Starting phenix.real_space_refine on Tue Feb 11 19:20:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i9g_35270/02_2025/8i9g_35270.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i9g_35270/02_2025/8i9g_35270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i9g_35270/02_2025/8i9g_35270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i9g_35270/02_2025/8i9g_35270.map" model { file = "/net/cci-nas-00/data/ceres_data/8i9g_35270/02_2025/8i9g_35270.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i9g_35270/02_2025/8i9g_35270.cif" } resolution = 3.2 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= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 4159 2.51 5 N 1061 2.21 5 O 1251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6507 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "A" Number of atoms: 1455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1455 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 10, 'TRANS': 170} Chain breaks: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.33, per 1000 atoms: 0.67 Number of scatterers: 6507 At special positions: 0 Unit cell: (104.352, 90.221, 107.613, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1251 8.00 N 1061 7.00 C 4159 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG B 1 " - " ASN D 53 " " NAG C 1 " - " ASN D 90 " " NAG D 701 " - " ASN D 322 " " NAG E 1 " - " ASN D 103 " " NAG F 1 " - " ASN D 432 " " NAG G 1 " - " ASN D 546 " " NAG H 1 " - " ASN A 343 " Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 844.5 milliseconds 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1466 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 4 sheets defined 51.7% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'D' and resid 22 through 53 removed outlier: 3.776A pdb=" N LYS D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN D 53 " --> pdb=" O ASN D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 80 removed outlier: 3.797A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.893A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.944A pdb=" N ALA D 153 " --> pdb=" O ASN D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.779A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 193 removed outlier: 3.909A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.640A pdb=" N TYR D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 230 removed outlier: 4.122A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 249 removed outlier: 3.833A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.728A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 300 Processing helix chain 'D' and resid 305 through 318 removed outlier: 3.858A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.857A pdb=" N ASN D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 326 through 331' Processing helix chain 'D' and resid 366 through 385 removed outlier: 4.070A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.692A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 412 removed outlier: 3.877A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 3.913A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE D 421 " --> pdb=" O HIS D 417 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.631A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 4.162A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN D 531 " --> pdb=" O GLU D 527 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.608A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.897A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 570 Processing helix chain 'D' and resid 570 through 575 Processing helix chain 'D' and resid 581 through 599 removed outlier: 3.532A pdb=" N LEU D 585 " --> pdb=" O VAL D 581 " (cutoff:3.500A) Proline residue: D 590 - end of helix Processing helix chain 'A' and resid 337 through 342 removed outlier: 4.380A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.699A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 4.976A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.921A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.243A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.655A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 259 hydrogen bonds defined for protein. 735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2058 1.34 - 1.47: 1773 1.47 - 1.59: 2798 1.59 - 1.71: 0 1.71 - 1.84: 57 Bond restraints: 6686 Sorted by residual: bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.84e+00 bond pdb=" C ALA A 372 " pdb=" N PRO A 373 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.38e-02 5.25e+03 2.82e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.70e+00 bond pdb=" C VAL A 382 " pdb=" N SER A 383 " ideal model delta sigma weight residual 1.329 1.354 -0.025 1.60e-02 3.91e+03 2.47e+00 bond pdb=" C1 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.46e+00 ... (remaining 6681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 8652 1.44 - 2.88: 361 2.88 - 4.32: 57 4.32 - 5.76: 8 5.76 - 7.20: 5 Bond angle restraints: 9083 Sorted by residual: angle pdb=" N GLY D 326 " pdb=" CA GLY D 326 " pdb=" C GLY D 326 " ideal model delta sigma weight residual 115.61 108.41 7.20 1.74e+00 3.30e-01 1.71e+01 angle pdb=" N ARG A 452 " pdb=" CA ARG A 452 " pdb=" C ARG A 452 " ideal model delta sigma weight residual 110.44 114.92 -4.48 1.20e+00 6.94e-01 1.39e+01 angle pdb=" C PHE A 371 " pdb=" N ALA A 372 " pdb=" CA ALA A 372 " ideal model delta sigma weight residual 123.96 119.34 4.62 1.44e+00 4.82e-01 1.03e+01 angle pdb=" C GLN A 493 " pdb=" N SER A 494 " pdb=" CA SER A 494 " ideal model delta sigma weight residual 121.31 125.48 -4.17 1.49e+00 4.50e-01 7.85e+00 angle pdb=" N GLY D 337 " pdb=" CA GLY D 337 " pdb=" C GLY D 337 " ideal model delta sigma weight residual 113.18 119.63 -6.45 2.37e+00 1.78e-01 7.42e+00 ... (remaining 9078 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 3531 17.70 - 35.40: 426 35.40 - 53.10: 108 53.10 - 70.79: 31 70.79 - 88.49: 6 Dihedral angle restraints: 4102 sinusoidal: 1819 harmonic: 2283 Sorted by residual: dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual -86.00 -15.34 -70.66 1 1.00e+01 1.00e-02 6.42e+01 dihedral pdb=" CA TYR A 451 " pdb=" C TYR A 451 " pdb=" N ARG A 452 " pdb=" CA ARG A 452 " ideal model delta harmonic sigma weight residual -180.00 -154.66 -25.34 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA PHE A 371 " pdb=" C PHE A 371 " pdb=" N ALA A 372 " pdb=" CA ALA A 372 " ideal model delta harmonic sigma weight residual -180.00 -158.37 -21.63 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 4099 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 668 0.043 - 0.086: 243 0.086 - 0.129: 68 0.129 - 0.172: 2 0.172 - 0.215: 4 Chirality restraints: 985 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.71e+01 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN D 90 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C4 NAG E 1 " pdb=" C3 NAG E 1 " pdb=" C5 NAG E 1 " pdb=" O4 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.33 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 982 not shown) Planarity restraints: 1166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " -0.082 2.00e-02 2.50e+03 6.72e-02 5.64e+01 pdb=" C7 NAG H 2 " 0.022 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " -0.062 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " 0.106 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " 0.035 2.00e-02 2.50e+03 3.84e-02 1.84e+01 pdb=" CG ASN A 343 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " -0.061 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " -0.046 2.00e-02 2.50e+03 3.75e-02 1.76e+01 pdb=" C7 NAG H 1 " 0.013 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " -0.035 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " 0.059 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.009 2.00e-02 2.50e+03 ... (remaining 1163 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1003 2.75 - 3.29: 5898 3.29 - 3.83: 9954 3.83 - 4.36: 11729 4.36 - 4.90: 20829 Nonbonded interactions: 49413 Sorted by model distance: nonbonded pdb=" O PHE A 392 " pdb=" OG1 THR A 523 " model vdw 2.213 3.040 nonbonded pdb=" NZ LYS D 288 " pdb=" OE1 GLU D 433 " model vdw 2.239 3.120 nonbonded pdb=" ND2 ASN D 134 " pdb=" OD1 ASP D 136 " model vdw 2.278 3.120 nonbonded pdb=" N ASP D 431 " pdb=" OD1 ASP D 431 " model vdw 2.347 3.120 nonbonded pdb=" OG SER A 438 " pdb=" OD2 ASP A 442 " model vdw 2.352 3.040 ... (remaining 49408 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.770 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6686 Z= 0.306 Angle : 0.670 7.201 9083 Z= 0.372 Chirality : 0.046 0.215 985 Planarity : 0.005 0.067 1159 Dihedral : 16.413 88.492 2621 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 4.97 % Allowed : 16.23 % Favored : 78.80 % 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: -3.28 (0.26), residues: 770 helix: -1.15 (0.26), residues: 358 sheet: -2.17 (0.67), residues: 49 loop : -3.31 (0.25), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS D 241 PHE 0.012 0.001 PHE A 375 TYR 0.013 0.001 TYR D 183 ARG 0.003 0.000 ARG D 245 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 0.689 Fit side-chains REVERT: D 86 GLN cc_start: 0.8299 (tm-30) cc_final: 0.7680 (tm-30) REVERT: D 131 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8613 (mtmp) REVERT: D 140 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7231 (tm-30) REVERT: D 256 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8584 (mm) REVERT: D 332 MET cc_start: 0.8069 (ttp) cc_final: 0.7740 (ttm) REVERT: D 431 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7244 (p0) REVERT: D 522 GLN cc_start: 0.8445 (tt0) cc_final: 0.8227 (tt0) REVERT: A 420 ASP cc_start: 0.7387 (m-30) cc_final: 0.7168 (m-30) REVERT: A 467 ASP cc_start: 0.7523 (t0) cc_final: 0.6987 (t0) outliers start: 34 outliers final: 24 residues processed: 106 average time/residue: 0.1948 time to fit residues: 27.4065 Evaluate side-chains 87 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 139 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 247 LYS Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 409 SER Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 0.0010 chunk 19 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 0.0980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN D 58 ASN D 96 GLN D 239 HIS D 345 HIS D 378 HIS D 472 GLN D 493 HIS D 505 HIS D 522 GLN D 599 ASN A 354 ASN A 460 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.107174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.083644 restraints weight = 10361.818| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.15 r_work: 0.2866 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6686 Z= 0.175 Angle : 0.570 9.122 9083 Z= 0.290 Chirality : 0.043 0.277 985 Planarity : 0.004 0.050 1159 Dihedral : 9.357 79.840 1165 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.80 % Allowed : 18.86 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.28), residues: 770 helix: -0.26 (0.28), residues: 369 sheet: -1.63 (0.72), residues: 49 loop : -2.88 (0.26), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS D 241 PHE 0.011 0.001 PHE D 32 TYR 0.010 0.001 TYR A 495 ARG 0.002 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 0.728 Fit side-chains REVERT: D 86 GLN cc_start: 0.8494 (tm-30) cc_final: 0.7805 (tm-30) REVERT: D 131 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8728 (mtmp) REVERT: D 140 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7314 (pp20) REVERT: D 213 ASP cc_start: 0.8969 (t0) cc_final: 0.8759 (t0) REVERT: D 366 MET cc_start: 0.7260 (OUTLIER) cc_final: 0.6961 (tpp) REVERT: D 455 MET cc_start: 0.8874 (tmm) cc_final: 0.8575 (tmm) REVERT: A 364 ASP cc_start: 0.6464 (p0) cc_final: 0.6262 (p0) REVERT: A 420 ASP cc_start: 0.7939 (m-30) cc_final: 0.7689 (m-30) outliers start: 26 outliers final: 14 residues processed: 88 average time/residue: 0.1628 time to fit residues: 20.0655 Evaluate side-chains 77 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 139 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 445 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 16 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 48 optimal weight: 0.0570 chunk 76 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS D 277 ASN D 345 HIS D 522 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.107500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.084699 restraints weight = 10384.278| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.08 r_work: 0.2867 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6686 Z= 0.205 Angle : 0.563 9.349 9083 Z= 0.286 Chirality : 0.044 0.274 985 Planarity : 0.004 0.056 1159 Dihedral : 8.204 79.168 1140 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 4.09 % Allowed : 19.88 % Favored : 76.02 % 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: -1.63 (0.29), residues: 770 helix: 0.21 (0.28), residues: 363 sheet: -1.26 (0.73), residues: 49 loop : -2.50 (0.27), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.009 0.001 HIS D 345 PHE 0.011 0.001 PHE D 32 TYR 0.011 0.001 TYR A 495 ARG 0.002 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: D 86 GLN cc_start: 0.8457 (tm-30) cc_final: 0.7863 (tm-30) REVERT: D 134 ASN cc_start: 0.7595 (OUTLIER) cc_final: 0.6789 (m110) REVERT: D 366 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.6996 (tpp) REVERT: D 455 MET cc_start: 0.8926 (tmm) cc_final: 0.8653 (tmm) REVERT: A 420 ASP cc_start: 0.8008 (m-30) cc_final: 0.7719 (m-30) outliers start: 28 outliers final: 22 residues processed: 87 average time/residue: 0.1625 time to fit residues: 19.7931 Evaluate side-chains 83 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 139 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 522 GLN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 11 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS D 345 HIS D 522 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.107734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.084797 restraints weight = 10497.601| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.10 r_work: 0.2868 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6686 Z= 0.209 Angle : 0.561 9.340 9083 Z= 0.284 Chirality : 0.043 0.278 985 Planarity : 0.004 0.066 1159 Dihedral : 7.832 77.954 1140 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 4.39 % Allowed : 19.01 % Favored : 76.61 % 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: -1.28 (0.29), residues: 770 helix: 0.53 (0.28), residues: 360 sheet: -1.04 (0.74), residues: 49 loop : -2.35 (0.27), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS D 241 PHE 0.011 0.001 PHE D 32 TYR 0.011 0.001 TYR A 495 ARG 0.001 0.000 ARG D 245 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 67 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: D 86 GLN cc_start: 0.8472 (tm-30) cc_final: 0.7873 (tm-30) REVERT: D 134 ASN cc_start: 0.7521 (OUTLIER) cc_final: 0.6771 (m110) REVERT: D 256 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8632 (mm) REVERT: D 366 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6879 (tpp) REVERT: D 368 ASP cc_start: 0.7387 (m-30) cc_final: 0.7159 (m-30) REVERT: D 455 MET cc_start: 0.8913 (tmm) cc_final: 0.8630 (tmm) REVERT: A 364 ASP cc_start: 0.6374 (p0) cc_final: 0.6155 (p0) REVERT: A 420 ASP cc_start: 0.8027 (m-30) cc_final: 0.7714 (m-30) REVERT: A 454 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7578 (ttm170) outliers start: 30 outliers final: 21 residues processed: 93 average time/residue: 0.2098 time to fit residues: 26.4058 Evaluate side-chains 88 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 139 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 70 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 26 optimal weight: 0.0030 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS D 345 HIS D 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.106427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.083096 restraints weight = 10608.190| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.14 r_work: 0.2860 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6686 Z= 0.225 Angle : 0.562 9.362 9083 Z= 0.284 Chirality : 0.044 0.270 985 Planarity : 0.004 0.070 1159 Dihedral : 7.503 76.611 1137 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.97 % Allowed : 19.59 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.29), residues: 770 helix: 0.68 (0.28), residues: 360 sheet: -0.94 (0.74), residues: 49 loop : -2.14 (0.28), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS D 540 PHE 0.011 0.001 PHE D 32 TYR 0.012 0.001 TYR A 495 ARG 0.001 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 68 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: D 86 GLN cc_start: 0.8470 (tm-30) cc_final: 0.7874 (tm-30) REVERT: D 134 ASN cc_start: 0.7484 (OUTLIER) cc_final: 0.6733 (m110) REVERT: D 145 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7801 (tp30) REVERT: D 256 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8650 (mm) REVERT: D 366 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6940 (tpp) REVERT: D 368 ASP cc_start: 0.7298 (m-30) cc_final: 0.7053 (m-30) REVERT: D 376 MET cc_start: 0.8423 (mmm) cc_final: 0.8117 (mmm) REVERT: D 455 MET cc_start: 0.8900 (tmm) cc_final: 0.8609 (tmm) REVERT: A 364 ASP cc_start: 0.6506 (p0) cc_final: 0.6190 (p0) REVERT: A 420 ASP cc_start: 0.8057 (m-30) cc_final: 0.7685 (m-30) REVERT: A 454 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7566 (ttm170) REVERT: A 500 THR cc_start: 0.9200 (p) cc_final: 0.8799 (p) outliers start: 34 outliers final: 25 residues processed: 96 average time/residue: 0.1812 time to fit residues: 23.9118 Evaluate side-chains 95 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 139 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.105633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.082189 restraints weight = 10501.212| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.15 r_work: 0.2846 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6686 Z= 0.252 Angle : 0.570 9.304 9083 Z= 0.289 Chirality : 0.045 0.281 985 Planarity : 0.004 0.056 1159 Dihedral : 7.543 76.554 1137 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 4.97 % Allowed : 19.30 % Favored : 75.73 % 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: -0.86 (0.30), residues: 770 helix: 0.79 (0.28), residues: 360 sheet: -0.84 (0.74), residues: 49 loop : -2.02 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS D 241 PHE 0.011 0.001 PHE D 32 TYR 0.012 0.001 TYR D 183 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 68 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: D 86 GLN cc_start: 0.8479 (tm-30) cc_final: 0.7886 (tm-30) REVERT: D 134 ASN cc_start: 0.7420 (OUTLIER) cc_final: 0.6610 (m110) REVERT: D 256 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8655 (mm) REVERT: D 366 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.7011 (tpp) REVERT: D 376 MET cc_start: 0.8455 (mmm) cc_final: 0.8159 (mmm) REVERT: D 401 HIS cc_start: 0.8447 (OUTLIER) cc_final: 0.7401 (m90) REVERT: A 354 ASN cc_start: 0.7947 (OUTLIER) cc_final: 0.7364 (m110) REVERT: A 364 ASP cc_start: 0.6609 (p0) cc_final: 0.6321 (p0) REVERT: A 420 ASP cc_start: 0.8074 (m-30) cc_final: 0.7701 (m-30) REVERT: A 454 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7608 (ttm170) REVERT: A 500 THR cc_start: 0.9209 (p) cc_final: 0.8838 (p) outliers start: 34 outliers final: 25 residues processed: 98 average time/residue: 0.1735 time to fit residues: 23.1294 Evaluate side-chains 94 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 63 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 139 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 247 LYS Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 522 GLN Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 46 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS D 345 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.106253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.082501 restraints weight = 10559.422| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.19 r_work: 0.2850 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6686 Z= 0.237 Angle : 0.567 9.331 9083 Z= 0.287 Chirality : 0.044 0.276 985 Planarity : 0.004 0.072 1159 Dihedral : 6.927 58.254 1134 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 4.82 % Allowed : 20.18 % Favored : 75.00 % 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: -0.72 (0.30), residues: 770 helix: 0.91 (0.28), residues: 360 sheet: -0.82 (0.75), residues: 49 loop : -1.94 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS D 241 PHE 0.011 0.001 PHE D 32 TYR 0.012 0.001 TYR A 495 ARG 0.001 0.000 ARG D 245 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 66 time to evaluate : 0.663 Fit side-chains revert: symmetry clash REVERT: D 86 GLN cc_start: 0.8470 (tm-30) cc_final: 0.7865 (tm-30) REVERT: D 134 ASN cc_start: 0.7380 (OUTLIER) cc_final: 0.6593 (m110) REVERT: D 142 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8086 (pp) REVERT: D 145 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7681 (tp30) REVERT: D 198 ASP cc_start: 0.8606 (p0) cc_final: 0.8117 (p0) REVERT: D 256 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8653 (mm) REVERT: D 366 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.7017 (tpp) REVERT: D 376 MET cc_start: 0.8471 (mmm) cc_final: 0.8170 (mmm) REVERT: D 401 HIS cc_start: 0.8486 (OUTLIER) cc_final: 0.7470 (m90) REVERT: A 364 ASP cc_start: 0.6624 (p0) cc_final: 0.6323 (p0) REVERT: A 420 ASP cc_start: 0.8067 (m-30) cc_final: 0.7649 (m-30) REVERT: A 454 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7578 (ttm170) REVERT: A 500 THR cc_start: 0.9201 (p) cc_final: 0.8829 (p) outliers start: 33 outliers final: 22 residues processed: 94 average time/residue: 0.1744 time to fit residues: 22.4015 Evaluate side-chains 92 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 139 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 247 LYS Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 522 GLN Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 61 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.104920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.081241 restraints weight = 10575.155| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.20 r_work: 0.2826 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6686 Z= 0.303 Angle : 0.602 9.295 9083 Z= 0.307 Chirality : 0.046 0.273 985 Planarity : 0.004 0.064 1159 Dihedral : 6.878 58.180 1134 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 4.53 % Allowed : 20.32 % Favored : 75.15 % 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: -0.69 (0.30), residues: 770 helix: 0.90 (0.28), residues: 360 sheet: -0.70 (0.77), residues: 49 loop : -1.90 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS D 241 PHE 0.012 0.001 PHE D 32 TYR 0.015 0.001 TYR D 183 ARG 0.002 0.000 ARG D 245 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 65 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: D 86 GLN cc_start: 0.8511 (tm-30) cc_final: 0.7916 (tm-30) REVERT: D 134 ASN cc_start: 0.7544 (OUTLIER) cc_final: 0.6656 (m110) REVERT: D 142 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8221 (pp) REVERT: D 145 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7796 (tp30) REVERT: D 198 ASP cc_start: 0.8593 (p0) cc_final: 0.8172 (p0) REVERT: D 256 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8678 (mm) REVERT: D 366 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.7159 (tpp) REVERT: D 376 MET cc_start: 0.8510 (mmm) cc_final: 0.8202 (mmm) REVERT: D 401 HIS cc_start: 0.8566 (OUTLIER) cc_final: 0.7518 (m90) REVERT: A 420 ASP cc_start: 0.8078 (m-30) cc_final: 0.7689 (m-30) REVERT: A 454 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7619 (ttm170) REVERT: A 500 THR cc_start: 0.9255 (p) cc_final: 0.8908 (p) outliers start: 31 outliers final: 23 residues processed: 93 average time/residue: 0.1786 time to fit residues: 22.6381 Evaluate side-chains 94 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 139 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 247 LYS Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 522 GLN Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 70 optimal weight: 0.3980 chunk 28 optimal weight: 0.0670 chunk 18 optimal weight: 0.0670 chunk 41 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 26 optimal weight: 0.0030 chunk 34 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.2266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS A 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.109830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.086817 restraints weight = 10487.169| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.12 r_work: 0.2898 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6686 Z= 0.141 Angle : 0.537 9.411 9083 Z= 0.272 Chirality : 0.042 0.284 985 Planarity : 0.004 0.058 1159 Dihedral : 6.513 58.198 1134 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.36 % Allowed : 20.91 % Favored : 75.73 % 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: -0.40 (0.30), residues: 770 helix: 1.18 (0.29), residues: 357 sheet: -0.43 (0.77), residues: 49 loop : -1.80 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 163 HIS 0.003 0.001 HIS D 241 PHE 0.008 0.001 PHE D 315 TYR 0.010 0.001 TYR D 41 ARG 0.002 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: D 86 GLN cc_start: 0.8474 (tm-30) cc_final: 0.7861 (tm-30) REVERT: D 134 ASN cc_start: 0.7281 (OUTLIER) cc_final: 0.6725 (m110) REVERT: D 142 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7908 (pp) REVERT: D 145 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7569 (tp30) REVERT: D 198 ASP cc_start: 0.8617 (p0) cc_final: 0.8201 (p0) REVERT: D 256 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8657 (mm) REVERT: D 366 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.6766 (tpp) REVERT: D 376 MET cc_start: 0.8502 (mmm) cc_final: 0.8191 (mmm) REVERT: D 401 HIS cc_start: 0.8465 (OUTLIER) cc_final: 0.7443 (m90) REVERT: A 356 LYS cc_start: 0.7392 (ttpt) cc_final: 0.7065 (ttmm) REVERT: A 420 ASP cc_start: 0.8031 (m-30) cc_final: 0.7681 (m-30) REVERT: A 454 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7494 (ttm170) REVERT: A 500 THR cc_start: 0.9187 (p) cc_final: 0.8790 (p) outliers start: 23 outliers final: 13 residues processed: 90 average time/residue: 0.1988 time to fit residues: 24.0905 Evaluate side-chains 86 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 139 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 480 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 73 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 63 optimal weight: 0.0770 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.107662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.084471 restraints weight = 10570.991| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.15 r_work: 0.2865 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6686 Z= 0.226 Angle : 0.566 9.355 9083 Z= 0.287 Chirality : 0.044 0.275 985 Planarity : 0.004 0.055 1159 Dihedral : 6.482 58.292 1134 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.22 % Allowed : 21.64 % Favored : 75.15 % 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: -0.31 (0.30), residues: 770 helix: 1.21 (0.29), residues: 360 sheet: -0.43 (0.77), residues: 49 loop : -1.71 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS D 241 PHE 0.011 0.001 PHE D 32 TYR 0.011 0.001 TYR A 495 ARG 0.001 0.000 ARG D 245 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: D 86 GLN cc_start: 0.8472 (tm-30) cc_final: 0.7863 (tm-30) REVERT: D 134 ASN cc_start: 0.7309 (OUTLIER) cc_final: 0.6704 (m110) REVERT: D 142 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7937 (pp) REVERT: D 145 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7611 (tp30) REVERT: D 198 ASP cc_start: 0.8631 (p0) cc_final: 0.8179 (p0) REVERT: D 256 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8659 (mm) REVERT: D 366 MET cc_start: 0.7220 (OUTLIER) cc_final: 0.6904 (tpp) REVERT: D 376 MET cc_start: 0.8463 (mmm) cc_final: 0.8164 (mmm) REVERT: D 401 HIS cc_start: 0.8467 (OUTLIER) cc_final: 0.7501 (m90) REVERT: A 420 ASP cc_start: 0.8079 (m-30) cc_final: 0.7803 (m-30) REVERT: A 454 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7546 (ttm170) REVERT: A 500 THR cc_start: 0.9216 (p) cc_final: 0.8878 (p) outliers start: 22 outliers final: 14 residues processed: 86 average time/residue: 0.1888 time to fit residues: 21.7924 Evaluate side-chains 85 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 139 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 247 LYS Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 480 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 51 optimal weight: 0.0050 chunk 48 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 0.0470 chunk 43 optimal weight: 0.9990 chunk 31 optimal weight: 0.0970 chunk 32 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.3290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS A 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.110757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.087626 restraints weight = 10498.058| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.15 r_work: 0.2912 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6686 Z= 0.137 Angle : 0.537 9.431 9083 Z= 0.270 Chirality : 0.042 0.279 985 Planarity : 0.004 0.052 1159 Dihedral : 6.107 58.290 1130 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.07 % Allowed : 21.49 % Favored : 75.44 % 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: -0.15 (0.30), residues: 770 helix: 1.38 (0.29), residues: 357 sheet: -0.36 (0.77), residues: 49 loop : -1.64 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS D 241 PHE 0.009 0.001 PHE A 392 TYR 0.008 0.001 TYR D 41 ARG 0.001 0.000 ARG D 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2858.38 seconds wall clock time: 51 minutes 28.66 seconds (3088.66 seconds total)