Starting phenix.real_space_refine on Sun Aug 24 15:01:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fhk_29087/08_2025/8fhk_29087_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fhk_29087/08_2025/8fhk_29087.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fhk_29087/08_2025/8fhk_29087_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fhk_29087/08_2025/8fhk_29087_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fhk_29087/08_2025/8fhk_29087.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fhk_29087/08_2025/8fhk_29087.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.025 sd= 0.050 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: 7 Type Number sf(0) Gaussians P 19 5.49 5 Mg 2 5.21 5 S 40 5.16 5 C 6528 2.51 5 N 1652 2.21 5 O 1879 1.98 5 H 9827 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19947 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 10395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 10395 Classifications: {'peptide': 645} Link IDs: {'PTRANS': 13, 'TRANS': 631} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 9107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 9107 Classifications: {'peptide': 574} Link IDs: {'PTRANS': 19, 'TRANS': 554} Chain: "D" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 297 Unusual residues: {' MG': 1, 'ATP': 1, 'POV': 11} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 288 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-3': 6, 'POV:plan-1': 5, 'POV:plan-2': 2} Unresolved non-hydrogen planarities: 45 Chain: "C" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 148 Unusual residues: {' MG': 1, 'ATP': 1, 'POV': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 2, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 29 Time building chain proxies: 3.60, per 1000 atoms: 0.18 Number of scatterers: 19947 At special positions: 0 Unit cell: (74.405, 83.463, 158.515, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 40 16.00 P 19 15.00 Mg 2 11.99 O 1879 8.00 N 1652 7.00 C 6528 6.00 H 9827 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.01 Conformation dependent library (CDL) restraints added in 521.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2260 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 10 sheets defined 64.6% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'D' and resid 2 through 13 removed outlier: 3.868A pdb=" N THR D 6 " --> pdb=" O LYS D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 47 removed outlier: 4.164A pdb=" N LEU D 18 " --> pdb=" O TYR D 14 " (cutoff:3.500A) Proline residue: D 36 - end of helix removed outlier: 3.858A pdb=" N GLY D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP D 45 " --> pdb=" O LYS D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 142 removed outlier: 4.136A pdb=" N TYR D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 195 removed outlier: 3.999A pdb=" N VAL D 161 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE D 162 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE D 165 " --> pdb=" O VAL D 161 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET D 176 " --> pdb=" O TYR D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 203 removed outlier: 3.800A pdb=" N PHE D 201 " --> pdb=" O PRO D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 215 Processing helix chain 'D' and resid 216 through 226 removed outlier: 3.597A pdb=" N ILE D 220 " --> pdb=" O ASP D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 249 Processing helix chain 'D' and resid 251 through 273 removed outlier: 3.884A pdb=" N VAL D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL D 260 " --> pdb=" O ALA D 256 " (cutoff:3.500A) Proline residue: D 261 - end of helix Processing helix chain 'D' and resid 274 through 298 Processing helix chain 'D' and resid 298 through 305 Processing helix chain 'D' and resid 307 through 328 Processing helix chain 'D' and resid 336 through 361 removed outlier: 4.106A pdb=" N VAL D 343 " --> pdb=" O ASN D 339 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE D 356 " --> pdb=" O LEU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 391 removed outlier: 3.641A pdb=" N TYR D 373 " --> pdb=" O ILE D 369 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE D 383 " --> pdb=" O LEU D 379 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN D 384 " --> pdb=" O ASN D 380 " (cutoff:3.500A) Proline residue: D 385 - end of helix Processing helix chain 'D' and resid 392 through 411 removed outlier: 3.898A pdb=" N VAL D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 442 No H-bonds generated for 'chain 'D' and resid 440 through 442' Processing helix chain 'D' and resid 468 through 477 Processing helix chain 'D' and resid 495 through 497 No H-bonds generated for 'chain 'D' and resid 495 through 497' Processing helix chain 'D' and resid 498 through 503 Processing helix chain 'D' and resid 519 through 526 Processing helix chain 'D' and resid 535 through 543 removed outlier: 3.636A pdb=" N ALA D 539 " --> pdb=" O GLU D 535 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN D 542 " --> pdb=" O ASN D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 550 Processing helix chain 'D' and resid 568 through 583 Processing helix chain 'D' and resid 599 through 604 Processing helix chain 'D' and resid 604 through 609 Processing helix chain 'D' and resid 624 through 629 removed outlier: 3.606A pdb=" N THR D 627 " --> pdb=" O ARG D 624 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG D 629 " --> pdb=" O SER D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 641 Processing helix chain 'D' and resid 653 through 663 removed outlier: 3.627A pdb=" N GLN D 657 " --> pdb=" O ALA D 653 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR D 658 " --> pdb=" O LEU D 654 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU D 663 " --> pdb=" O TYR D 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 15 removed outlier: 5.162A pdb=" N TRP C 10 " --> pdb=" O LYS C 6 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N PHE C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE C 12 " --> pdb=" O LEU C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 49 removed outlier: 3.542A pdb=" N VAL C 24 " --> pdb=" O THR C 20 " (cutoff:3.500A) Proline residue: C 36 - end of helix Processing helix chain 'C' and resid 53 through 102 removed outlier: 4.179A pdb=" N TRP C 78 " --> pdb=" O MET C 74 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN C 87 " --> pdb=" O PHE C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 109 removed outlier: 3.681A pdb=" N PHE C 108 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 157 removed outlier: 4.258A pdb=" N ASP C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE C 136 " --> pdb=" O THR C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 207 removed outlier: 4.331A pdb=" N GLU C 185 " --> pdb=" O SER C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 216 through 270 removed outlier: 3.844A pdb=" N ARG C 223 " --> pdb=" O ASN C 219 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE C 241 " --> pdb=" O LYS C 237 " (cutoff:3.500A) Proline residue: C 247 - end of helix Processing helix chain 'C' and resid 274 through 290 removed outlier: 3.612A pdb=" N TRP C 290 " --> pdb=" O GLY C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 294 through 317 Processing helix chain 'C' and resid 376 through 386 Processing helix chain 'C' and resid 406 through 414 Processing helix chain 'C' and resid 428 through 433 Processing helix chain 'C' and resid 442 through 449 Processing helix chain 'C' and resid 455 through 460 removed outlier: 4.042A pdb=" N MET C 459 " --> pdb=" O LYS C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 490 Processing helix chain 'C' and resid 506 through 521 Processing helix chain 'C' and resid 534 through 538 removed outlier: 4.091A pdb=" N HIS C 538 " --> pdb=" O ALA C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 562 removed outlier: 3.528A pdb=" N LEU C 559 " --> pdb=" O THR C 555 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU C 560 " --> pdb=" O HIS C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 576 removed outlier: 4.073A pdb=" N GLU C 571 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG C 572 " --> pdb=" O GLU C 568 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE C 576 " --> pdb=" O ARG C 572 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 89 through 93 removed outlier: 3.647A pdb=" N PHE D 99 " --> pdb=" O GLU D 131 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU D 131 " --> pdb=" O PHE D 99 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 117 through 118 Processing sheet with id=AA3, first strand: chain 'D' and resid 430 through 431 Processing sheet with id=AA4, first strand: chain 'D' and resid 438 through 439 Processing sheet with id=AA5, first strand: chain 'D' and resid 458 through 460 Processing sheet with id=AA6, first strand: chain 'D' and resid 488 through 489 Processing sheet with id=AA7, first strand: chain 'D' and resid 506 through 509 removed outlier: 5.800A pdb=" N GLY D 507 " --> pdb=" O ILE D 589 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ASP D 591 " --> pdb=" O GLY D 507 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL D 509 " --> pdb=" O ASP D 591 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU D 588 " --> pdb=" O PHE D 619 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ILE D 621 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU D 590 " --> pdb=" O ILE D 621 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 337 through 338 Processing sheet with id=AA9, first strand: chain 'C' and resid 496 through 499 removed outlier: 6.136A pdb=" N GLY C 368 " --> pdb=" O LEU C 543 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N MET C 545 " --> pdb=" O GLY C 368 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE C 542 " --> pdb=" O ARG C 553 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG C 553 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL C 544 " --> pdb=" O ALA C 551 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 426 through 427 564 hydrogen bonds defined for protein. 1647 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: 4.23 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.06: 3231 1.06 - 1.25: 8189 1.25 - 1.45: 2808 1.45 - 1.65: 5814 1.65 - 1.85: 80 Bond restraints: 20122 Sorted by residual: bond pdb=" NE1 TRP C 78 " pdb=" HE1 TRP C 78 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP D 54 " pdb=" HE1 TRP D 54 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP C 10 " pdb=" HE1 TRP C 10 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" NE1 TRP C 290 " pdb=" HE1 TRP C 290 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" NE1 TRP C 565 " pdb=" HE1 TRP C 565 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 ... (remaining 20117 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.06: 36137 13.06 - 26.12: 5 26.12 - 39.18: 1 39.18 - 52.24: 0 52.24 - 65.29: 1 Bond angle restraints: 36144 Sorted by residual: angle pdb=" CA GLY D 108 " pdb=" N GLY D 108 " pdb=" H GLY D 108 " ideal model delta sigma weight residual 114.00 179.29 -65.29 3.00e+00 1.11e-01 4.74e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 122.12 14.71 1.00e+00 1.00e+00 2.16e+02 angle pdb=" O2G ATP C 601 " pdb=" PG ATP C 601 " pdb=" O3B ATP C 601 " ideal model delta sigma weight residual 104.48 118.62 -14.14 1.14e+00 7.76e-01 1.55e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 128.40 11.47 1.00e+00 1.00e+00 1.32e+02 angle pdb=" CA ALA D 64 " pdb=" N ALA D 64 " pdb=" H ALA D 64 " ideal model delta sigma weight residual 114.00 145.63 -31.63 3.00e+00 1.11e-01 1.11e+02 ... (remaining 36139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 9146 35.94 - 71.88: 334 71.88 - 107.82: 28 107.82 - 143.76: 6 143.76 - 179.70: 4 Dihedral angle restraints: 9518 sinusoidal: 5328 harmonic: 4190 Sorted by residual: dihedral pdb=" CA GLU D 80 " pdb=" C GLU D 80 " pdb=" N PRO D 81 " pdb=" CA PRO D 81 " ideal model delta harmonic sigma weight residual 180.00 153.07 26.93 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" C29 POV D 711 " pdb="C210 POV D 711 " pdb="C211 POV D 711 " pdb="C212 POV D 711 " ideal model delta sinusoidal sigma weight residual 112.25 -68.05 -179.70 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C27 POV D 705 " pdb=" C28 POV D 705 " pdb=" C29 POV D 705 " pdb="C210 POV D 705 " ideal model delta sinusoidal sigma weight residual 127.48 -61.85 -170.67 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 9515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1290 0.071 - 0.141: 196 0.141 - 0.212: 38 0.212 - 0.283: 7 0.283 - 0.353: 3 Chirality restraints: 1534 Sorted by residual: chirality pdb=" CA VAL C 215 " pdb=" N VAL C 215 " pdb=" C VAL C 215 " pdb=" CB VAL C 215 " both_signs ideal model delta sigma weight residual False 2.44 2.09 0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CA ILE D 236 " pdb=" N ILE D 236 " pdb=" C ILE D 236 " pdb=" CB ILE D 236 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA ILE D 369 " pdb=" N ILE D 369 " pdb=" C ILE D 369 " pdb=" CB ILE D 369 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 1531 not shown) Planarity restraints: 2896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV D 706 " -0.212 2.00e-02 2.50e+03 2.59e-01 6.70e+02 pdb=" C29 POV D 706 " 0.432 2.00e-02 2.50e+03 pdb="C210 POV D 706 " -0.187 2.00e-02 2.50e+03 pdb="C211 POV D 706 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C 605 " -0.079 2.00e-02 2.50e+03 2.55e-01 6.48e+02 pdb=" C29 POV C 605 " 0.321 2.00e-02 2.50e+03 pdb="C210 POV C 605 " -0.367 2.00e-02 2.50e+03 pdb="C211 POV C 605 " 0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 704 " 0.098 2.00e-02 2.50e+03 2.35e-01 5.54e+02 pdb=" C29 POV D 704 " -0.315 2.00e-02 2.50e+03 pdb="C210 POV D 704 " 0.320 2.00e-02 2.50e+03 pdb="C211 POV D 704 " -0.103 2.00e-02 2.50e+03 ... (remaining 2893 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 948 2.10 - 2.72: 33155 2.72 - 3.35: 57671 3.35 - 3.97: 76992 3.97 - 4.60: 116515 Nonbonded interactions: 285281 Sorted by model distance: nonbonded pdb=" HB1 ALA D 244 " pdb=" HH TYR D 378 " model vdw 1.469 2.270 nonbonded pdb=" HA3 GLY D 428 " pdb=" HG1 THR D 617 " model vdw 1.526 2.270 nonbonded pdb="HG13 VAL D 612 " pdb=" HG1 THR D 618 " model vdw 1.537 2.270 nonbonded pdb=" HG1 THR C 131 " pdb=" HA3 GLY C 305 " model vdw 1.565 2.270 nonbonded pdb=" HB2 HIS C 421 " pdb=" HZ2 LYS C 480 " model vdw 1.570 2.270 ... (remaining 285276 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: 9.500 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: 0.160 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.850 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.156 10295 Z= 0.501 Angle : 1.175 16.977 13872 Z= 0.764 Chirality : 0.057 0.353 1534 Planarity : 0.016 0.259 1716 Dihedral : 18.883 179.695 3961 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.39 % Allowed : 2.90 % Favored : 96.71 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.24), residues: 1207 helix: -0.13 (0.19), residues: 756 sheet: -1.62 (0.62), residues: 62 loop : -2.76 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 411 TYR 0.019 0.002 TYR C 76 PHE 0.026 0.002 PHE D 254 TRP 0.029 0.002 TRP C 290 HIS 0.007 0.001 HIS D 192 Details of bonding type rmsd covalent geometry : bond 0.00811 (10295) covalent geometry : angle 1.17466 (13872) hydrogen bonds : bond 0.17615 ( 564) hydrogen bonds : angle 7.12845 ( 1647) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 262 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 181 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.6242 (ppp) cc_final: 0.6017 (tmt) REVERT: C 420 ASP cc_start: 0.7079 (m-30) cc_final: 0.6867 (m-30) outliers start: 4 outliers final: 3 residues processed: 183 average time/residue: 0.9361 time to fit residues: 187.4043 Evaluate side-chains 128 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain C residue 108 PHE Chi-restraints excluded: chain C residue 416 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 GLN C 458 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.112579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.100866 restraints weight = 64779.388| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 1.89 r_work: 0.3994 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3877 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10295 Z= 0.170 Angle : 0.633 8.863 13872 Z= 0.343 Chirality : 0.040 0.172 1534 Planarity : 0.006 0.086 1716 Dihedral : 17.968 175.500 1667 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 1.64 % Allowed : 12.67 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.24), residues: 1207 helix: 0.27 (0.19), residues: 750 sheet: -1.00 (0.69), residues: 52 loop : -2.55 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 328 TYR 0.015 0.001 TYR C 19 PHE 0.020 0.002 PHE C 108 TRP 0.016 0.001 TRP C 290 HIS 0.005 0.001 HIS D 322 Details of bonding type rmsd covalent geometry : bond 0.00358 (10295) covalent geometry : angle 0.63302 (13872) hydrogen bonds : bond 0.06092 ( 564) hydrogen bonds : angle 5.31822 ( 1647) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 262 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 86 LYS cc_start: 0.4280 (mptt) cc_final: 0.3996 (mptt) REVERT: D 159 LEU cc_start: 0.6861 (tm) cc_final: 0.6572 (tp) REVERT: C 108 PHE cc_start: 0.7113 (OUTLIER) cc_final: 0.6855 (t80) outliers start: 17 outliers final: 10 residues processed: 148 average time/residue: 0.8653 time to fit residues: 141.4651 Evaluate side-chains 128 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain D residue 538 ASN Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 108 PHE Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain C residue 458 HIS Chi-restraints excluded: chain C residue 550 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 1 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN C 216 GLN C 458 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.109638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.097675 restraints weight = 65028.993| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 1.90 r_work: 0.3923 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3801 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 10295 Z= 0.238 Angle : 0.666 8.375 13872 Z= 0.367 Chirality : 0.042 0.164 1534 Planarity : 0.006 0.066 1716 Dihedral : 17.286 163.605 1665 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 1.93 % Allowed : 13.54 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.23), residues: 1207 helix: -0.09 (0.18), residues: 755 sheet: -0.78 (0.68), residues: 52 loop : -2.69 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 120 TYR 0.019 0.002 TYR C 19 PHE 0.019 0.002 PHE C 108 TRP 0.020 0.002 TRP C 290 HIS 0.014 0.001 HIS C 458 Details of bonding type rmsd covalent geometry : bond 0.00504 (10295) covalent geometry : angle 0.66586 (13872) hydrogen bonds : bond 0.06138 ( 564) hydrogen bonds : angle 5.21946 ( 1647) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 262 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.569 Fit side-chains TARDY: cannot create tardy model for: "TYR D 142 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 86 LYS cc_start: 0.4327 (mptt) cc_final: 0.4079 (mptt) REVERT: D 159 LEU cc_start: 0.6958 (tm) cc_final: 0.6693 (tp) REVERT: C 8 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.6988 (mp) REVERT: C 358 SER cc_start: 0.8086 (m) cc_final: 0.7488 (t) outliers start: 20 outliers final: 10 residues processed: 139 average time/residue: 1.0328 time to fit residues: 158.5674 Evaluate side-chains 128 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain C residue 458 HIS Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 550 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 100 optimal weight: 0.0980 chunk 20 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 GLN C 574 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.110545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.098627 restraints weight = 64601.112| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 1.89 r_work: 0.3939 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3820 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 10295 Z= 0.158 Angle : 0.592 8.310 13872 Z= 0.320 Chirality : 0.039 0.167 1534 Planarity : 0.005 0.056 1716 Dihedral : 15.872 106.146 1663 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 2.42 % Allowed : 14.41 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.24), residues: 1207 helix: 0.25 (0.19), residues: 755 sheet: -0.65 (0.68), residues: 52 loop : -2.62 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 362 TYR 0.016 0.001 TYR C 19 PHE 0.017 0.002 PHE D 315 TRP 0.016 0.001 TRP C 290 HIS 0.006 0.001 HIS C 458 Details of bonding type rmsd covalent geometry : bond 0.00342 (10295) covalent geometry : angle 0.59238 (13872) hydrogen bonds : bond 0.05425 ( 564) hydrogen bonds : angle 4.96873 ( 1647) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 262 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.565 Fit side-chains TARDY: cannot create tardy model for: "TYR D 142 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 86 LYS cc_start: 0.4291 (mptt) cc_final: 0.4066 (mptt) REVERT: D 159 LEU cc_start: 0.6919 (tm) cc_final: 0.6676 (tp) REVERT: D 259 ILE cc_start: 0.5825 (OUTLIER) cc_final: 0.5391 (mp) REVERT: C 8 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.7089 (mp) REVERT: C 166 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7523 (mp) REVERT: C 358 SER cc_start: 0.8088 (m) cc_final: 0.7488 (t) outliers start: 25 outliers final: 12 residues processed: 140 average time/residue: 1.0729 time to fit residues: 165.8030 Evaluate side-chains 128 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain D residue 538 ASN Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 550 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 93 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN C 458 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.108930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.096967 restraints weight = 65159.689| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 1.88 r_work: 0.3910 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3792 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 10295 Z= 0.215 Angle : 0.624 9.029 13872 Z= 0.341 Chirality : 0.040 0.188 1534 Planarity : 0.005 0.055 1716 Dihedral : 15.734 103.103 1663 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 2.22 % Allowed : 16.44 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.23), residues: 1207 helix: 0.04 (0.18), residues: 755 sheet: -0.59 (0.69), residues: 52 loop : -2.65 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 624 TYR 0.020 0.002 TYR C 19 PHE 0.021 0.002 PHE D 315 TRP 0.019 0.002 TRP C 290 HIS 0.007 0.001 HIS D 322 Details of bonding type rmsd covalent geometry : bond 0.00469 (10295) covalent geometry : angle 0.62440 (13872) hydrogen bonds : bond 0.05731 ( 564) hydrogen bonds : angle 5.05146 ( 1647) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 262 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 146 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7649 (mt) REVERT: D 159 LEU cc_start: 0.6964 (tm) cc_final: 0.6730 (tp) REVERT: D 255 VAL cc_start: 0.7398 (OUTLIER) cc_final: 0.7039 (m) REVERT: D 259 ILE cc_start: 0.5902 (OUTLIER) cc_final: 0.5435 (mp) REVERT: D 398 LEU cc_start: 0.7958 (tp) cc_final: 0.7752 (mp) REVERT: C 166 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7505 (mp) outliers start: 23 outliers final: 14 residues processed: 134 average time/residue: 1.0529 time to fit residues: 156.2903 Evaluate side-chains 132 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain D residue 538 ASN Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 550 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 52 optimal weight: 1.9990 chunk 93 optimal weight: 0.0570 chunk 1 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN C 458 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.109824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.097885 restraints weight = 64919.219| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 1.88 r_work: 0.3925 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3807 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 10295 Z= 0.156 Angle : 0.582 8.610 13872 Z= 0.316 Chirality : 0.039 0.176 1534 Planarity : 0.005 0.055 1716 Dihedral : 15.087 88.680 1663 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 2.32 % Allowed : 16.83 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.24), residues: 1207 helix: 0.28 (0.19), residues: 755 sheet: -0.62 (0.66), residues: 57 loop : -2.61 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 362 TYR 0.017 0.001 TYR C 19 PHE 0.011 0.001 PHE D 383 TRP 0.017 0.001 TRP C 290 HIS 0.005 0.001 HIS C 458 Details of bonding type rmsd covalent geometry : bond 0.00336 (10295) covalent geometry : angle 0.58203 (13872) hydrogen bonds : bond 0.05290 ( 564) hydrogen bonds : angle 4.88575 ( 1647) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 262 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 146 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7588 (mt) REVERT: D 159 LEU cc_start: 0.6944 (tm) cc_final: 0.6721 (tp) REVERT: D 259 ILE cc_start: 0.5910 (OUTLIER) cc_final: 0.5461 (mp) REVERT: C 166 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7503 (mp) outliers start: 24 outliers final: 13 residues processed: 138 average time/residue: 1.1111 time to fit residues: 168.6597 Evaluate side-chains 132 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain C residue 458 HIS Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 550 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 56 optimal weight: 0.0770 chunk 60 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN C 458 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.109557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.097619 restraints weight = 65138.352| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 1.89 r_work: 0.3922 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3799 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10295 Z= 0.170 Angle : 0.595 8.793 13872 Z= 0.324 Chirality : 0.039 0.183 1534 Planarity : 0.005 0.054 1716 Dihedral : 14.936 89.068 1663 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 2.32 % Allowed : 17.41 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.24), residues: 1207 helix: 0.30 (0.19), residues: 754 sheet: -0.59 (0.66), residues: 57 loop : -2.56 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 362 TYR 0.016 0.002 TYR C 19 PHE 0.023 0.002 PHE D 315 TRP 0.017 0.001 TRP C 290 HIS 0.005 0.001 HIS D 322 Details of bonding type rmsd covalent geometry : bond 0.00369 (10295) covalent geometry : angle 0.59470 (13872) hydrogen bonds : bond 0.05314 ( 564) hydrogen bonds : angle 4.87150 ( 1647) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 262 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 146 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7559 (mt) REVERT: D 159 LEU cc_start: 0.6950 (tm) cc_final: 0.6735 (tp) REVERT: D 259 ILE cc_start: 0.5967 (OUTLIER) cc_final: 0.5508 (mp) REVERT: C 166 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7488 (mp) outliers start: 24 outliers final: 12 residues processed: 136 average time/residue: 1.1050 time to fit residues: 164.6709 Evaluate side-chains 133 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 550 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 2 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 115 optimal weight: 0.5980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.108829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.096802 restraints weight = 65084.664| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 1.89 r_work: 0.3906 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3782 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 10295 Z= 0.191 Angle : 0.617 8.907 13872 Z= 0.334 Chirality : 0.040 0.234 1534 Planarity : 0.005 0.061 1716 Dihedral : 15.045 91.222 1663 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 2.22 % Allowed : 17.89 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.23), residues: 1207 helix: 0.14 (0.18), residues: 756 sheet: -0.52 (0.67), residues: 57 loop : -2.56 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 624 TYR 0.020 0.002 TYR C 19 PHE 0.016 0.002 PHE D 375 TRP 0.020 0.002 TRP C 290 HIS 0.006 0.001 HIS D 322 Details of bonding type rmsd covalent geometry : bond 0.00417 (10295) covalent geometry : angle 0.61704 (13872) hydrogen bonds : bond 0.05465 ( 564) hydrogen bonds : angle 4.92849 ( 1647) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 262 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 146 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7571 (mt) REVERT: D 159 LEU cc_start: 0.6906 (tm) cc_final: 0.6704 (tp) REVERT: D 255 VAL cc_start: 0.7296 (OUTLIER) cc_final: 0.6928 (m) REVERT: D 259 ILE cc_start: 0.6018 (OUTLIER) cc_final: 0.5562 (mp) REVERT: D 347 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7772 (mm) REVERT: D 375 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7914 (t80) REVERT: C 166 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7487 (mp) REVERT: C 290 TRP cc_start: 0.6204 (m100) cc_final: 0.5811 (m100) outliers start: 23 outliers final: 13 residues processed: 136 average time/residue: 1.0777 time to fit residues: 161.7057 Evaluate side-chains 139 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 550 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 36 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 chunk 105 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.109932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.098020 restraints weight = 64457.560| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 1.88 r_work: 0.3928 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3806 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10295 Z= 0.141 Angle : 0.584 8.851 13872 Z= 0.315 Chirality : 0.039 0.205 1534 Planarity : 0.005 0.056 1716 Dihedral : 14.480 87.232 1663 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 2.13 % Allowed : 17.89 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.24), residues: 1207 helix: 0.43 (0.19), residues: 754 sheet: -0.54 (0.66), residues: 57 loop : -2.52 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 624 TYR 0.016 0.001 TYR C 19 PHE 0.026 0.001 PHE D 315 TRP 0.018 0.001 TRP C 290 HIS 0.003 0.001 HIS C 458 Details of bonding type rmsd covalent geometry : bond 0.00306 (10295) covalent geometry : angle 0.58437 (13872) hydrogen bonds : bond 0.05060 ( 564) hydrogen bonds : angle 4.78037 ( 1647) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 262 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 135 LYS cc_start: 0.8231 (pptt) cc_final: 0.7358 (mttm) REVERT: D 146 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7534 (mt) REVERT: D 159 LEU cc_start: 0.6940 (tm) cc_final: 0.6732 (tp) REVERT: D 255 VAL cc_start: 0.7222 (OUTLIER) cc_final: 0.6826 (m) REVERT: D 259 ILE cc_start: 0.6040 (OUTLIER) cc_final: 0.5599 (mp) REVERT: D 347 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7782 (mm) REVERT: C 166 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7468 (mp) REVERT: C 273 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6859 (tt) REVERT: C 290 TRP cc_start: 0.6132 (m100) cc_final: 0.5841 (m100) outliers start: 22 outliers final: 12 residues processed: 140 average time/residue: 0.8563 time to fit residues: 132.2469 Evaluate side-chains 133 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 550 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 10 optimal weight: 0.0770 chunk 1 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.110555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.098645 restraints weight = 64893.982| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 1.89 r_work: 0.3937 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3815 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10295 Z= 0.137 Angle : 0.589 8.848 13872 Z= 0.315 Chirality : 0.039 0.262 1534 Planarity : 0.005 0.054 1716 Dihedral : 13.951 84.512 1663 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 1.84 % Allowed : 18.47 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.24), residues: 1207 helix: 0.55 (0.19), residues: 758 sheet: -0.48 (0.67), residues: 57 loop : -2.49 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 624 TYR 0.016 0.001 TYR C 19 PHE 0.024 0.001 PHE D 315 TRP 0.018 0.001 TRP C 290 HIS 0.003 0.001 HIS D 322 Details of bonding type rmsd covalent geometry : bond 0.00299 (10295) covalent geometry : angle 0.58870 (13872) hydrogen bonds : bond 0.04868 ( 564) hydrogen bonds : angle 4.68293 ( 1647) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 262 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 146 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7497 (mt) REVERT: D 159 LEU cc_start: 0.6921 (tm) cc_final: 0.6705 (tp) REVERT: D 347 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7812 (mm) REVERT: D 375 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7841 (t80) REVERT: C 166 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7509 (mp) REVERT: C 273 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6858 (tt) outliers start: 19 outliers final: 11 residues processed: 132 average time/residue: 0.9629 time to fit residues: 140.3982 Evaluate side-chains 126 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 550 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 70 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 60 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.110153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.098164 restraints weight = 65014.463| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 1.90 r_work: 0.3928 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3807 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10295 Z= 0.152 Angle : 0.596 9.529 13872 Z= 0.319 Chirality : 0.038 0.203 1534 Planarity : 0.005 0.054 1716 Dihedral : 13.864 85.317 1663 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 1.64 % Allowed : 18.96 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.24), residues: 1207 helix: 0.49 (0.19), residues: 760 sheet: -0.35 (0.68), residues: 57 loop : -2.49 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 624 TYR 0.020 0.001 TYR C 19 PHE 0.025 0.001 PHE D 315 TRP 0.019 0.001 TRP C 290 HIS 0.004 0.001 HIS D 322 Details of bonding type rmsd covalent geometry : bond 0.00335 (10295) covalent geometry : angle 0.59560 (13872) hydrogen bonds : bond 0.04938 ( 564) hydrogen bonds : angle 4.71218 ( 1647) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6533.22 seconds wall clock time: 111 minutes 32.41 seconds (6692.41 seconds total)