Starting phenix.real_space_refine on Wed Aug 7 19:53:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhk_29087/08_2024/8fhk_29087_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhk_29087/08_2024/8fhk_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhk_29087/08_2024/8fhk_29087.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhk_29087/08_2024/8fhk_29087.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhk_29087/08_2024/8fhk_29087_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhk_29087/08_2024/8fhk_29087_trim.cif" } resolution = 2.9 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= 0.025 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 Residue "C TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/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-2': 2, 'POV:plan-1': 5} 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-3': 3, 'POV:plan-2': 2, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 29 Time building chain proxies: 11.68, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.05 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.73 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: 7.67 Time building geometry restraints manager: 16.91 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: 94.37 - 111.35: 21883 111.35 - 128.34: 14187 128.34 - 145.32: 72 145.32 - 162.31: 1 162.31 - 179.29: 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: 12.490 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: 0.170 Extract box with map and model: 0.820 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 68.480 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 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:11.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.270 ------------------------------------------------------------------------------- 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= 0.537 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 (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: -1.60 (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 TRP 0.029 0.002 TRP C 290 HIS 0.007 0.001 HIS D 192 PHE 0.026 0.002 PHE D 254 TYR 0.019 0.002 TYR C 76 ARG 0.011 0.001 ARG C 411 *********************** 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 fitting. rotamer outliers: 4 poor density : 181 time to evaluate : 1.548 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: C 144 MET cc_start: 0.6242 (ppp) cc_final: 0.6008 (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: 2.0609 time to fit residues: 415.7548 Evaluate side-chains 128 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 1.575 ------------------------------------------------------------------------------- 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 102 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 C 574 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10295 Z= 0.225 Angle : 0.626 6.068 13872 Z= 0.339 Chirality : 0.040 0.170 1534 Planarity : 0.006 0.084 1716 Dihedral : 17.873 175.565 1667 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 1.84 % Allowed : 12.48 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.24), residues: 1207 helix: 0.31 (0.19), residues: 750 sheet: -0.99 (0.69), residues: 52 loop : -2.54 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 290 HIS 0.004 0.001 HIS D 322 PHE 0.018 0.002 PHE C 108 TYR 0.015 0.001 TYR C 109 ARG 0.005 0.001 ARG D 624 *********************** 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 156 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 137 time to evaluate : 1.592 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 86 LYS cc_start: 0.3841 (mptt) cc_final: 0.3565 (mptt) REVERT: D 159 LEU cc_start: 0.6666 (tm) cc_final: 0.6407 (tp) REVERT: C 108 PHE cc_start: 0.6944 (OUTLIER) cc_final: 0.6712 (t80) REVERT: C 420 ASP cc_start: 0.7235 (m-30) cc_final: 0.7033 (m-30) outliers start: 19 outliers final: 9 residues processed: 148 average time/residue: 1.8137 time to fit residues: 298.1033 Evaluate side-chains 129 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 119 time to evaluate : 1.517 ------------------------------------------------------------------------------- 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 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 61 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 98 optimal weight: 0.1980 chunk 109 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10295 Z= 0.218 Angle : 0.593 6.960 13872 Z= 0.325 Chirality : 0.039 0.167 1534 Planarity : 0.005 0.065 1716 Dihedral : 16.977 171.409 1665 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 1.93 % Allowed : 13.15 % Favored : 84.91 % 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: -0.88 (0.24), residues: 1207 helix: 0.44 (0.19), residues: 750 sheet: -0.72 (0.68), residues: 52 loop : -2.53 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 290 HIS 0.028 0.001 HIS C 458 PHE 0.016 0.002 PHE C 108 TYR 0.015 0.002 TYR C 19 ARG 0.004 0.000 ARG C 362 *********************** 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 148 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 1.519 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: 0.3909 (mptt) cc_final: 0.3666 (mptt) REVERT: D 159 LEU cc_start: 0.6632 (tm) cc_final: 0.6379 (tp) REVERT: C 8 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6773 (mp) REVERT: C 358 SER cc_start: 0.7953 (m) cc_final: 0.7435 (t) outliers start: 20 outliers final: 11 residues processed: 139 average time/residue: 1.8757 time to fit residues: 288.8968 Evaluate side-chains 134 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 122 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 108 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 104 optimal weight: 0.0570 chunk 31 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.9904 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 10295 Z= 0.299 Angle : 0.628 9.860 13872 Z= 0.343 Chirality : 0.040 0.176 1534 Planarity : 0.005 0.058 1716 Dihedral : 16.195 102.000 1663 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 2.71 % Allowed : 13.64 % Favored : 83.66 % 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: -1.25 (0.23), residues: 1207 helix: 0.10 (0.18), residues: 754 sheet: -0.60 (0.66), residues: 57 loop : -2.67 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 290 HIS 0.008 0.001 HIS D 322 PHE 0.015 0.002 PHE C 108 TYR 0.017 0.002 TYR C 19 ARG 0.005 0.001 ARG D 624 *********************** 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 156 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 128 time to evaluate : 1.562 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: D 86 LYS cc_start: 0.3933 (mptt) cc_final: 0.3716 (mptt) REVERT: D 159 LEU cc_start: 0.6757 (tm) cc_final: 0.6521 (tp) REVERT: C 166 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7455 (mp) REVERT: C 273 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.7040 (tt) REVERT: C 358 SER cc_start: 0.8144 (m) cc_final: 0.7587 (t) outliers start: 28 outliers final: 14 residues processed: 143 average time/residue: 1.8522 time to fit residues: 293.2873 Evaluate side-chains 128 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 MET 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 166 ILE Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 273 LEU 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 66 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10295 Z= 0.339 Angle : 0.657 7.045 13872 Z= 0.362 Chirality : 0.042 0.207 1534 Planarity : 0.006 0.060 1716 Dihedral : 15.837 100.165 1663 Min Nonbonded Distance : 1.520 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 3.19 % Allowed : 15.76 % Favored : 81.04 % 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: -1.61 (0.23), residues: 1207 helix: -0.25 (0.18), residues: 757 sheet: -0.63 (0.65), residues: 57 loop : -2.68 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 290 HIS 0.008 0.001 HIS D 322 PHE 0.019 0.002 PHE C 65 TYR 0.020 0.002 TYR C 19 ARG 0.011 0.001 ARG C 362 *********************** 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 153 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 120 time to evaluate : 1.544 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: D 146 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7410 (mt) REVERT: C 166 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7472 (mp) REVERT: C 273 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.7045 (tt) outliers start: 33 outliers final: 12 residues processed: 141 average time/residue: 1.9289 time to fit residues: 302.0089 Evaluate side-chains 127 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 1.531 ------------------------------------------------------------------------------- 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 259 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 117 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 458 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10295 Z= 0.309 Angle : 0.637 8.908 13872 Z= 0.347 Chirality : 0.040 0.183 1534 Planarity : 0.006 0.053 1716 Dihedral : 15.649 95.490 1663 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % 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 (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: -1.57 (0.23), residues: 1207 helix: -0.21 (0.18), residues: 756 sheet: -0.54 (0.67), residues: 57 loop : -2.69 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 290 HIS 0.007 0.001 HIS D 322 PHE 0.026 0.002 PHE D 315 TYR 0.019 0.002 TYR C 19 ARG 0.008 0.001 ARG C 362 *********************** 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 138 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 114 time to evaluate : 1.654 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 86 LYS cc_start: 0.4014 (mptt) cc_final: 0.3808 (mptt) REVERT: D 146 ILE cc_start: 0.7677 (OUTLIER) cc_final: 0.7352 (mt) REVERT: C 166 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7430 (mp) REVERT: C 273 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7112 (tt) outliers start: 24 outliers final: 15 residues processed: 129 average time/residue: 2.0479 time to fit residues: 291.2467 Evaluate side-chains 129 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 1.605 ------------------------------------------------------------------------------- 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 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 273 LEU 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 13 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: