Starting phenix.real_space_refine on Tue Mar 11 18:49:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i9g_35270/03_2025/8i9g_35270.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i9g_35270/03_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_35270/03_2025/8i9g_35270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i9g_35270/03_2025/8i9g_35270.map" model { file = "/net/cci-nas-00/data/ceres_data/8i9g_35270/03_2025/8i9g_35270.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i9g_35270/03_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-5624/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: 4.72, per 1000 atoms: 0.73 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: 1.81 Conformation dependent library (CDL) restraints added in 918.3 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: 0.64 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: 2.13 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: 1.530 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 19.730 Find NCS groups from input model: 0.100 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.610 ------------------------------------------------------------------------------- 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 : 0.771 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: 0.1927 time to fit residues: 27.1885 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 : 0.775 ------------------------------------------------------------------------------- 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 = 0.3350 r_free = 0.3350 target = 0.107085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.083647 restraints weight = 10351.719| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.14 r_work: 0.2867 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- 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 9.121 9083 Z= 0.290 Chirality : 0.043 0.277 985 Planarity : 0.004 0.050 1159 Dihedral : 9.357 79.839 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 : 0.775 Fit side-chains REVERT: D 86 GLN cc_start: 0.8495 (tm-30) cc_final: 0.7806 (tm-30) REVERT: D 131 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8729 (mtmp) REVERT: D 140 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7317 (pp20) REVERT: D 213 ASP cc_start: 0.8966 (t0) cc_final: 0.8756 (t0) REVERT: D 366 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.6966 (tpp) REVERT: D 455 MET cc_start: 0.8874 (tmm) cc_final: 0.8574 (tmm) REVERT: A 420 ASP cc_start: 0.7937 (m-30) cc_final: 0.7687 (m-30) outliers start: 26 outliers final: 14 residues processed: 88 average time/residue: 0.1625 time to fit residues: 20.2125 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 : 0.700 ------------------------------------------------------------------------------- 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: 2.9990 chunk 53 optimal weight: 0.7980 chunk 72 optimal weight: 0.0970 chunk 60 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 48 optimal weight: 0.0670 chunk 76 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- 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 = 0.3385 r_free = 0.3385 target = 0.109184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.086386 restraints weight = 10335.991| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.09 r_work: 0.2893 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6686 Z= 0.155 Angle : 0.549 9.370 9083 Z= 0.278 Chirality : 0.042 0.282 985 Planarity : 0.004 0.055 1159 Dihedral : 8.035 78.457 1140 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.80 % Allowed : 19.88 % Favored : 76.32 % 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: -1.52 (0.29), residues: 770 helix: 0.32 (0.28), residues: 360 sheet: -1.25 (0.73), residues: 49 loop : -2.44 (0.27), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.005 0.001 HIS D 345 PHE 0.009 0.001 PHE D 32 TYR 0.010 0.001 TYR A 495 ARG 0.001 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 92 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: D 86 GLN cc_start: 0.8456 (tm-30) cc_final: 0.7863 (tm-30) REVERT: D 134 ASN cc_start: 0.7531 (OUTLIER) cc_final: 0.6786 (m110) REVERT: D 366 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6942 (tpp) REVERT: D 455 MET cc_start: 0.8913 (tmm) cc_final: 0.8643 (tmm) REVERT: A 420 ASP cc_start: 0.7994 (m-30) cc_final: 0.7707 (m-30) outliers start: 26 outliers final: 16 residues processed: 87 average time/residue: 0.1706 time to fit residues: 20.6084 Evaluate side-chains 78 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 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 167 SER Chi-restraints excluded: chain D residue 233 ILE 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 480 CYS 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: 1.9990 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 60 optimal weight: 0.0980 chunk 19 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 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 = 0.3356 r_free = 0.3356 target = 0.107374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.083902 restraints weight = 10581.445| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.17 r_work: 0.2869 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6686 Z= 0.212 Angle : 0.557 9.346 9083 Z= 0.281 Chirality : 0.043 0.274 985 Planarity : 0.004 0.065 1159 Dihedral : 7.568 76.629 1138 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 4.39 % Allowed : 18.57 % Favored : 77.05 % 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: -1.17 (0.29), residues: 770 helix: 0.63 (0.28), residues: 357 sheet: -1.01 (0.74), residues: 49 loop : -2.26 (0.27), 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 0.011 0.001 PHE D 32 TYR 0.012 0.001 TYR A 495 ARG 0.001 0.000 ARG D 245 *********************** REFINEMENT MACRO_CYCLE 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 95 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: D 86 GLN cc_start: 0.8461 (tm-30) cc_final: 0.7861 (tm-30) REVERT: D 134 ASN cc_start: 0.7471 (OUTLIER) cc_final: 0.6794 (m110) REVERT: D 366 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6831 (tpp) REVERT: D 368 ASP cc_start: 0.7349 (m-30) cc_final: 0.7116 (m-30) REVERT: D 455 MET cc_start: 0.8910 (tmm) cc_final: 0.8622 (tmm) REVERT: A 420 ASP cc_start: 0.8046 (m-30) cc_final: 0.7709 (m-30) REVERT: A 454 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7550 (ttm170) REVERT: A 500 THR cc_start: 0.9210 (p) cc_final: 0.8863 (p) outliers start: 30 outliers final: 21 residues processed: 89 average time/residue: 0.1689 time to fit residues: 20.8214 Evaluate side-chains 86 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 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 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 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: 2.9990 chunk 75 optimal weight: 2.9990 chunk 26 optimal weight: 0.0370 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 31 optimal weight: 0.2980 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 = 0.3384 r_free = 0.3384 target = 0.109038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.086122 restraints weight = 10456.772| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.10 r_work: 0.2881 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1569 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= 0.177 Angle : 0.545 9.391 9083 Z= 0.275 Chirality : 0.043 0.273 985 Planarity : 0.004 0.053 1159 Dihedral : 7.320 74.891 1137 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.24 % Allowed : 19.59 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.90 (0.29), residues: 770 helix: 0.82 (0.28), residues: 357 sheet: -0.88 (0.74), residues: 49 loop : -2.10 (0.28), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS D 345 PHE 0.010 0.001 PHE D 32 TYR 0.011 0.001 TYR A 495 ARG 0.001 0.000 ARG D 245 *********************** 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 95 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: D 86 GLN cc_start: 0.8445 (tm-30) cc_final: 0.7840 (tm-30) REVERT: D 134 ASN cc_start: 0.7398 (OUTLIER) cc_final: 0.6762 (m110) REVERT: D 145 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7853 (tp30) REVERT: D 256 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8700 (mm) REVERT: D 366 MET cc_start: 0.7157 (OUTLIER) cc_final: 0.6818 (tpp) REVERT: D 368 ASP cc_start: 0.7160 (m-30) cc_final: 0.6924 (m-30) REVERT: D 376 MET cc_start: 0.8416 (mmm) cc_final: 0.8117 (mmm) REVERT: D 455 MET cc_start: 0.8897 (tmm) cc_final: 0.8619 (tmm) REVERT: A 420 ASP cc_start: 0.8024 (m-30) cc_final: 0.7675 (m-30) REVERT: A 500 THR cc_start: 0.9208 (p) cc_final: 0.8860 (p) outliers start: 29 outliers final: 20 residues processed: 90 average time/residue: 0.1587 time to fit residues: 20.0014 Evaluate side-chains 86 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE 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 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 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 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 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: 0.7980 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 A 354 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.106339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.082611 restraints weight = 10541.327| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.17 r_work: 0.2851 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6686 Z= 0.279 Angle : 0.582 9.347 9083 Z= 0.296 Chirality : 0.045 0.267 985 Planarity : 0.004 0.050 1159 Dihedral : 7.298 74.126 1133 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.80 % Allowed : 20.47 % 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: -0.83 (0.30), residues: 770 helix: 0.84 (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 0.010 0.001 HIS D 345 PHE 0.012 0.001 PHE D 32 TYR 0.013 0.001 TYR D 183 ARG 0.001 0.000 ARG D 245 *********************** 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 94 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: D 86 GLN cc_start: 0.8455 (tm-30) cc_final: 0.7849 (tm-30) REVERT: D 134 ASN cc_start: 0.7432 (OUTLIER) cc_final: 0.6678 (m110) REVERT: D 198 ASP cc_start: 0.8625 (p0) cc_final: 0.8189 (p0) REVERT: D 256 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8702 (mm) REVERT: D 366 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.7007 (tpp) REVERT: D 376 MET cc_start: 0.8433 (mmm) cc_final: 0.8137 (mmm) REVERT: D 455 MET cc_start: 0.8910 (tmm) cc_final: 0.8616 (tmm) REVERT: A 356 LYS cc_start: 0.7620 (ttmm) cc_final: 0.7354 (ttmm) REVERT: A 420 ASP cc_start: 0.8061 (m-30) cc_final: 0.7691 (m-30) REVERT: A 454 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7576 (ttm170) REVERT: A 500 THR cc_start: 0.9209 (p) cc_final: 0.8863 (p) outliers start: 26 outliers final: 19 residues processed: 89 average time/residue: 0.1731 time to fit residues: 21.1806 Evaluate side-chains 85 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE 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 134 ASN Chi-restraints excluded: chain D residue 139 GLN Chi-restraints excluded: chain D residue 142 LEU 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 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: 3.9990 chunk 25 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 48 optimal weight: 0.1980 chunk 66 optimal weight: 0.0030 chunk 28 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 = 0.3379 r_free = 0.3379 target = 0.108693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.085803 restraints weight = 10393.356| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.09 r_work: 0.2881 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1689 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= 0.171 Angle : 0.542 9.375 9083 Z= 0.274 Chirality : 0.042 0.278 985 Planarity : 0.004 0.073 1159 Dihedral : 7.120 73.095 1133 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.65 % Allowed : 21.05 % Favored : 75.29 % 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: -0.61 (0.30), residues: 770 helix: 1.04 (0.29), residues: 357 sheet: -0.81 (0.74), residues: 49 loop : -1.90 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS D 241 PHE 0.009 0.001 PHE D 32 TYR 0.010 0.001 TYR A 495 ARG 0.001 0.000 ARG A 357 *********************** 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 92 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: D 86 GLN cc_start: 0.8443 (tm-30) cc_final: 0.7827 (tm-30) REVERT: D 134 ASN cc_start: 0.7314 (OUTLIER) cc_final: 0.6773 (m110) REVERT: D 145 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7721 (tp30) REVERT: D 198 ASP cc_start: 0.8613 (p0) cc_final: 0.8156 (p0) REVERT: D 256 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8657 (mm) REVERT: D 366 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6807 (tpp) REVERT: D 376 MET cc_start: 0.8398 (mmm) cc_final: 0.8113 (mmm) REVERT: A 356 LYS cc_start: 0.7531 (ttmm) cc_final: 0.7289 (ttmm) REVERT: A 420 ASP cc_start: 0.7993 (m-30) cc_final: 0.7565 (m-30) REVERT: A 454 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7501 (ttm170) REVERT: A 500 THR cc_start: 0.9167 (p) cc_final: 0.8770 (p) outliers start: 25 outliers final: 19 residues processed: 88 average time/residue: 0.1648 time to fit residues: 20.2650 Evaluate side-chains 86 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE 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 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 345 HIS 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 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: 2.9990 chunk 11 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3341 r_free = 0.3341 target = 0.106285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.082521 restraints weight = 10519.584| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.19 r_work: 0.2855 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6686 Z= 0.260 Angle : 0.581 9.328 9083 Z= 0.295 Chirality : 0.045 0.274 985 Planarity : 0.004 0.062 1159 Dihedral : 6.577 58.324 1130 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.80 % Allowed : 21.20 % 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: -0.58 (0.30), residues: 770 helix: 1.01 (0.28), residues: 360 sheet: -0.75 (0.75), residues: 49 loop : -1.84 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.007 0.001 HIS D 345 PHE 0.011 0.001 PHE D 32 TYR 0.013 0.001 TYR D 183 ARG 0.001 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 92 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: D 86 GLN cc_start: 0.8452 (tm-30) cc_final: 0.7835 (tm-30) REVERT: D 134 ASN cc_start: 0.7337 (OUTLIER) cc_final: 0.6671 (m110) REVERT: D 142 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8059 (pp) REVERT: D 145 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7934 (tp30) REVERT: D 198 ASP cc_start: 0.8641 (p0) cc_final: 0.8105 (p0) REVERT: D 256 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8684 (mm) REVERT: D 366 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.6975 (tpp) REVERT: D 376 MET cc_start: 0.8437 (mmm) cc_final: 0.8140 (mmm) REVERT: A 356 LYS cc_start: 0.7575 (ttmm) cc_final: 0.7344 (ttmm) REVERT: A 420 ASP cc_start: 0.8074 (m-30) cc_final: 0.7744 (m-30) REVERT: A 454 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7585 (ttm170) REVERT: A 500 THR cc_start: 0.9188 (p) cc_final: 0.8789 (p) outliers start: 26 outliers final: 18 residues processed: 89 average time/residue: 0.1768 time to fit residues: 21.6251 Evaluate side-chains 88 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE 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 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 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 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: 3.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 70 optimal weight: 0.0060 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 26 optimal weight: 0.0170 chunk 34 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.4034 ------------------------------------------------------------------------------- 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 A 422 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.110281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.087181 restraints weight = 10492.232| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.13 r_work: 0.2908 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6686 Z= 0.148 Angle : 0.529 9.437 9083 Z= 0.267 Chirality : 0.042 0.279 985 Planarity : 0.004 0.056 1159 Dihedral : 6.165 58.270 1130 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.07 % Allowed : 21.78 % 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: -0.33 (0.30), residues: 770 helix: 1.23 (0.29), residues: 357 sheet: -0.40 (0.76), residues: 49 loop : -1.75 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 163 HIS 0.003 0.001 HIS D 241 PHE 0.007 0.001 PHE D 315 TYR 0.008 0.001 TYR D 41 ARG 0.001 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 90 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: D 86 GLN cc_start: 0.8421 (tm-30) cc_final: 0.7795 (tm-30) REVERT: D 134 ASN cc_start: 0.7106 (OUTLIER) cc_final: 0.6692 (m110) REVERT: D 142 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7812 (pp) REVERT: D 145 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7779 (tp30) REVERT: D 198 ASP cc_start: 0.8614 (p0) cc_final: 0.8141 (p0) REVERT: D 256 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8613 (mm) REVERT: D 332 MET cc_start: 0.7888 (ttm) cc_final: 0.7406 (ttp) REVERT: D 366 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6776 (tpp) REVERT: D 376 MET cc_start: 0.8400 (mmm) cc_final: 0.8118 (mmm) REVERT: A 420 ASP cc_start: 0.8014 (m-30) cc_final: 0.7659 (m-30) REVERT: A 454 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7490 (ttm170) REVERT: A 500 THR cc_start: 0.9143 (p) cc_final: 0.8749 (p) outliers start: 21 outliers final: 14 residues processed: 87 average time/residue: 0.1912 time to fit residues: 23.1245 Evaluate side-chains 85 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 73 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3372 r_free = 0.3372 target = 0.108321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.085736 restraints weight = 10493.465| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.08 r_work: 0.2904 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.233 6686 Z= 0.373 Angle : 1.011 59.198 9083 Z= 0.580 Chirality : 0.048 0.506 985 Planarity : 0.004 0.054 1159 Dihedral : 6.176 58.054 1130 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.51 % Allowed : 21.20 % Favored : 75.29 % Cbeta Deviations : 0.14 % 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: -0.37 (0.30), residues: 770 helix: 1.18 (0.28), residues: 357 sheet: -0.38 (0.76), residues: 49 loop : -1.75 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.003 0.001 HIS D 241 PHE 0.010 0.001 PHE A 400 TYR 0.027 0.001 TYR A 421 ARG 0.002 0.000 ARG D 161 ********************** 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 92 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.788 Fit side-chains REVERT: D 86 GLN cc_start: 0.8429 (tm-30) cc_final: 0.7802 (tm-30) REVERT: D 134 ASN cc_start: 0.7097 (OUTLIER) cc_final: 0.6751 (m110) REVERT: D 140 GLU cc_start: 0.7765 (tm-30) cc_final: 0.6957 (tt0) REVERT: D 142 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7722 (pp) REVERT: D 145 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7792 (tp30) REVERT: D 198 ASP cc_start: 0.8625 (p0) cc_final: 0.8156 (p0) REVERT: D 256 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8635 (mm) REVERT: D 332 MET cc_start: 0.7910 (ttm) cc_final: 0.7427 (ttp) REVERT: D 366 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6799 (tpp) REVERT: D 376 MET cc_start: 0.8420 (mmm) cc_final: 0.8131 (mmm) REVERT: A 420 ASP cc_start: 0.8014 (m-30) cc_final: 0.7672 (m-30) REVERT: A 454 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7563 (ttm170) REVERT: A 500 THR cc_start: 0.9135 (p) cc_final: 0.8738 (p) outliers start: 24 outliers final: 16 residues processed: 90 average time/residue: 0.1786 time to fit residues: 21.9146 Evaluate side-chains 86 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE 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 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 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 454 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 51 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 31 optimal weight: 0.2980 chunk 32 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 63 optimal weight: 0.0060 chunk 57 optimal weight: 0.6980 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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 = 0.3380 r_free = 0.3380 target = 0.109143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.085518 restraints weight = 10602.360| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.19 r_work: 0.2893 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.234 6686 Z= 0.373 Angle : 1.010 59.182 9083 Z= 0.580 Chirality : 0.048 0.506 985 Planarity : 0.004 0.054 1159 Dihedral : 6.176 58.054 1130 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.07 % Allowed : 21.49 % Favored : 75.44 % Cbeta Deviations : 0.14 % 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: -0.37 (0.30), residues: 770 helix: 1.18 (0.28), residues: 357 sheet: -0.38 (0.76), residues: 49 loop : -1.75 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.003 0.001 HIS D 241 PHE 0.010 0.001 PHE A 400 TYR 0.027 0.001 TYR A 421 ARG 0.002 0.000 ARG D 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2937.95 seconds wall clock time: 51 minutes 10.39 seconds (3070.39 seconds total)