Starting phenix.real_space_refine on Fri Feb 6 04:17:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cur_45939/02_2026/9cur_45939_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cur_45939/02_2026/9cur_45939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cur_45939/02_2026/9cur_45939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cur_45939/02_2026/9cur_45939.map" model { file = "/net/cci-nas-00/data/ceres_data/9cur_45939/02_2026/9cur_45939_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cur_45939/02_2026/9cur_45939_trim.cif" } resolution = 3.4 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= -0.000 sd= 0.012 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 32 5.49 5 Mg 1 5.21 5 S 43 5.16 5 C 7073 2.51 5 N 1675 2.21 5 O 2007 1.98 5 H 9834 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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20665 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 10535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 10535 Classifications: {'peptide': 657} Link IDs: {'PTRANS': 13, 'TRANS': 643} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 9015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 9015 Classifications: {'peptide': 568} Link IDs: {'PTRANS': 19, 'TRANS': 548} Chain breaks: 1 Chain: "D" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 590 Unusual residues: {' MG': 1, 'ATP': 1, 'HT1': 2, 'POV': 13} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-3': 2} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 525 Unusual residues: {'ATP': 1, 'POV': 14} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 6, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 4.23, per 1000 atoms: 0.20 Number of scatterers: 20665 At special positions: 0 Unit cell: (80.228, 106.755, 154.633, 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 43 16.00 P 32 15.00 Mg 1 11.99 O 2007 8.00 N 1675 7.00 C 7073 6.00 H 9834 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: 2.19 Conformation dependent library (CDL) restraints added in 540.4 milliseconds 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2276 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 8 sheets defined 64.7% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'D' and resid 3 through 13 removed outlier: 3.624A pdb=" N LEU D 13 " --> pdb=" O ARG D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 46 removed outlier: 3.741A pdb=" N LEU D 18 " --> pdb=" O TYR D 14 " (cutoff:3.500A) Proline residue: D 36 - end of helix Processing helix chain 'D' and resid 48 through 52 Processing helix chain 'D' and resid 134 through 143 Processing helix chain 'D' and resid 145 through 195 Processing helix chain 'D' and resid 197 through 204 removed outlier: 3.550A pdb=" N PHE D 201 " --> pdb=" O PRO D 197 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN D 203 " --> pdb=" O ARG D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 249 removed outlier: 3.501A pdb=" N VAL D 209 " --> pdb=" O PRO D 205 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASP D 216 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR D 217 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR D 233 " --> pdb=" O SER D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 297 removed outlier: 4.167A pdb=" N CYS D 256 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Proline residue: D 261 - end of helix removed outlier: 3.571A pdb=" N TRP D 264 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR D 276 " --> pdb=" O ARG D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.631A pdb=" N ILE D 302 " --> pdb=" O GLY D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 309 removed outlier: 4.387A pdb=" N LYS D 309 " --> pdb=" O ARG D 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 310 through 337 Processing helix chain 'D' and resid 337 through 362 removed outlier: 4.280A pdb=" N ASN D 362 " --> pdb=" O GLY D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 383 removed outlier: 3.590A pdb=" N LEU D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 411 removed outlier: 5.038A pdb=" N GLU D 397 " --> pdb=" O PHE D 393 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N LEU D 398 " --> pdb=" O SER D 394 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 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 506 removed outlier: 3.531A pdb=" N SER D 504 " --> pdb=" O GLN D 500 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS D 505 " --> pdb=" O GLU D 501 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 526 Processing helix chain 'D' and resid 532 through 542 removed outlier: 3.891A pdb=" N ILE D 536 " --> pdb=" O THR D 532 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN D 538 " --> pdb=" O GLU D 534 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D 539 " --> pdb=" O GLU D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 549 removed outlier: 4.108A pdb=" N LEU D 548 " --> pdb=" O GLY D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 583 removed outlier: 3.861A pdb=" N GLN D 573 " --> pdb=" O SER D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 604 Processing helix chain 'D' and resid 604 through 613 Processing helix chain 'D' and resid 624 through 629 removed outlier: 3.714A pdb=" N THR D 627 " --> pdb=" O ARG D 624 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG D 629 " --> pdb=" O SER D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 655 removed outlier: 4.278A pdb=" N LEU D 654 " --> pdb=" O LEU D 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 8 through 15 Processing helix chain 'C' and resid 16 through 33 Processing helix chain 'C' and resid 34 through 49 removed outlier: 4.020A pdb=" N LYS C 38 " --> pdb=" O MET C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 102 removed outlier: 3.801A pdb=" N GLY C 85 " --> pdb=" O GLN C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 112 removed outlier: 3.544A pdb=" N TYR C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 123 Processing helix chain 'C' and resid 123 through 144 removed outlier: 4.238A pdb=" N ILE C 136 " --> pdb=" O THR C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 156 Processing helix chain 'C' and resid 158 through 167 removed outlier: 3.738A pdb=" N THR C 162 " --> pdb=" O SER C 158 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE C 163 " --> pdb=" O TRP C 159 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE C 167 " --> pdb=" O PHE C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 207 removed outlier: 4.017A pdb=" N VAL C 171 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY C 207 " --> pdb=" O GLU C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 214 Processing helix chain 'C' and resid 218 through 243 removed outlier: 3.831A pdb=" N ILE C 241 " --> pdb=" O LYS C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 269 removed outlier: 3.658A pdb=" N THR C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE C 269 " --> pdb=" O ALA C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 317 removed outlier: 4.995A pdb=" N TRP C 290 " --> pdb=" O GLY C 286 " (cutoff:3.500A) Proline residue: C 291 - end of helix removed outlier: 3.862A pdb=" N GLY C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 385 removed outlier: 4.390A pdb=" N ILE C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 427 through 432 Processing helix chain 'C' and resid 433 through 436 Processing helix chain 'C' and resid 442 through 451 Processing helix chain 'C' and resid 452 through 456 removed outlier: 3.730A pdb=" N LYS C 455 " --> pdb=" O HIS C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 491 removed outlier: 4.313A pdb=" N ARG C 482 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 521 Processing helix chain 'C' and resid 555 through 562 Processing sheet with id=AA1, first strand: chain 'D' and resid 54 through 56 Processing sheet with id=AA2, first strand: chain 'D' and resid 89 through 93 Processing sheet with id=AA3, first strand: chain 'D' and resid 110 through 111 Processing sheet with id=AA4, first strand: chain 'D' and resid 451 through 453 removed outlier: 4.906A pdb=" N PHE D 432 " --> pdb=" O LEU D 488 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU D 488 " --> pdb=" O PHE D 432 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP D 434 " --> pdb=" O ASP D 486 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 617 through 620 removed outlier: 6.214A pdb=" N GLU D 457 " --> pdb=" O THR D 618 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL D 620 " --> pdb=" O GLU D 457 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL D 459 " --> pdb=" O VAL D 620 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU D 635 " --> pdb=" O THR D 458 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ALA D 460 " --> pdb=" O LEU D 635 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 360 through 361 removed outlier: 3.708A pdb=" N VAL C 400 " --> pdb=" O PHE C 397 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 367 through 369 removed outlier: 6.419A pdb=" N LEU C 496 " --> pdb=" O PHE C 527 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU C 529 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU C 498 " --> pdb=" O LEU C 529 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLY C 415 " --> pdb=" O ILE C 497 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ASP C 499 " --> pdb=" O GLY C 415 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL C 417 " --> pdb=" O ASP C 499 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 544 through 546 removed outlier: 7.354A pdb=" N VAL C 544 " --> pdb=" O ALA C 551 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1680 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: 5.43 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9831 1.03 - 1.23: 163 1.23 - 1.43: 4175 1.43 - 1.62: 6587 1.62 - 1.82: 84 Bond restraints: 20840 Sorted by residual: bond pdb=" C THR C 95 " pdb=" O THR C 95 " ideal model delta sigma weight residual 1.236 1.195 0.041 1.26e-02 6.30e+03 1.06e+01 bond pdb=" N GLU D 534 " pdb=" H GLU D 534 " ideal model delta sigma weight residual 0.860 0.921 -0.061 2.00e-02 2.50e+03 9.42e+00 bond pdb=" N ARG C 567 " pdb=" H ARG C 567 " ideal model delta sigma weight residual 0.860 0.919 -0.059 2.00e-02 2.50e+03 8.72e+00 bond pdb=" N VAL C 312 " pdb=" CA VAL C 312 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 8.03e+00 bond pdb=" O12 POV D 713 " pdb=" P POV D 713 " ideal model delta sigma weight residual 1.657 1.602 0.055 2.00e-02 2.50e+03 7.52e+00 ... (remaining 20835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 36898 3.58 - 7.15: 126 7.15 - 10.73: 5 10.73 - 14.30: 0 14.30 - 17.88: 2 Bond angle restraints: 37031 Sorted by residual: angle pdb=" PA ATP D 714 " pdb=" O3A ATP D 714 " pdb=" PB ATP D 714 " ideal model delta sigma weight residual 136.83 118.95 17.88 1.00e+00 1.00e+00 3.20e+02 angle pdb=" PB ATP C 615 " pdb=" O3B ATP C 615 " pdb=" PG ATP C 615 " ideal model delta sigma weight residual 139.87 123.96 15.91 1.00e+00 1.00e+00 2.53e+02 angle pdb=" N ARG C 567 " pdb=" CA ARG C 567 " pdb=" C ARG C 567 " ideal model delta sigma weight residual 113.41 103.41 10.00 1.22e+00 6.72e-01 6.72e+01 angle pdb=" PA ATP C 615 " pdb=" O3A ATP C 615 " pdb=" PB ATP C 615 " ideal model delta sigma weight residual 136.83 130.90 5.93 1.00e+00 1.00e+00 3.52e+01 angle pdb=" O3B ATP D 714 " pdb=" PG ATP D 714 " pdb=" O3G ATP D 714 " ideal model delta sigma weight residual 104.48 110.05 -5.57 1.14e+00 7.76e-01 2.41e+01 ... (remaining 37026 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.13: 9463 35.13 - 70.26: 538 70.26 - 105.39: 54 105.39 - 140.52: 13 140.52 - 175.65: 1 Dihedral angle restraints: 10069 sinusoidal: 5857 harmonic: 4212 Sorted by residual: dihedral pdb=" CA SER D 337 " pdb=" C SER D 337 " pdb=" N HIS D 338 " pdb=" CA HIS D 338 " ideal model delta harmonic sigma weight residual -180.00 -155.37 -24.63 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" C29 POV C 605 " pdb="C210 POV C 605 " pdb="C211 POV C 605 " pdb="C212 POV C 605 " ideal model delta sinusoidal sigma weight residual 112.25 -63.40 175.65 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA THR D 599 " pdb=" C THR D 599 " pdb=" N GLU D 600 " pdb=" CA GLU D 600 " ideal model delta harmonic sigma weight residual -180.00 -157.61 -22.39 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 10066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1173 0.041 - 0.083: 307 0.083 - 0.124: 64 0.124 - 0.165: 12 0.165 - 0.207: 1 Chirality restraints: 1557 Sorted by residual: chirality pdb=" CA TYR C 566 " pdb=" N TYR C 566 " pdb=" C TYR C 566 " pdb=" CB TYR C 566 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB THR C 95 " pdb=" CA THR C 95 " pdb=" OG1 THR C 95 " pdb=" CG2 THR C 95 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CA VAL C 312 " pdb=" N VAL C 312 " pdb=" C VAL C 312 " pdb=" CB VAL C 312 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.06e-01 ... (remaining 1554 not shown) Planarity restraints: 2964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 567 " 0.074 9.50e-02 1.11e+02 2.28e-01 1.16e+03 pdb=" NE ARG C 567 " 0.159 2.00e-02 2.50e+03 pdb=" CZ ARG C 567 " 0.045 2.00e-02 2.50e+03 pdb=" NH1 ARG C 567 " 0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG C 567 " -0.054 2.00e-02 2.50e+03 pdb="HH11 ARG C 567 " -0.454 2.00e-02 2.50e+03 pdb="HH12 ARG C 567 " 0.450 2.00e-02 2.50e+03 pdb="HH21 ARG C 567 " -0.011 2.00e-02 2.50e+03 pdb="HH22 ARG C 567 " -0.156 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 633 " 0.156 2.00e-02 2.50e+03 1.70e-01 4.31e+02 pdb=" CD GLN D 633 " -0.008 2.00e-02 2.50e+03 pdb=" OE1 GLN D 633 " -0.149 2.00e-02 2.50e+03 pdb=" NE2 GLN D 633 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN D 633 " -0.251 2.00e-02 2.50e+03 pdb="HE22 GLN D 633 " 0.251 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 707 " 0.183 2.00e-02 2.50e+03 1.84e-01 3.40e+02 pdb=" C29 POV D 707 " -0.179 2.00e-02 2.50e+03 pdb="C210 POV D 707 " -0.190 2.00e-02 2.50e+03 pdb="C211 POV D 707 " 0.186 2.00e-02 2.50e+03 ... (remaining 2961 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.20: 1480 2.20 - 2.80: 40881 2.80 - 3.40: 55673 3.40 - 4.00: 71386 4.00 - 4.60: 111034 Nonbonded interactions: 280454 Sorted by model distance: nonbonded pdb=" H ASP D 638 " pdb=" O GLU D 641 " model vdw 1.605 2.450 nonbonded pdb=" H PHE D 516 " pdb=" OD1 ASN D 523 " model vdw 1.644 2.450 nonbonded pdb=" O HIS D 505 " pdb=" H ALA D 586 " model vdw 1.663 2.450 nonbonded pdb=" H LYS D 447 " pdb=" O GLY D 640 " model vdw 1.673 2.450 nonbonded pdb=" O LEU C 496 " pdb=" H PHE C 527 " model vdw 1.673 2.450 ... (remaining 280449 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 0.440 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 22.680 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 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 : 0.007 0.062 11006 Z= 0.362 Angle : 0.834 17.880 14736 Z= 0.444 Chirality : 0.040 0.207 1557 Planarity : 0.011 0.184 1776 Dihedral : 22.179 175.651 4493 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 22.40 % Favored : 77.60 % 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 are not related in a simple way. whole: 0.12 (0.24), residues: 1215 helix: 1.44 (0.19), residues: 742 sheet: -0.17 (0.65), residues: 62 loop : -2.55 (0.27), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 126 TYR 0.013 0.001 TYR C 566 PHE 0.012 0.001 PHE D 231 TRP 0.016 0.002 TRP D 266 HIS 0.007 0.001 HIS D 338 Details of bonding type rmsd covalent geometry : bond 0.00712 (11006) covalent geometry : angle 0.83401 (14736) hydrogen bonds : bond 0.12583 ( 577) hydrogen bonds : angle 5.52138 ( 1680) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 124 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 310 ASP cc_start: 0.8150 (t0) cc_final: 0.7913 (t0) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2509 time to fit residues: 47.3389 Evaluate side-chains 124 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 440 GLN C 353 ASN ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.175946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.145289 restraints weight = 38295.251| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.04 r_work: 0.3636 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11006 Z= 0.145 Angle : 0.547 6.509 14736 Z= 0.289 Chirality : 0.038 0.151 1557 Planarity : 0.004 0.056 1776 Dihedral : 21.301 171.857 2188 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.15 % Allowed : 23.08 % Favored : 75.77 % 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 are not related in a simple way. whole: 0.20 (0.25), residues: 1215 helix: 1.49 (0.19), residues: 746 sheet: -0.39 (0.67), residues: 62 loop : -2.49 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 567 TYR 0.017 0.001 TYR D 200 PHE 0.011 0.001 PHE D 451 TRP 0.013 0.001 TRP C 78 HIS 0.005 0.001 HIS D 338 Details of bonding type rmsd covalent geometry : bond 0.00317 (11006) covalent geometry : angle 0.54665 (14736) hydrogen bonds : bond 0.04813 ( 577) hydrogen bonds : angle 4.44893 ( 1680) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 124 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 310 ASP cc_start: 0.8287 (t0) cc_final: 0.8025 (t0) outliers start: 12 outliers final: 8 residues processed: 136 average time/residue: 0.1947 time to fit residues: 38.9733 Evaluate side-chains 133 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 648 HIS Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 295 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 440 GLN C 216 GLN C 353 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.172873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.141649 restraints weight = 38680.873| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.06 r_work: 0.3590 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11006 Z= 0.193 Angle : 0.552 6.775 14736 Z= 0.294 Chirality : 0.038 0.158 1557 Planarity : 0.004 0.056 1776 Dihedral : 20.518 166.961 2188 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.21 % Allowed : 23.27 % Favored : 74.52 % 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 are not related in a simple way. whole: -0.01 (0.24), residues: 1215 helix: 1.29 (0.19), residues: 749 sheet: -0.51 (0.68), residues: 62 loop : -2.52 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 487 TYR 0.016 0.002 TYR D 200 PHE 0.009 0.001 PHE C 339 TRP 0.012 0.002 TRP C 78 HIS 0.004 0.001 HIS D 338 Details of bonding type rmsd covalent geometry : bond 0.00437 (11006) covalent geometry : angle 0.55176 (14736) hydrogen bonds : bond 0.04970 ( 577) hydrogen bonds : angle 4.44515 ( 1680) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 124 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8456 (mp) REVERT: C 310 ASP cc_start: 0.8378 (t0) cc_final: 0.8114 (t0) REVERT: C 366 THR cc_start: 0.8368 (p) cc_final: 0.7935 (t) outliers start: 23 outliers final: 15 residues processed: 143 average time/residue: 0.2029 time to fit residues: 43.2617 Evaluate side-chains 144 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 353 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 440 GLN C 216 GLN C 353 ASN ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.173920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.142879 restraints weight = 38496.162| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.05 r_work: 0.3602 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11006 Z= 0.156 Angle : 0.528 7.087 14736 Z= 0.280 Chirality : 0.038 0.168 1557 Planarity : 0.004 0.056 1776 Dihedral : 20.028 162.491 2188 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.12 % Allowed : 23.46 % Favored : 74.42 % 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 are not related in a simple way. whole: -0.00 (0.24), residues: 1215 helix: 1.31 (0.19), residues: 758 sheet: -0.60 (0.68), residues: 62 loop : -2.60 (0.27), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 487 TYR 0.015 0.001 TYR D 200 PHE 0.009 0.001 PHE C 339 TRP 0.013 0.001 TRP C 78 HIS 0.003 0.001 HIS C 538 Details of bonding type rmsd covalent geometry : bond 0.00347 (11006) covalent geometry : angle 0.52752 (14736) hydrogen bonds : bond 0.04747 ( 577) hydrogen bonds : angle 4.30887 ( 1680) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 124 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8458 (mp) REVERT: C 310 ASP cc_start: 0.8343 (t0) cc_final: 0.8092 (t0) REVERT: C 366 THR cc_start: 0.8332 (p) cc_final: 0.7899 (t) outliers start: 22 outliers final: 18 residues processed: 140 average time/residue: 0.2081 time to fit residues: 43.0096 Evaluate side-chains 143 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 500 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 93 optimal weight: 0.9990 chunk 55 optimal weight: 0.0070 chunk 53 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 overall best weight: 1.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 440 GLN ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.174056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.143120 restraints weight = 38240.523| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.03 r_work: 0.3609 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11006 Z= 0.146 Angle : 0.511 7.781 14736 Z= 0.271 Chirality : 0.037 0.140 1557 Planarity : 0.004 0.057 1776 Dihedral : 19.402 157.828 2188 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.31 % Allowed : 23.65 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.24), residues: 1215 helix: 1.40 (0.19), residues: 757 sheet: -0.67 (0.69), residues: 62 loop : -2.58 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 381 TYR 0.013 0.001 TYR D 200 PHE 0.009 0.001 PHE C 339 TRP 0.013 0.001 TRP C 78 HIS 0.003 0.001 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00326 (11006) covalent geometry : angle 0.51144 (14736) hydrogen bonds : bond 0.04590 ( 577) hydrogen bonds : angle 4.20789 ( 1680) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 124 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8508 (mp) REVERT: C 310 ASP cc_start: 0.8329 (t0) cc_final: 0.8086 (t0) REVERT: C 366 THR cc_start: 0.8323 (p) cc_final: 0.7883 (t) outliers start: 24 outliers final: 19 residues processed: 142 average time/residue: 0.2065 time to fit residues: 43.3492 Evaluate side-chains 141 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 573 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 81 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 117 optimal weight: 0.4980 chunk 103 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 440 GLN D 523 ASN ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.175553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.144637 restraints weight = 38270.042| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.04 r_work: 0.3626 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11006 Z= 0.116 Angle : 0.491 8.743 14736 Z= 0.260 Chirality : 0.036 0.140 1557 Planarity : 0.004 0.057 1776 Dihedral : 18.838 154.746 2188 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.31 % Allowed : 23.65 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.25), residues: 1215 helix: 1.57 (0.19), residues: 754 sheet: -0.71 (0.70), residues: 62 loop : -2.53 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 426 TYR 0.012 0.001 TYR D 200 PHE 0.008 0.001 PHE C 339 TRP 0.013 0.001 TRP C 78 HIS 0.004 0.001 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00252 (11006) covalent geometry : angle 0.49117 (14736) hydrogen bonds : bond 0.04388 ( 577) hydrogen bonds : angle 4.07085 ( 1680) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 124 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8527 (mp) REVERT: D 661 MET cc_start: 0.5783 (tpp) cc_final: 0.5517 (tpp) REVERT: C 310 ASP cc_start: 0.8299 (t0) cc_final: 0.8058 (t0) REVERT: C 366 THR cc_start: 0.8309 (p) cc_final: 0.7895 (t) outliers start: 24 outliers final: 20 residues processed: 149 average time/residue: 0.2055 time to fit residues: 44.8392 Evaluate side-chains 147 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 484 LYS Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 500 ASP Chi-restraints excluded: chain C residue 573 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 24 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 440 GLN D 523 ASN ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.173103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.142080 restraints weight = 38465.355| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.04 r_work: 0.3595 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11006 Z= 0.170 Angle : 0.527 7.624 14736 Z= 0.280 Chirality : 0.037 0.140 1557 Planarity : 0.004 0.056 1776 Dihedral : 18.663 154.301 2188 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.79 % Allowed : 23.37 % Favored : 73.85 % 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 are not related in a simple way. whole: 0.13 (0.25), residues: 1215 helix: 1.42 (0.19), residues: 758 sheet: -0.76 (0.69), residues: 63 loop : -2.54 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 487 TYR 0.014 0.001 TYR D 200 PHE 0.008 0.001 PHE C 397 TRP 0.023 0.002 TRP C 565 HIS 0.003 0.001 HIS C 538 Details of bonding type rmsd covalent geometry : bond 0.00384 (11006) covalent geometry : angle 0.52709 (14736) hydrogen bonds : bond 0.04628 ( 577) hydrogen bonds : angle 4.18638 ( 1680) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 124 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 48 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8544 (mp) REVERT: D 523 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7586 (t0) REVERT: D 661 MET cc_start: 0.5923 (tpp) cc_final: 0.5629 (tpp) REVERT: C 310 ASP cc_start: 0.8322 (t0) cc_final: 0.8086 (t0) REVERT: C 366 THR cc_start: 0.8326 (p) cc_final: 0.7895 (t) outliers start: 29 outliers final: 25 residues processed: 147 average time/residue: 0.1793 time to fit residues: 39.2095 Evaluate side-chains 150 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 500 ASP Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 573 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 81 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 440 GLN D 523 ASN ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.174318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.143285 restraints weight = 38459.057| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.03 r_work: 0.3607 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11006 Z= 0.134 Angle : 0.499 5.231 14736 Z= 0.268 Chirality : 0.037 0.138 1557 Planarity : 0.004 0.056 1776 Dihedral : 18.385 152.862 2188 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.88 % Allowed : 23.65 % Favored : 73.46 % 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 are not related in a simple way. whole: 0.21 (0.25), residues: 1215 helix: 1.50 (0.19), residues: 756 sheet: -0.80 (0.68), residues: 63 loop : -2.52 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 426 TYR 0.012 0.001 TYR D 200 PHE 0.008 0.001 PHE D 67 TRP 0.025 0.002 TRP C 565 HIS 0.003 0.001 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00298 (11006) covalent geometry : angle 0.49866 (14736) hydrogen bonds : bond 0.04505 ( 577) hydrogen bonds : angle 4.11950 ( 1680) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 124 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8558 (mp) REVERT: D 523 ASN cc_start: 0.7759 (OUTLIER) cc_final: 0.7544 (t0) REVERT: C 310 ASP cc_start: 0.8321 (t0) cc_final: 0.8088 (t0) REVERT: C 366 THR cc_start: 0.8319 (p) cc_final: 0.7900 (t) outliers start: 30 outliers final: 25 residues processed: 151 average time/residue: 0.1967 time to fit residues: 43.3930 Evaluate side-chains 152 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 500 ASP Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 573 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 76 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 440 GLN ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.173147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.141858 restraints weight = 38548.727| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.05 r_work: 0.3588 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11006 Z= 0.177 Angle : 0.531 7.904 14736 Z= 0.283 Chirality : 0.038 0.172 1557 Planarity : 0.004 0.056 1776 Dihedral : 18.317 152.473 2188 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.79 % Allowed : 23.85 % Favored : 73.37 % 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 are not related in a simple way. whole: 0.11 (0.24), residues: 1215 helix: 1.42 (0.19), residues: 754 sheet: -0.89 (0.67), residues: 63 loop : -2.50 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 487 TYR 0.014 0.001 TYR D 200 PHE 0.008 0.001 PHE C 397 TRP 0.021 0.002 TRP C 565 HIS 0.003 0.001 HIS C 538 Details of bonding type rmsd covalent geometry : bond 0.00404 (11006) covalent geometry : angle 0.53094 (14736) hydrogen bonds : bond 0.04641 ( 577) hydrogen bonds : angle 4.22687 ( 1680) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 124 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8596 (mp) REVERT: C 310 ASP cc_start: 0.8341 (t0) cc_final: 0.8109 (t0) REVERT: C 366 THR cc_start: 0.8322 (p) cc_final: 0.7901 (t) outliers start: 29 outliers final: 27 residues processed: 144 average time/residue: 0.2036 time to fit residues: 43.7505 Evaluate side-chains 150 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 500 ASP Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 573 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 83 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 440 GLN ** D 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.175008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.144057 restraints weight = 38151.477| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.03 r_work: 0.3620 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11006 Z= 0.123 Angle : 0.495 6.905 14736 Z= 0.263 Chirality : 0.037 0.139 1557 Planarity : 0.004 0.057 1776 Dihedral : 17.775 149.174 2188 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.40 % Allowed : 24.23 % Favored : 73.37 % 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 are not related in a simple way. whole: 0.32 (0.25), residues: 1215 helix: 1.60 (0.19), residues: 751 sheet: -1.00 (0.67), residues: 62 loop : -2.37 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 409 TYR 0.012 0.001 TYR D 200 PHE 0.008 0.001 PHE C 339 TRP 0.019 0.001 TRP C 565 HIS 0.003 0.001 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00274 (11006) covalent geometry : angle 0.49492 (14736) hydrogen bonds : bond 0.04378 ( 577) hydrogen bonds : angle 4.05925 ( 1680) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 124 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8608 (mp) REVERT: C 310 ASP cc_start: 0.8316 (t0) cc_final: 0.8083 (t0) REVERT: C 366 THR cc_start: 0.8303 (p) cc_final: 0.7908 (t) outliers start: 25 outliers final: 23 residues processed: 140 average time/residue: 0.1624 time to fit residues: 35.0671 Evaluate side-chains 145 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 500 ASP Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 573 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 82 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 109 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 440 GLN ** D 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.175161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.144249 restraints weight = 38433.057| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.04 r_work: 0.3617 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11006 Z= 0.123 Angle : 0.488 6.785 14736 Z= 0.261 Chirality : 0.036 0.140 1557 Planarity : 0.004 0.056 1776 Dihedral : 17.323 147.489 2188 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.50 % Allowed : 24.42 % Favored : 73.08 % 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 are not related in a simple way. whole: 0.38 (0.25), residues: 1215 helix: 1.63 (0.19), residues: 752 sheet: -1.02 (0.67), residues: 62 loop : -2.32 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 409 TYR 0.012 0.001 TYR D 200 PHE 0.011 0.001 PHE D 67 TRP 0.017 0.001 TRP C 565 HIS 0.003 0.001 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00275 (11006) covalent geometry : angle 0.48806 (14736) hydrogen bonds : bond 0.04294 ( 577) hydrogen bonds : angle 4.00854 ( 1680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5532.19 seconds wall clock time: 94 minutes 32.40 seconds (5672.40 seconds total)