Starting phenix.real_space_refine on Thu Jun 5 18:33:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wpb_32681/06_2025/7wpb_32681_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wpb_32681/06_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_32681/06_2025/7wpb_32681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wpb_32681/06_2025/7wpb_32681.map" model { file = "/net/cci-nas-00/data/ceres_data/7wpb_32681/06_2025/7wpb_32681_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wpb_32681/06_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-5710/modules/chem_data/mon_lib" Total number of atoms: 6491 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1590 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.81, per 1000 atoms: 0.90 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: 1.49 Conformation dependent library (CDL) restraints added in 926.0 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: 0.69 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: 1.63 Time building geometry restraints manager: 1.80 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: 10.180 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: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.660 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.260 ------------------------------------------------------------------------------- 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 6683 Z= 0.228 Angle : 0.747 8.114 9091 Z= 0.415 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00170 ( 3) link_NAG-ASN : angle 3.18285 ( 9) hydrogen bonds : bond 0.30417 ( 277) hydrogen bonds : angle 9.81234 ( 783) metal coordination : bond 0.03751 ( 1) SS BOND : bond 0.00348 ( 6) SS BOND : angle 0.85168 ( 12) covalent geometry : bond 0.00533 ( 6673) covalent geometry : angle 0.74029 ( 9070) *********************** 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 : 0.768 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: 1.2606 time to fit residues: 156.1690 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 : 0.755 ------------------------------------------------------------------------------- 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 6683 Z= 0.120 Angle : 0.546 7.788 9091 Z= 0.287 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 3) link_NAG-ASN : angle 2.16407 ( 9) hydrogen bonds : bond 0.05078 ( 277) hydrogen bonds : angle 4.64301 ( 783) metal coordination : bond 0.00008 ( 1) SS BOND : bond 0.00631 ( 6) SS BOND : angle 1.59652 ( 12) covalent geometry : bond 0.00258 ( 6673) covalent geometry : angle 0.53965 ( 9070) *********************** 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 : 0.636 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: 1.2695 time to fit residues: 132.1874 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 : 0.795 ------------------------------------------------------------------------------- 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: 0.0870 chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 194 ASN D 401 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.140755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.110748 restraints weight = 7747.883| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.69 r_work: 0.3081 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6683 Z= 0.166 Angle : 0.572 7.029 9091 Z= 0.298 Chirality : 0.045 0.219 957 Planarity : 0.005 0.056 1172 Dihedral : 5.536 57.840 926 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.43 % Allowed : 11.44 % 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: -1.19 (0.29), residues: 789 helix: -0.56 (0.26), residues: 393 sheet: 0.47 (0.74), residues: 48 loop : -1.12 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 478 HIS 0.003 0.001 HIS D 535 PHE 0.013 0.001 PHE D 32 TYR 0.017 0.001 TYR D 385 ARG 0.007 0.001 ARG A 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00160 ( 3) link_NAG-ASN : angle 2.22814 ( 9) hydrogen bonds : bond 0.05161 ( 277) hydrogen bonds : angle 4.29937 ( 783) metal coordination : bond 0.00214 ( 1) SS BOND : bond 0.00540 ( 6) SS BOND : angle 2.28672 ( 12) covalent geometry : bond 0.00392 ( 6673) covalent geometry : angle 0.56188 ( 9070) *********************** 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 107 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 GLU cc_start: 0.8113 (pt0) cc_final: 0.7662 (pp20) REVERT: A 439 ASP cc_start: 0.8515 (m-30) cc_final: 0.8269 (m-30) REVERT: D 22 GLU cc_start: 0.8364 (tt0) cc_final: 0.8146 (tt0) REVERT: D 118 THR cc_start: 0.8401 (p) cc_final: 0.7965 (t) REVERT: D 295 ASP cc_start: 0.7361 (t70) cc_final: 0.6803 (t0) REVERT: D 470 LYS cc_start: 0.8260 (pttp) cc_final: 0.7442 (mttm) REVERT: D 582 ARG cc_start: 0.8070 (tpp-160) cc_final: 0.7460 (tpm170) outliers start: 17 outliers final: 6 residues processed: 97 average time/residue: 1.3225 time to fit residues: 134.8505 Evaluate side-chains 87 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 29 optimal weight: 0.5980 chunk 45 optimal weight: 0.1980 chunk 35 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 67 optimal weight: 0.0670 overall best weight: 0.3918 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.143741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.115389 restraints weight = 7725.637| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.72 r_work: 0.3154 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 6683 Z= 0.106 Angle : 0.501 6.235 9091 Z= 0.261 Chirality : 0.042 0.228 957 Planarity : 0.005 0.076 1172 Dihedral : 5.036 55.290 926 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.00 % Allowed : 12.45 % Favored : 85.55 % 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: -0.62 (0.29), residues: 789 helix: -0.03 (0.26), residues: 396 sheet: 0.48 (0.74), residues: 48 loop : -0.88 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 433 HIS 0.003 0.001 HIS D 241 PHE 0.010 0.001 PHE D 315 TYR 0.013 0.001 TYR D 50 ARG 0.009 0.000 ARG A 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 3) link_NAG-ASN : angle 1.91756 ( 9) hydrogen bonds : bond 0.04059 ( 277) hydrogen bonds : angle 4.06698 ( 783) metal coordination : bond 0.00059 ( 1) SS BOND : bond 0.00574 ( 6) SS BOND : angle 2.06403 ( 12) covalent geometry : bond 0.00236 ( 6673) covalent geometry : angle 0.49177 ( 9070) *********************** 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 106 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 GLU cc_start: 0.8020 (pt0) cc_final: 0.7587 (pp20) REVERT: A 439 ASP cc_start: 0.8279 (m-30) cc_final: 0.8018 (m-30) REVERT: D 23 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7366 (mt-10) REVERT: D 118 THR cc_start: 0.8385 (p) cc_final: 0.7992 (t) REVERT: D 295 ASP cc_start: 0.7348 (t70) cc_final: 0.6832 (t0) REVERT: D 470 LYS cc_start: 0.8159 (pttp) cc_final: 0.7422 (mttm) REVERT: D 582 ARG cc_start: 0.8051 (tpp-160) cc_final: 0.7444 (tpm170) REVERT: D 597 ASP cc_start: 0.8266 (t70) cc_final: 0.7361 (m-30) outliers start: 14 outliers final: 6 residues processed: 101 average time/residue: 1.3710 time to fit residues: 145.6640 Evaluate side-chains 91 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 190 MET 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: 1.9990 chunk 65 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 49 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 401 HIS D 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.141445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.112900 restraints weight = 7693.526| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.74 r_work: 0.3119 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 6683 Z= 0.148 Angle : 0.560 13.750 9091 Z= 0.290 Chirality : 0.044 0.311 957 Planarity : 0.004 0.063 1172 Dihedral : 5.219 57.078 926 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.72 % Allowed : 13.30 % Favored : 83.98 % 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: -0.38 (0.30), residues: 789 helix: 0.19 (0.27), residues: 396 sheet: 0.71 (0.76), residues: 47 loop : -0.82 (0.33), residues: 346 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 523 TYR 0.016 0.001 TYR D 385 ARG 0.008 0.000 ARG A 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00157 ( 3) link_NAG-ASN : angle 2.11423 ( 9) hydrogen bonds : bond 0.04557 ( 277) hydrogen bonds : angle 4.10677 ( 783) metal coordination : bond 0.00149 ( 1) SS BOND : bond 0.00891 ( 6) SS BOND : angle 2.87964 ( 12) covalent geometry : bond 0.00354 ( 6673) covalent geometry : angle 0.54722 ( 9070) *********************** 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 105 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 GLU cc_start: 0.8038 (pt0) cc_final: 0.7645 (pp20) REVERT: A 375 LYS cc_start: 0.8075 (mttm) cc_final: 0.7186 (tptp) REVERT: A 439 ASP cc_start: 0.8374 (m-30) cc_final: 0.8132 (m-30) REVERT: A 525 LYS cc_start: 0.6397 (mtmm) cc_final: 0.6028 (pmtt) REVERT: D 23 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7391 (mt-10) REVERT: D 118 THR cc_start: 0.8373 (p) cc_final: 0.8038 (t) REVERT: D 121 ASN cc_start: 0.7877 (m-40) cc_final: 0.7483 (m-40) REVERT: D 295 ASP cc_start: 0.7390 (t70) cc_final: 0.6834 (t0) REVERT: D 470 LYS cc_start: 0.8149 (pttp) cc_final: 0.7447 (mttm) REVERT: D 582 ARG cc_start: 0.8083 (tpp-160) cc_final: 0.7493 (tpm170) REVERT: D 597 ASP cc_start: 0.8283 (t70) cc_final: 0.7385 (m-30) outliers start: 19 outliers final: 10 residues processed: 97 average time/residue: 1.2004 time to fit residues: 122.6589 Evaluate side-chains 92 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 276 THR 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: 0.0170 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 401 HIS D 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.142959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.114034 restraints weight = 7653.279| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.68 r_work: 0.3134 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6683 Z= 0.121 Angle : 0.529 11.228 9091 Z= 0.275 Chirality : 0.043 0.270 957 Planarity : 0.004 0.057 1172 Dihedral : 5.034 56.011 926 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.86 % Allowed : 13.73 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.30), residues: 789 helix: 0.38 (0.27), residues: 396 sheet: 0.73 (0.79), residues: 47 loop : -0.72 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 566 HIS 0.003 0.001 HIS D 241 PHE 0.011 0.001 PHE D 315 TYR 0.013 0.001 TYR D 385 ARG 0.007 0.000 ARG A 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00190 ( 3) link_NAG-ASN : angle 2.00574 ( 9) hydrogen bonds : bond 0.04195 ( 277) hydrogen bonds : angle 4.09084 ( 783) metal coordination : bond 0.00083 ( 1) SS BOND : bond 0.00779 ( 6) SS BOND : angle 2.39522 ( 12) covalent geometry : bond 0.00282 ( 6673) covalent geometry : angle 0.51897 ( 9070) *********************** 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 98 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 GLU cc_start: 0.8072 (pt0) cc_final: 0.7600 (pp20) REVERT: A 375 LYS cc_start: 0.7999 (mttm) cc_final: 0.7039 (tptp) REVERT: A 439 ASP cc_start: 0.8316 (m-30) cc_final: 0.8076 (m-30) REVERT: A 525 LYS cc_start: 0.6431 (mtmm) cc_final: 0.5997 (pmtt) REVERT: D 23 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7351 (mt-10) REVERT: D 118 THR cc_start: 0.8367 (p) cc_final: 0.8020 (t) REVERT: D 121 ASN cc_start: 0.7896 (m-40) cc_final: 0.7684 (m-40) REVERT: D 295 ASP cc_start: 0.7306 (t70) cc_final: 0.6748 (t0) REVERT: D 470 LYS cc_start: 0.8103 (pttp) cc_final: 0.7410 (mttm) REVERT: D 582 ARG cc_start: 0.8038 (tpp-160) cc_final: 0.7438 (tpm170) REVERT: D 597 ASP cc_start: 0.8294 (t70) cc_final: 0.7365 (m-30) outliers start: 13 outliers final: 7 residues processed: 94 average time/residue: 1.1856 time to fit residues: 117.6219 Evaluate side-chains 93 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 0.0570 chunk 23 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.3980 chunk 26 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 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 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 = 0.3592 r_free = 0.3592 target = 0.142710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.113551 restraints weight = 7663.192| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.81 r_work: 0.3124 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 6683 Z= 0.126 Angle : 0.541 14.269 9091 Z= 0.280 Chirality : 0.043 0.279 957 Planarity : 0.004 0.053 1172 Dihedral : 5.055 56.426 926 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.15 % Allowed : 14.16 % Favored : 83.69 % 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: -0.04 (0.30), residues: 789 helix: 0.48 (0.27), residues: 396 sheet: 0.83 (0.80), residues: 47 loop : -0.65 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 566 HIS 0.003 0.001 HIS D 241 PHE 0.010 0.001 PHE D 315 TYR 0.013 0.001 TYR D 385 ARG 0.007 0.000 ARG A 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00174 ( 3) link_NAG-ASN : angle 2.00262 ( 9) hydrogen bonds : bond 0.04246 ( 277) hydrogen bonds : angle 4.10441 ( 783) metal coordination : bond 0.00102 ( 1) SS BOND : bond 0.01015 ( 6) SS BOND : angle 2.38663 ( 12) covalent geometry : bond 0.00296 ( 6673) covalent geometry : angle 0.53136 ( 9070) *********************** 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 104 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 GLU cc_start: 0.8068 (pt0) cc_final: 0.7584 (pp20) REVERT: A 375 LYS cc_start: 0.7987 (mttm) cc_final: 0.7125 (tptp) REVERT: A 439 ASP cc_start: 0.8379 (m-30) cc_final: 0.8131 (m-30) REVERT: A 525 LYS cc_start: 0.6403 (mtmm) cc_final: 0.5970 (pmtt) REVERT: D 23 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7350 (mt-10) REVERT: D 118 THR cc_start: 0.8321 (p) cc_final: 0.7993 (t) REVERT: D 121 ASN cc_start: 0.7889 (m-40) cc_final: 0.7667 (m-40) REVERT: D 295 ASP cc_start: 0.7154 (t70) cc_final: 0.6605 (t0) REVERT: D 470 LYS cc_start: 0.8102 (pttp) cc_final: 0.7424 (mttm) REVERT: D 582 ARG cc_start: 0.8063 (tpp-160) cc_final: 0.7469 (tpm170) REVERT: D 597 ASP cc_start: 0.8302 (t70) cc_final: 0.7359 (m-30) outliers start: 15 outliers final: 8 residues processed: 99 average time/residue: 1.2278 time to fit residues: 128.2474 Evaluate side-chains 93 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 276 THR Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 67 optimal weight: 0.1980 chunk 58 optimal weight: 3.9990 chunk 50 optimal weight: 0.0470 chunk 18 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN D 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.143463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.114643 restraints weight = 7673.953| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.65 r_work: 0.3156 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 6683 Z= 0.117 Angle : 0.527 13.441 9091 Z= 0.272 Chirality : 0.043 0.266 957 Planarity : 0.004 0.050 1172 Dihedral : 4.959 55.949 926 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.00 % Allowed : 14.16 % Favored : 83.83 % 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: 0.08 (0.30), residues: 789 helix: 0.60 (0.27), residues: 393 sheet: 0.89 (0.81), residues: 47 loop : -0.61 (0.33), residues: 349 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 0.013 0.001 TYR D 385 ARG 0.009 0.000 ARG A 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00178 ( 3) link_NAG-ASN : angle 1.93197 ( 9) hydrogen bonds : bond 0.04060 ( 277) hydrogen bonds : angle 4.04220 ( 783) metal coordination : bond 0.00086 ( 1) SS BOND : bond 0.00906 ( 6) SS BOND : angle 2.19184 ( 12) covalent geometry : bond 0.00272 ( 6673) covalent geometry : angle 0.51801 ( 9070) *********************** 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 102 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 GLU cc_start: 0.8029 (pt0) cc_final: 0.7576 (pp20) REVERT: A 375 LYS cc_start: 0.7915 (mttm) cc_final: 0.7098 (tptp) REVERT: A 439 ASP cc_start: 0.8356 (m-30) cc_final: 0.8130 (m-30) REVERT: A 525 LYS cc_start: 0.6412 (mtmm) cc_final: 0.5905 (pmtt) REVERT: D 117 ASN cc_start: 0.7738 (t0) cc_final: 0.7525 (t160) REVERT: D 118 THR cc_start: 0.8303 (p) cc_final: 0.7989 (t) REVERT: D 295 ASP cc_start: 0.7127 (t70) cc_final: 0.6585 (t0) REVERT: D 470 LYS cc_start: 0.8094 (pttp) cc_final: 0.7452 (mttm) REVERT: D 582 ARG cc_start: 0.8028 (tpp-160) cc_final: 0.7447 (tpm170) REVERT: D 597 ASP cc_start: 0.8294 (t70) cc_final: 0.7340 (m-30) outliers start: 14 outliers final: 10 residues processed: 99 average time/residue: 1.3832 time to fit residues: 144.7518 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 : 1.070 ------------------------------------------------------------------------------- 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 339 VAL 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: 0.9980 chunk 45 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.141312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.112476 restraints weight = 7764.716| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.75 r_work: 0.3108 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 6683 Z= 0.156 Angle : 0.573 13.556 9091 Z= 0.295 Chirality : 0.045 0.275 957 Planarity : 0.004 0.051 1172 Dihedral : 5.235 57.549 926 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.43 % Allowed : 14.45 % Favored : 83.12 % 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: -0.03 (0.30), residues: 789 helix: 0.49 (0.27), residues: 397 sheet: 0.90 (0.80), residues: 47 loop : -0.67 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 566 HIS 0.003 0.001 HIS D 241 PHE 0.012 0.001 PHE D 308 TYR 0.017 0.001 TYR D 385 ARG 0.008 0.000 ARG A 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00151 ( 3) link_NAG-ASN : angle 2.10257 ( 9) hydrogen bonds : bond 0.04557 ( 277) hydrogen bonds : angle 4.08832 ( 783) metal coordination : bond 0.00162 ( 1) SS BOND : bond 0.00978 ( 6) SS BOND : angle 2.33040 ( 12) covalent geometry : bond 0.00376 ( 6673) covalent geometry : angle 0.56318 ( 9070) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 GLU cc_start: 0.8070 (pt0) cc_final: 0.7606 (pp20) REVERT: A 375 LYS cc_start: 0.7967 (mttm) cc_final: 0.7101 (tptp) REVERT: A 439 ASP cc_start: 0.8522 (m-30) cc_final: 0.8287 (m-30) REVERT: D 118 THR cc_start: 0.8247 (p) cc_final: 0.7939 (t) REVERT: D 295 ASP cc_start: 0.7147 (t70) cc_final: 0.6600 (t0) REVERT: D 470 LYS cc_start: 0.8128 (pttp) cc_final: 0.7460 (mttm) REVERT: D 582 ARG cc_start: 0.8030 (tpp-160) cc_final: 0.7435 (tpm170) REVERT: D 597 ASP cc_start: 0.8286 (t70) cc_final: 0.7336 (m-30) outliers start: 17 outliers final: 10 residues processed: 98 average time/residue: 1.3806 time to fit residues: 142.7515 Evaluate side-chains 90 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 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 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 339 VAL 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: 3.9990 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.139686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.110427 restraints weight = 7338.807| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.74 r_work: 0.3051 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 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 0.068 6683 Z= 0.154 Angle : 0.575 13.501 9091 Z= 0.297 Chirality : 0.045 0.272 957 Planarity : 0.004 0.051 1172 Dihedral : 5.285 57.209 926 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.86 % Allowed : 14.74 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.30), residues: 789 helix: 0.48 (0.26), residues: 398 sheet: 0.05 (0.75), residues: 57 loop : -0.52 (0.34), residues: 334 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 0.011 0.001 PHE D 32 TYR 0.016 0.001 TYR D 385 ARG 0.009 0.000 ARG A 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00158 ( 3) link_NAG-ASN : angle 2.09204 ( 9) hydrogen bonds : bond 0.04545 ( 277) hydrogen bonds : angle 4.08577 ( 783) metal coordination : bond 0.00156 ( 1) SS BOND : bond 0.00978 ( 6) SS BOND : angle 2.32663 ( 12) covalent geometry : bond 0.00369 ( 6673) covalent geometry : angle 0.56566 ( 9070) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 GLU cc_start: 0.8086 (pt0) cc_final: 0.7634 (pp20) REVERT: A 375 LYS cc_start: 0.8044 (mttm) cc_final: 0.7207 (tptp) REVERT: A 439 ASP cc_start: 0.8596 (m-30) cc_final: 0.8322 (m-30) REVERT: A 525 LYS cc_start: 0.6363 (mtmm) cc_final: 0.5958 (pmtt) REVERT: D 118 THR cc_start: 0.8246 (p) cc_final: 0.7940 (t) REVERT: D 121 ASN cc_start: 0.7731 (m-40) cc_final: 0.7404 (m-40) REVERT: D 295 ASP cc_start: 0.7175 (t70) cc_final: 0.6645 (t0) REVERT: D 470 LYS cc_start: 0.8166 (pttp) cc_final: 0.7524 (mttm) REVERT: D 582 ARG cc_start: 0.8086 (tpp-160) cc_final: 0.7491 (tpm170) outliers start: 13 outliers final: 10 residues processed: 94 average time/residue: 1.6423 time to fit residues: 165.1277 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 : 0.787 ------------------------------------------------------------------------------- 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 339 VAL 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: 0.9990 chunk 54 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 340 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.140035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.110625 restraints weight = 7416.895| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.76 r_work: 0.3047 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 6683 Z= 0.148 Angle : 0.571 13.311 9091 Z= 0.294 Chirality : 0.044 0.270 957 Planarity : 0.004 0.051 1172 Dihedral : 5.271 57.047 926 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.72 % Allowed : 14.59 % Favored : 83.69 % 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: 0.03 (0.30), residues: 789 helix: 0.52 (0.26), residues: 398 sheet: 0.87 (0.80), residues: 47 loop : -0.59 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 566 HIS 0.003 0.001 HIS D 241 PHE 0.011 0.001 PHE D 315 TYR 0.016 0.001 TYR D 385 ARG 0.009 0.000 ARG A 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00146 ( 3) link_NAG-ASN : angle 2.06370 ( 9) hydrogen bonds : bond 0.04471 ( 277) hydrogen bonds : angle 4.08224 ( 783) metal coordination : bond 0.00148 ( 1) SS BOND : bond 0.00951 ( 6) SS BOND : angle 2.29429 ( 12) covalent geometry : bond 0.00355 ( 6673) covalent geometry : angle 0.56227 ( 9070) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7236.85 seconds wall clock time: 127 minutes 52.08 seconds (7672.08 seconds total)