> "OE2" Residue "D GLU 483": "OE1" <-> "OE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D GLU 549": "OE1" <-> "OE2" Residue "D ARG 559": "NH1" <-> "NH2" Residue "D GLU 564": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6491 Number of models: 1 Model: "" Number of chains: 2 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: 4901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4901 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 3} Classifications: {'peptide': 595, 'undetermined': 5} Link IDs: {'PTRANS': 27, 'TRANS': 567, None: 5} Not linked: pdbres="TYR D 613 " pdbres="NAG D 901 " Not linked: pdbres="NAG D 901 " pdbres="NAG D 902 " Not linked: pdbres="NAG D 902 " pdbres="NAG D 903 " Not linked: pdbres="NAG D 903 " pdbres=" CL D 904 " Not linked: pdbres=" CL D 904 " pdbres=" ZN D 905 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.06, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 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: 2.32 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.64 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: 1.78 Time building geometry restraints manager: 2.55 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: 98.90 - 105.94: 155 105.94 - 112.98: 3415 112.98 - 120.02: 2504 120.02 - 127.06: 2896 127.06 - 134.10: 100 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 2.440 nonbonded pdb=" OH TYR D 183 " pdb=" OD1 ASP D 509 " model vdw 2.299 2.440 nonbonded pdb=" O LYS D 114 " pdb=" OG1 THR D 118 " model vdw 2.303 2.440 nonbonded pdb=" OE1 GLU A 403 " pdb=" OH TYR A 492 " model vdw 2.304 2.440 ... (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 ========== 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: 5.630 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: 24.470 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 22.660 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.380 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 0.726 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: 1.4103 time to fit residues: 175.0709 Evaluate side-chains 86 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 4.9990 chunk 59 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN A 436 ASN A 471 GLN A 474 ASN D 76 GLN D 98 GLN D 101 GLN 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6673 Z= 0.211 Angle : 0.556 7.669 9070 Z= 0.294 Chirality : 0.043 0.209 957 Planarity : 0.006 0.063 1172 Dihedral : 5.763 57.731 926 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.86 % Allowed : 9.87 % Favored : 88.27 % 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: -2.27 (0.26), residues: 789 helix: -1.68 (0.23), residues: 392 sheet: 0.54 (0.74), residues: 48 loop : -1.44 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 433 HIS 0.004 0.001 HIS D 241 PHE 0.012 0.001 PHE D 315 TYR 0.015 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 108 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 GLU cc_start: 0.7566 (pt0) cc_final: 0.7248 (pp20) REVERT: D 22 GLU cc_start: 0.7929 (tt0) cc_final: 0.7650 (tt0) REVERT: D 201 ASP cc_start: 0.8749 (t0) cc_final: 0.8455 (t0) REVERT: D 295 ASP cc_start: 0.7045 (t70) cc_final: 0.6682 (t0) REVERT: D 470 LYS cc_start: 0.7826 (pttp) cc_final: 0.7135 (mttm) REVERT: D 578 ASN cc_start: 0.8233 (p0) cc_final: 0.7582 (t0) REVERT: D 582 ARG cc_start: 0.7623 (tpp-160) cc_final: 0.7087 (tpm170) outliers start: 13 outliers final: 5 residues processed: 102 average time/residue: 1.2872 time to fit residues: 138.0114 Evaluate side-chains 85 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 118 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 0.2980 chunk 59 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 57 optimal weight: 0.0970 chunk 54 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN D 117 ASN D 401 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6673 Z= 0.168 Angle : 0.506 6.311 9070 Z= 0.264 Chirality : 0.042 0.209 957 Planarity : 0.004 0.056 1172 Dihedral : 5.179 55.751 926 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.29 % Allowed : 11.73 % Favored : 85.98 % 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: -1.03 (0.29), residues: 789 helix: -0.40 (0.26), residues: 391 sheet: 0.40 (0.74), residues: 48 loop : -1.05 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 433 HIS 0.004 0.001 HIS D 535 PHE 0.011 0.001 PHE D 315 TYR 0.013 0.001 TYR D 385 ARG 0.007 0.000 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 111 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 GLU cc_start: 0.7549 (pt0) cc_final: 0.7132 (pp20) REVERT: D 22 GLU cc_start: 0.7819 (tt0) cc_final: 0.7581 (tt0) REVERT: D 295 ASP cc_start: 0.7027 (t70) cc_final: 0.6579 (t0) REVERT: D 470 LYS cc_start: 0.7730 (pttp) cc_final: 0.7133 (mttm) REVERT: D 578 ASN cc_start: 0.8168 (p0) cc_final: 0.7578 (t0) REVERT: D 582 ARG cc_start: 0.7637 (tpp-160) cc_final: 0.7121 (tpm170) outliers start: 16 outliers final: 7 residues processed: 104 average time/residue: 1.2343 time to fit residues: 135.0354 Evaluate side-chains 91 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 351 ASN 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 298 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN D 154 ASN D 401 HIS D 531 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6673 Z= 0.216 Angle : 0.526 6.877 9070 Z= 0.275 Chirality : 0.043 0.235 957 Planarity : 0.005 0.076 1172 Dihedral : 5.294 57.607 926 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.15 % Allowed : 12.59 % Favored : 84.26 % 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: -0.62 (0.29), residues: 789 helix: 0.02 (0.26), residues: 396 sheet: 0.43 (0.74), residues: 48 loop : -0.94 (0.32), 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 535 PHE 0.011 0.001 PHE D 32 TYR 0.016 0.001 TYR D 385 ARG 0.007 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 110 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 88 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 GLU cc_start: 0.7570 (pt0) cc_final: 0.7178 (pp20) REVERT: A 525 LYS cc_start: 0.6188 (mtmm) cc_final: 0.5936 (pmtt) REVERT: D 22 GLU cc_start: 0.7741 (tt0) cc_final: 0.7486 (tt0) REVERT: D 295 ASP cc_start: 0.7053 (t70) cc_final: 0.6593 (t0) REVERT: D 470 LYS cc_start: 0.7706 (pttp) cc_final: 0.7202 (mttm) REVERT: D 578 ASN cc_start: 0.8181 (p0) cc_final: 0.7579 (t0) REVERT: D 582 ARG cc_start: 0.7615 (tpp-160) cc_final: 0.7078 (tpm170) outliers start: 22 outliers final: 8 residues processed: 101 average time/residue: 1.2840 time to fit residues: 136.8612 Evaluate side-chains 91 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 351 ASN 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 118 THR 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: 79 random chunks: chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 0.0980 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN D 401 HIS D 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 6673 Z= 0.268 Angle : 0.568 13.782 9070 Z= 0.296 Chirality : 0.045 0.321 957 Planarity : 0.005 0.065 1172 Dihedral : 5.481 58.446 926 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.00 % Allowed : 14.02 % 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: -0.52 (0.30), residues: 789 helix: 0.07 (0.27), residues: 395 sheet: -0.12 (0.71), residues: 57 loop : -0.76 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 478 HIS 0.004 0.001 HIS D 535 PHE 0.012 0.001 PHE D 32 TYR 0.017 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 fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 GLU cc_start: 0.7600 (pt0) cc_final: 0.7231 (pp20) REVERT: A 375 LYS cc_start: 0.7881 (mttm) cc_final: 0.6951 (tptp) REVERT: A 525 LYS cc_start: 0.6211 (mtmm) cc_final: 0.5970 (pmtt) REVERT: D 22 GLU cc_start: 0.7755 (tt0) cc_final: 0.7525 (tt0) REVERT: D 182 GLU cc_start: 0.7415 (tt0) cc_final: 0.7200 (pt0) REVERT: D 295 ASP cc_start: 0.7021 (t70) cc_final: 0.6497 (t0) REVERT: D 470 LYS cc_start: 0.7896 (pttp) cc_final: 0.7219 (mttm) REVERT: D 578 ASN cc_start: 0.8195 (p0) cc_final: 0.7573 (t0) REVERT: D 582 ARG cc_start: 0.7611 (tpp-160) cc_final: 0.7079 (tpm170) outliers start: 21 outliers final: 9 residues processed: 100 average time/residue: 1.2552 time to fit residues: 132.1553 Evaluate side-chains 94 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 351 ASN 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 522 CYS Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 298 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 0.0570 chunk 55 optimal weight: 0.9980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN A 391 ASN D 401 HIS D 531 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2240 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= 0.178 Angle : 0.512 11.368 9070 Z= 0.266 Chirality : 0.043 0.275 957 Planarity : 0.004 0.057 1172 Dihedral : 5.111 56.142 926 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.43 % Allowed : 15.02 % 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: -0.23 (0.30), residues: 789 helix: 0.33 (0.27), residues: 396 sheet: 0.70 (0.76), residues: 47 loop : -0.76 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 566 HIS 0.003 0.001 HIS D 535 PHE 0.011 0.001 PHE D 315 TYR 0.013 0.001 TYR D 385 ARG 0.008 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 106 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 GLU cc_start: 0.7582 (pt0) cc_final: 0.7195 (pp20) REVERT: A 375 LYS cc_start: 0.7779 (mttm) cc_final: 0.6837 (tptp) REVERT: A 525 LYS cc_start: 0.6211 (mtmm) cc_final: 0.5886 (pmtt) REVERT: D 22 GLU cc_start: 0.7617 (tt0) cc_final: 0.7397 (tt0) REVERT: D 121 ASN cc_start: 0.7620 (m-40) cc_final: 0.7232 (m-40) REVERT: D 295 ASP cc_start: 0.6921 (t70) cc_final: 0.6431 (t0) REVERT: D 470 LYS cc_start: 0.7765 (pttp) cc_final: 0.7179 (mttm) REVERT: D 582 ARG cc_start: 0.7587 (tpp-160) cc_final: 0.7062 (tpm170) outliers start: 17 outliers final: 10 residues processed: 99 average time/residue: 1.2757 time to fit residues: 133.1416 Evaluate side-chains 95 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ASN 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 497 THR Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.1980 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN A 351 ASN D 401 HIS D 531 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 6673 Z= 0.177 Angle : 0.516 14.115 9070 Z= 0.268 Chirality : 0.043 0.281 957 Planarity : 0.004 0.053 1172 Dihedral : 5.054 56.615 926 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.43 % Allowed : 15.45 % Favored : 82.12 % 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: -0.00 (0.30), residues: 789 helix: 0.52 (0.27), residues: 393 sheet: 0.87 (0.78), residues: 47 loop : -0.65 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 566 HIS 0.003 0.001 HIS D 535 PHE 0.010 0.001 PHE D 315 TYR 0.012 0.001 TYR D 50 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 103 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 GLU cc_start: 0.7579 (pt0) cc_final: 0.7147 (pp20) REVERT: A 375 LYS cc_start: 0.7741 (mttm) cc_final: 0.6945 (tptp) REVERT: D 22 GLU cc_start: 0.7627 (tt0) cc_final: 0.7403 (tt0) REVERT: D 156 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8497 (mp) REVERT: D 295 ASP cc_start: 0.6762 (t70) cc_final: 0.6237 (t0) REVERT: D 470 LYS cc_start: 0.7697 (pttp) cc_final: 0.7215 (mttm) REVERT: D 582 ARG cc_start: 0.7594 (tpp-160) cc_final: 0.7082 (tpm170) outliers start: 17 outliers final: 9 residues processed: 96 average time/residue: 1.3686 time to fit residues: 138.5966 Evaluate side-chains 92 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 513 GLU Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 156 LEU 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: 79 random chunks: chunk 14 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 42 optimal weight: 0.0020 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN A 351 ASN A 391 ASN D 531 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2340 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= 0.190 Angle : 0.526 13.693 9070 Z= 0.274 Chirality : 0.044 0.271 957 Planarity : 0.004 0.050 1172 Dihedral : 5.073 56.842 926 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.72 % Allowed : 15.31 % Favored : 81.97 % 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: 0.03 (0.30), residues: 789 helix: 0.53 (0.27), residues: 394 sheet: 0.89 (0.79), residues: 47 loop : -0.61 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 566 HIS 0.003 0.001 HIS D 535 PHE 0.010 0.001 PHE D 315 TYR 0.013 0.001 TYR D 50 ARG 0.009 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 107 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 88 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 GLU cc_start: 0.7589 (pt0) cc_final: 0.7173 (pp20) REVERT: A 375 LYS cc_start: 0.7743 (mttm) cc_final: 0.6979 (tptp) REVERT: D 22 GLU cc_start: 0.7629 (tt0) cc_final: 0.7397 (tt0) REVERT: D 118 THR cc_start: 0.8369 (p) cc_final: 0.7911 (t) REVERT: D 121 ASN cc_start: 0.7647 (m-40) cc_final: 0.7257 (m-40) REVERT: D 295 ASP cc_start: 0.6749 (t70) cc_final: 0.6252 (t0) REVERT: D 470 LYS cc_start: 0.7702 (pttp) cc_final: 0.7217 (mttm) REVERT: D 582 ARG cc_start: 0.7581 (tpp-160) cc_final: 0.7066 (tpm170) outliers start: 19 outliers final: 11 residues processed: 101 average time/residue: 1.2064 time to fit residues: 128.5086 Evaluate side-chains 94 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 513 GLU Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain D residue 96 GLN 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: 79 random chunks: chunk 30 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 chunk 75 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN A 351 ASN D 401 HIS D 531 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2349 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= 0.228 Angle : 0.549 13.639 9070 Z= 0.286 Chirality : 0.044 0.273 957 Planarity : 0.004 0.051 1172 Dihedral : 5.244 57.608 926 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.15 % Allowed : 16.60 % Favored : 81.26 % 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: -0.03 (0.30), residues: 789 helix: 0.43 (0.27), residues: 401 sheet: 0.05 (0.73), residues: 57 loop : -0.46 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 478 HIS 0.004 0.001 HIS D 535 PHE 0.011 0.001 PHE D 308 TYR 0.015 0.001 TYR D 385 ARG 0.009 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 99 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 GLU cc_start: 0.7637 (pt0) cc_final: 0.7218 (pp20) REVERT: A 375 LYS cc_start: 0.7758 (mttm) cc_final: 0.6944 (tptp) REVERT: D 22 GLU cc_start: 0.7657 (tt0) cc_final: 0.7436 (tt0) REVERT: D 118 THR cc_start: 0.8329 (p) cc_final: 0.7875 (t) REVERT: D 121 ASN cc_start: 0.7676 (m-40) cc_final: 0.7304 (m-40) REVERT: D 295 ASP cc_start: 0.6758 (t70) cc_final: 0.6261 (t0) REVERT: D 383 MET cc_start: 0.9036 (mtp) cc_final: 0.8797 (mtp) REVERT: D 470 LYS cc_start: 0.7715 (pttp) cc_final: 0.7209 (mttm) REVERT: D 582 ARG cc_start: 0.7604 (tpp-160) cc_final: 0.7088 (tpm170) outliers start: 15 outliers final: 11 residues processed: 95 average time/residue: 1.1506 time to fit residues: 115.6821 Evaluate side-chains 94 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 513 GLU Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain D residue 96 GLN 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: 79 random chunks: chunk 78 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN A 351 ASN D 340 GLN D 531 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 6673 Z= 0.335 Angle : 0.613 14.104 9070 Z= 0.319 Chirality : 0.048 0.294 957 Planarity : 0.005 0.055 1172 Dihedral : 5.756 59.054 926 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.43 % Allowed : 16.17 % 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: -0.32 (0.30), residues: 789 helix: 0.22 (0.26), residues: 401 sheet: 0.02 (0.74), residues: 57 loop : -0.66 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 349 HIS 0.005 0.001 HIS D 535 PHE 0.014 0.002 PHE D 32 TYR 0.017 0.002 TYR D 385 ARG 0.009 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 98 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 GLU cc_start: 0.7610 (pt0) cc_final: 0.7286 (pp20) REVERT: A 375 LYS cc_start: 0.7869 (mttm) cc_final: 0.6967 (tptp) REVERT: D 22 GLU cc_start: 0.7842 (tt0) cc_final: 0.7628 (tt0) REVERT: D 118 THR cc_start: 0.8328 (p) cc_final: 0.7869 (t) REVERT: D 121 ASN cc_start: 0.7729 (m-40) cc_final: 0.7453 (m-40) REVERT: D 232 GLU cc_start: 0.7941 (mp0) cc_final: 0.7740 (mp0) REVERT: D 295 ASP cc_start: 0.6949 (t70) cc_final: 0.6460 (t0) REVERT: D 383 MET cc_start: 0.9016 (mtp) cc_final: 0.8807 (mtp) REVERT: D 470 LYS cc_start: 0.7826 (pttp) cc_final: 0.7181 (mttm) REVERT: D 582 ARG cc_start: 0.7635 (tpp-160) cc_final: 0.7105 (tpm170) outliers start: 17 outliers final: 10 residues processed: 94 average time/residue: 1.3823 time to fit residues: 137.8691 Evaluate side-chains 89 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 96 GLN 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: 79 random chunks: chunk 17 optimal weight: 0.0870 chunk 62 optimal weight: 0.0870 chunk 26 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 0.3980 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN A 351 ASN D 290 ASN D 340 GLN D 531 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.143874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.113891 restraints weight = 7601.161| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.72 r_work: 0.3123 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2494 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= 0.162 Angle : 0.514 13.094 9070 Z= 0.267 Chirality : 0.043 0.260 957 Planarity : 0.004 0.048 1172 Dihedral : 5.033 55.091 926 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.57 % Allowed : 17.60 % Favored : 80.83 % 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: 0.18 (0.30), residues: 789 helix: 0.60 (0.27), residues: 398 sheet: 0.92 (0.80), residues: 47 loop : -0.47 (0.33), residues: 344 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 0.010 0.001 TYR D 50 ARG 0.009 0.000 ARG A 354 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3124.14 seconds wall clock time: 56 minutes 47.13 seconds (3407.13 seconds total)