Starting phenix.real_space_refine on Tue Feb 11 18:27:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xoc_33344/02_2025/7xoc_33344.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xoc_33344/02_2025/7xoc_33344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xoc_33344/02_2025/7xoc_33344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xoc_33344/02_2025/7xoc_33344.map" model { file = "/net/cci-nas-00/data/ceres_data/7xoc_33344/02_2025/7xoc_33344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xoc_33344/02_2025/7xoc_33344.cif" } resolution = 3.0 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4109 2.51 5 N 1074 2.21 5 O 1211 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 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: 6432 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4824 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 25, 'TRANS': 566} Chain breaks: 1 Chain: "A" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1551 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} 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: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" 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: 6.15, per 1000 atoms: 0.96 Number of scatterers: 6432 At special positions: 0 Unit cell: (97.232, 71.688, 121.952, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1211 8.00 N 1074 7.00 C 4109 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.23 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 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-ASN " NAG A1301 " - " ASN A 343 " " NAG B 1 " - " ASN D 53 " " NAG D 902 " - " ASN D 546 " Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 867.1 milliseconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1482 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 7 sheets defined 53.6% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.809A pdb=" N ASN D 24 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP D 38 " --> pdb=" O GLN D 34 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN D 53 " --> pdb=" O ASN D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.805A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 108 removed outlier: 3.754A pdb=" N ALA D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 104 through 108' Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 194 removed outlier: 4.176A pdb=" N ALA D 164 " --> pdb=" O SER D 160 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.742A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 218 through 233 removed outlier: 3.604A pdb=" N LEU D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLU D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 removed outlier: 4.347A pdb=" N ASP D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N THR D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 256 removed outlier: 4.235A pdb=" N ILE D 256 " --> pdb=" O PRO D 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 253 through 256' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 318 removed outlier: 3.510A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 328 Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.614A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 388 removed outlier: 4.183A pdb=" N ARG D 387 " --> pdb=" O ALA D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 397 through 413 removed outlier: 3.734A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 3.567A pdb=" N LYS D 419 " --> pdb=" O PRO D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.735A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 465 removed outlier: 4.516A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) 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: 3.665A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA D 533 " --> pdb=" O LEU D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.531A pdb=" N CYS D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.511A pdb=" N GLN D 552 " --> pdb=" O THR D 548 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU D 554 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.691A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'D' and resid 600 through 602 No H-bonds generated for 'chain 'D' and resid 600 through 602' Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 385 through 389 removed outlier: 4.199A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.595A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.698A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.606A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.511A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.519A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) 282 hydrogen bonds defined for protein. 798 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: 1.77 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1669 1.33 - 1.45: 1458 1.45 - 1.58: 3426 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6611 Sorted by residual: bond pdb=" CA ALA A 376 " pdb=" CB ALA A 376 " ideal model delta sigma weight residual 1.533 1.487 0.046 1.69e-02 3.50e+03 7.37e+00 bond pdb=" N PRO A 373 " pdb=" CA PRO A 373 " ideal model delta sigma weight residual 1.468 1.442 0.026 1.20e-02 6.94e+03 4.58e+00 bond pdb=" N ALA A 372 " pdb=" CA ALA A 372 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.41e-02 5.03e+03 4.38e+00 bond pdb=" N ASN A 370 " pdb=" CA ASN A 370 " ideal model delta sigma weight residual 1.456 1.482 -0.025 1.23e-02 6.61e+03 4.28e+00 bond pdb=" N PHE A 371 " pdb=" CA PHE A 371 " ideal model delta sigma weight residual 1.463 1.488 -0.025 1.31e-02 5.83e+03 3.76e+00 ... (remaining 6606 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 8826 1.57 - 3.14: 119 3.14 - 4.71: 21 4.71 - 6.27: 10 6.27 - 7.84: 1 Bond angle restraints: 8977 Sorted by residual: angle pdb=" N PRO A 373 " pdb=" CA PRO A 373 " pdb=" C PRO A 373 " ideal model delta sigma weight residual 111.03 103.19 7.84 1.54e+00 4.22e-01 2.59e+01 angle pdb=" CA TYR A 369 " pdb=" C TYR A 369 " pdb=" O TYR A 369 " ideal model delta sigma weight residual 121.88 117.65 4.23 1.13e+00 7.83e-01 1.40e+01 angle pdb=" N PHE A 371 " pdb=" CA PHE A 371 " pdb=" CB PHE A 371 " ideal model delta sigma weight residual 110.25 115.65 -5.40 1.50e+00 4.44e-01 1.30e+01 angle pdb=" CA PHE A 375 " pdb=" CB PHE A 375 " pdb=" CG PHE A 375 " ideal model delta sigma weight residual 113.80 117.14 -3.34 1.00e+00 1.00e+00 1.12e+01 angle pdb=" CA PHE A 371 " pdb=" C PHE A 371 " pdb=" O PHE A 371 " ideal model delta sigma weight residual 121.53 115.87 5.66 1.74e+00 3.30e-01 1.06e+01 ... (remaining 8972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.31: 3837 21.31 - 42.61: 91 42.61 - 63.92: 16 63.92 - 85.22: 6 85.22 - 106.53: 8 Dihedral angle restraints: 3958 sinusoidal: 1649 harmonic: 2309 Sorted by residual: dihedral pdb=" CB CYS D 344 " pdb=" SG CYS D 344 " pdb=" SG CYS D 361 " pdb=" CB CYS D 361 " ideal model delta sinusoidal sigma weight residual -86.00 -169.86 83.86 1 1.00e+01 1.00e-02 8.57e+01 dihedral pdb=" C2 NAG B 2 " pdb=" C3 NAG B 2 " pdb=" C4 NAG B 2 " pdb=" O4 NAG B 2 " ideal model delta sinusoidal sigma weight residual 175.11 68.58 106.53 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" C2 NAG B 2 " pdb=" C3 NAG B 2 " pdb=" C4 NAG B 2 " pdb=" C5 NAG B 2 " ideal model delta sinusoidal sigma weight residual 53.78 -52.73 106.51 1 3.00e+01 1.11e-03 1.37e+01 ... (remaining 3955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 874 0.077 - 0.154: 62 0.154 - 0.231: 3 0.231 - 0.307: 2 0.307 - 0.384: 1 Chirality restraints: 942 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN D 53 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA ASN A 370 " pdb=" N ASN A 370 " pdb=" C ASN A 370 " pdb=" CB ASN A 370 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA PHE A 371 " pdb=" N PHE A 371 " pdb=" C PHE A 371 " pdb=" CB PHE A 371 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 939 not shown) Planarity restraints: 1163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 499 " -0.039 5.00e-02 4.00e+02 5.84e-02 5.45e+00 pdb=" N PRO D 500 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 500 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 500 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 368 " 0.009 2.00e-02 2.50e+03 1.94e-02 3.76e+00 pdb=" C LEU A 368 " -0.034 2.00e-02 2.50e+03 pdb=" O LEU A 368 " 0.013 2.00e-02 2.50e+03 pdb=" N TYR A 369 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 372 " -0.009 2.00e-02 2.50e+03 1.69e-02 2.84e+00 pdb=" C ALA A 372 " 0.029 2.00e-02 2.50e+03 pdb=" O ALA A 372 " -0.011 2.00e-02 2.50e+03 pdb=" N PRO A 373 " -0.010 2.00e-02 2.50e+03 ... (remaining 1160 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 147 2.70 - 3.25: 6238 3.25 - 3.80: 10006 3.80 - 4.35: 13444 4.35 - 4.90: 22297 Nonbonded interactions: 52132 Sorted by model distance: nonbonded pdb=" CA CYS D 344 " pdb=" SG CYS D 361 " model vdw 2.149 3.064 nonbonded pdb=" O TYR D 279 " pdb=" CG2 VAL D 283 " model vdw 2.232 3.460 nonbonded pdb=" OG SER D 84 " pdb=" OE1 GLU D 87 " model vdw 2.241 3.040 nonbonded pdb=" OH TYR D 41 " pdb=" OG1 THR A 500 " model vdw 2.252 3.040 nonbonded pdb=" OD2 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.269 3.040 ... (remaining 52127 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.340 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.870 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:17.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 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 : 0.002 0.046 6611 Z= 0.149 Angle : 0.494 7.843 8977 Z= 0.293 Chirality : 0.042 0.384 942 Planarity : 0.004 0.058 1160 Dihedral : 10.956 106.527 2455 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.11 (0.27), residues: 780 helix: -0.53 (0.26), residues: 382 sheet: -1.52 (0.52), residues: 47 loop : -2.37 (0.29), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP D 165 HIS 0.001 0.000 HIS D 322 PHE 0.014 0.001 PHE A 371 TYR 0.009 0.001 TYR A 369 ARG 0.001 0.000 ARG D 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: D 302 TRP cc_start: 0.7000 (m-10) cc_final: 0.6668 (m-10) REVERT: D 477 TRP cc_start: 0.7441 (t-100) cc_final: 0.7223 (t-100) REVERT: A 489 TYR cc_start: 0.7850 (m-80) cc_final: 0.7618 (m-80) outliers start: 0 outliers final: 1 residues processed: 249 average time/residue: 1.0213 time to fit residues: 269.1139 Evaluate side-chains 189 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 0.0050 chunk 31 optimal weight: 0.0870 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 45 optimal weight: 0.2980 chunk 70 optimal weight: 0.9990 overall best weight: 0.2772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 ASN D 51 ASN D 60 GLN D 76 GLN D 86 GLN D 89 GLN D 96 GLN D 101 GLN D 188 ASN D 239 HIS D 394 ASN D 417 HIS D 472 GLN D 493 HIS D 522 GLN D 586 ASN D 599 ASN A 414 GLN A 505 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.125600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.113112 restraints weight = 9252.052| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.07 r_work: 0.3343 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6611 Z= 0.228 Angle : 0.576 7.827 8977 Z= 0.286 Chirality : 0.044 0.404 942 Planarity : 0.004 0.062 1160 Dihedral : 7.175 56.448 946 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.64 % Allowed : 16.42 % Favored : 80.94 % 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: -0.80 (0.30), residues: 780 helix: 0.55 (0.28), residues: 380 sheet: -0.29 (0.54), residues: 43 loop : -1.78 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.007 0.002 HIS D 265 PHE 0.030 0.002 PHE D 308 TYR 0.019 0.002 TYR A 453 ARG 0.004 0.001 ARG D 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 201 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: D 75 GLU cc_start: 0.8046 (tp30) cc_final: 0.7763 (tp30) REVERT: D 94 LYS cc_start: 0.8427 (ttmt) cc_final: 0.8215 (ttmt) REVERT: D 206 ASP cc_start: 0.7688 (t70) cc_final: 0.7358 (t0) REVERT: D 225 ASP cc_start: 0.8043 (t0) cc_final: 0.7773 (t0) REVERT: D 229 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8311 (t) REVERT: D 232 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7501 (mm-30) REVERT: D 364 VAL cc_start: 0.8559 (m) cc_final: 0.8246 (t) REVERT: D 368 ASN cc_start: 0.7484 (m-40) cc_final: 0.7145 (m-40) REVERT: D 496 THR cc_start: 0.8143 (m) cc_final: 0.7860 (t) REVERT: D 514 ARG cc_start: 0.8249 (ptm-80) cc_final: 0.7979 (pmm-80) REVERT: D 517 THR cc_start: 0.7791 (p) cc_final: 0.7526 (p) REVERT: D 539 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8302 (tt) REVERT: D 549 GLU cc_start: 0.7281 (tp30) cc_final: 0.7071 (tp30) REVERT: A 453 TYR cc_start: 0.7955 (p90) cc_final: 0.7570 (p90) outliers start: 18 outliers final: 4 residues processed: 209 average time/residue: 1.0961 time to fit residues: 241.3728 Evaluate side-chains 198 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 192 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain A residue 367 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 50 optimal weight: 0.0770 chunk 54 optimal weight: 0.6980 chunk 75 optimal weight: 0.0570 chunk 65 optimal weight: 0.1980 chunk 26 optimal weight: 0.2980 chunk 35 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 42 optimal weight: 0.1980 chunk 6 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 overall best weight: 0.1656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 345 HIS D 493 HIS D 586 ASN A 388 ASN A 417 ASN A 450 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.123792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.111397 restraints weight = 9341.786| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.08 r_work: 0.3327 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6611 Z= 0.185 Angle : 0.560 9.716 8977 Z= 0.272 Chirality : 0.041 0.197 942 Planarity : 0.004 0.062 1160 Dihedral : 6.454 82.484 944 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.08 % Allowed : 19.79 % Favored : 77.13 % 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: -0.20 (0.31), residues: 780 helix: 1.02 (0.28), residues: 379 sheet: 0.32 (0.62), residues: 43 loop : -1.50 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 163 HIS 0.004 0.001 HIS D 353 PHE 0.021 0.001 PHE D 428 TYR 0.015 0.001 TYR A 453 ARG 0.003 0.000 ARG D 161 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: D 22 GLU cc_start: 0.6856 (tm-30) cc_final: 0.6429 (tm-30) REVERT: D 75 GLU cc_start: 0.8095 (tp30) cc_final: 0.7825 (tp30) REVERT: D 94 LYS cc_start: 0.8464 (ttmt) cc_final: 0.8125 (ttpp) REVERT: D 95 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7622 (ttp-110) REVERT: D 169 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.6107 (mtm-85) REVERT: D 206 ASP cc_start: 0.7730 (t70) cc_final: 0.7470 (t0) REVERT: D 225 ASP cc_start: 0.8097 (t0) cc_final: 0.7833 (t0) REVERT: D 229 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8340 (t) REVERT: D 232 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7675 (mm-30) REVERT: D 305 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7597 (mm-30) REVERT: D 368 ASN cc_start: 0.7500 (m-40) cc_final: 0.7235 (m-40) REVERT: D 496 THR cc_start: 0.8198 (m) cc_final: 0.7968 (t) REVERT: D 514 ARG cc_start: 0.8174 (ptm-80) cc_final: 0.7791 (ptm160) REVERT: D 517 THR cc_start: 0.7757 (p) cc_final: 0.6992 (t) REVERT: D 534 LYS cc_start: 0.7717 (mttp) cc_final: 0.7490 (mmtp) REVERT: D 539 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8345 (tt) REVERT: D 571 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7471 (tt0) REVERT: D 577 ARG cc_start: 0.7759 (ptp90) cc_final: 0.7475 (mtm-85) REVERT: D 578 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7877 (t160) REVERT: D 609 GLU cc_start: 0.6743 (pm20) cc_final: 0.6322 (pm20) REVERT: A 453 TYR cc_start: 0.8115 (p90) cc_final: 0.7803 (p90) outliers start: 21 outliers final: 2 residues processed: 201 average time/residue: 1.0490 time to fit residues: 223.1461 Evaluate side-chains 196 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 188 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 571 GLU Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain A residue 367 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 28 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 61 optimal weight: 0.0070 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 68 optimal weight: 0.0570 chunk 44 optimal weight: 0.0050 overall best weight: 0.1730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 197 ASN D 322 HIS D 586 ASN A 450 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.122800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.110517 restraints weight = 9331.602| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.06 r_work: 0.3298 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6611 Z= 0.179 Angle : 0.542 8.698 8977 Z= 0.264 Chirality : 0.040 0.172 942 Planarity : 0.004 0.061 1160 Dihedral : 5.895 78.774 944 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.79 % Allowed : 21.11 % Favored : 76.10 % 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: 0.24 (0.31), residues: 780 helix: 1.35 (0.28), residues: 377 sheet: 0.74 (0.65), residues: 43 loop : -1.24 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 163 HIS 0.003 0.001 HIS D 265 PHE 0.022 0.001 PHE D 428 TYR 0.015 0.001 TYR A 453 ARG 0.004 0.000 ARG D 246 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 22 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6663 (tm-30) REVERT: D 75 GLU cc_start: 0.8075 (tp30) cc_final: 0.7816 (tp30) REVERT: D 95 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8080 (ttp-110) REVERT: D 98 GLN cc_start: 0.8229 (tt0) cc_final: 0.7933 (mt0) REVERT: D 152 MET cc_start: 0.8121 (mmm) cc_final: 0.7865 (mmp) REVERT: D 206 ASP cc_start: 0.7766 (t70) cc_final: 0.7489 (t0) REVERT: D 232 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7817 (mm-30) REVERT: D 320 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8276 (mt) REVERT: D 368 ASN cc_start: 0.7581 (m-40) cc_final: 0.7290 (m-40) REVERT: D 429 GLN cc_start: 0.7512 (pm20) cc_final: 0.7031 (pm20) REVERT: D 430 GLU cc_start: 0.7528 (mp0) cc_final: 0.7272 (mp0) REVERT: D 471 GLU cc_start: 0.7888 (mp0) cc_final: 0.7490 (mp0) REVERT: D 496 THR cc_start: 0.8185 (m) cc_final: 0.7966 (t) REVERT: D 514 ARG cc_start: 0.8134 (ptm-80) cc_final: 0.7784 (ptm160) REVERT: D 517 THR cc_start: 0.7793 (p) cc_final: 0.6964 (t) REVERT: D 539 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8354 (tt) REVERT: D 577 ARG cc_start: 0.7818 (ptp90) cc_final: 0.7513 (mtm-85) REVERT: D 578 ASN cc_start: 0.8246 (OUTLIER) cc_final: 0.8000 (t160) REVERT: D 581 VAL cc_start: 0.8321 (OUTLIER) cc_final: 0.8044 (t) REVERT: D 606 TRP cc_start: 0.8473 (p90) cc_final: 0.7935 (p90) REVERT: D 609 GLU cc_start: 0.6820 (pm20) cc_final: 0.6386 (pm20) REVERT: A 421 TYR cc_start: 0.8540 (m-10) cc_final: 0.8197 (m-80) REVERT: A 451 TYR cc_start: 0.8402 (m-80) cc_final: 0.8159 (m-80) REVERT: A 453 TYR cc_start: 0.8214 (p90) cc_final: 0.7896 (p90) REVERT: A 464 PHE cc_start: 0.8001 (m-10) cc_final: 0.7758 (m-80) outliers start: 19 outliers final: 7 residues processed: 202 average time/residue: 1.0781 time to fit residues: 229.5064 Evaluate side-chains 197 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 185 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain A residue 367 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 22 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 3 optimal weight: 0.3980 chunk 8 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 30 optimal weight: 0.2980 chunk 49 optimal weight: 0.0970 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 536 ASN D 552 GLN D 586 ASN A 450 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.120214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.107805 restraints weight = 9168.230| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.01 r_work: 0.3274 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6611 Z= 0.238 Angle : 0.566 8.984 8977 Z= 0.278 Chirality : 0.041 0.141 942 Planarity : 0.004 0.058 1160 Dihedral : 5.623 71.055 944 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.23 % Allowed : 21.85 % Favored : 74.93 % 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: 0.51 (0.31), residues: 780 helix: 1.54 (0.28), residues: 375 sheet: 1.01 (0.68), residues: 43 loop : -1.07 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 163 HIS 0.004 0.001 HIS D 373 PHE 0.024 0.002 PHE D 428 TYR 0.017 0.002 TYR A 453 ARG 0.003 0.000 ARG D 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 22 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6585 (tm-30) REVERT: D 75 GLU cc_start: 0.8181 (tp30) cc_final: 0.7923 (tp30) REVERT: D 95 ARG cc_start: 0.8345 (ttp-170) cc_final: 0.8094 (ttp-110) REVERT: D 152 MET cc_start: 0.8165 (mmm) cc_final: 0.7904 (mmp) REVERT: D 169 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8236 (ttm-80) REVERT: D 206 ASP cc_start: 0.7931 (t70) cc_final: 0.7491 (t0) REVERT: D 368 ASN cc_start: 0.7710 (m-40) cc_final: 0.7492 (m-40) REVERT: D 429 GLN cc_start: 0.7578 (pm20) cc_final: 0.7143 (pm20) REVERT: D 430 GLU cc_start: 0.7463 (mp0) cc_final: 0.7187 (mp0) REVERT: D 471 GLU cc_start: 0.8069 (mp0) cc_final: 0.7692 (mp0) REVERT: D 510 TYR cc_start: 0.8014 (m-10) cc_final: 0.7686 (m-10) REVERT: D 534 LYS cc_start: 0.8299 (mmtp) cc_final: 0.8093 (mtpp) REVERT: D 536 ASN cc_start: 0.6955 (m-40) cc_final: 0.6495 (p0) REVERT: A 350 VAL cc_start: 0.8214 (p) cc_final: 0.7856 (t) REVERT: A 421 TYR cc_start: 0.8639 (m-10) cc_final: 0.8232 (m-80) REVERT: A 453 TYR cc_start: 0.8300 (p90) cc_final: 0.7922 (p90) outliers start: 22 outliers final: 12 residues processed: 202 average time/residue: 1.0968 time to fit residues: 233.4097 Evaluate side-chains 194 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 611 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 71 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 73 optimal weight: 0.0070 chunk 43 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 0.0050 chunk 36 optimal weight: 0.4980 overall best weight: 0.2812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 239 HIS D 378 HIS D 578 ASN D 586 ASN A 414 GLN A 450 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.118071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.105982 restraints weight = 9339.980| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.04 r_work: 0.3246 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6611 Z= 0.235 Angle : 0.584 8.817 8977 Z= 0.284 Chirality : 0.043 0.207 942 Planarity : 0.003 0.032 1160 Dihedral : 5.368 61.556 944 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.64 % Allowed : 22.73 % Favored : 74.63 % 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: 0.60 (0.31), residues: 780 helix: 1.58 (0.28), residues: 380 sheet: 1.15 (0.71), residues: 43 loop : -1.03 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 163 HIS 0.004 0.001 HIS D 373 PHE 0.027 0.002 PHE D 428 TYR 0.017 0.001 TYR A 453 ARG 0.006 0.000 ARG D 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 22 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6611 (tp30) REVERT: D 75 GLU cc_start: 0.8039 (tp30) cc_final: 0.7814 (tp30) REVERT: D 88 ILE cc_start: 0.8223 (mp) cc_final: 0.7771 (mm) REVERT: D 95 ARG cc_start: 0.8295 (ttp-170) cc_final: 0.8069 (ttp-110) REVERT: D 152 MET cc_start: 0.7957 (mmm) cc_final: 0.7704 (mmt) REVERT: D 163 TRP cc_start: 0.8507 (p-90) cc_final: 0.8117 (p-90) REVERT: D 197 ASN cc_start: 0.7995 (t0) cc_final: 0.7643 (t0) REVERT: D 206 ASP cc_start: 0.7766 (t70) cc_final: 0.7372 (t0) REVERT: D 249 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7383 (mtt) REVERT: D 292 ASP cc_start: 0.7626 (p0) cc_final: 0.7390 (p0) REVERT: D 368 ASN cc_start: 0.7730 (m-40) cc_final: 0.7497 (m-40) REVERT: D 429 GLN cc_start: 0.7559 (pm20) cc_final: 0.7123 (pm20) REVERT: D 430 GLU cc_start: 0.7598 (mp0) cc_final: 0.7333 (mp0) REVERT: D 471 GLU cc_start: 0.7996 (mp0) cc_final: 0.7621 (mp0) REVERT: D 483 GLU cc_start: 0.7633 (tp30) cc_final: 0.7384 (mt-10) REVERT: D 487 VAL cc_start: 0.8124 (t) cc_final: 0.7697 (m) REVERT: D 510 TYR cc_start: 0.8015 (m-10) cc_final: 0.7683 (m-10) REVERT: D 536 ASN cc_start: 0.6916 (m-40) cc_final: 0.6540 (p0) REVERT: D 562 ASN cc_start: 0.8393 (t0) cc_final: 0.8127 (t160) REVERT: D 581 VAL cc_start: 0.8088 (OUTLIER) cc_final: 0.7824 (t) REVERT: D 606 TRP cc_start: 0.8448 (p90) cc_final: 0.7886 (p90) REVERT: D 609 GLU cc_start: 0.6881 (pm20) cc_final: 0.6476 (pm20) REVERT: A 350 VAL cc_start: 0.8238 (p) cc_final: 0.7861 (t) outliers start: 18 outliers final: 3 residues processed: 186 average time/residue: 1.1403 time to fit residues: 223.3301 Evaluate side-chains 173 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 168 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 611 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 0.0970 chunk 25 optimal weight: 0.0870 chunk 41 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 16 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 36 optimal weight: 0.0970 chunk 54 optimal weight: 0.0770 overall best weight: 0.1312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 578 ASN D 586 ASN A 450 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.119745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.107748 restraints weight = 9315.478| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.99 r_work: 0.3264 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6611 Z= 0.170 Angle : 0.561 8.490 8977 Z= 0.271 Chirality : 0.041 0.188 942 Planarity : 0.003 0.030 1160 Dihedral : 5.211 59.278 944 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.91 % Allowed : 23.75 % Favored : 74.34 % 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: 0.72 (0.31), residues: 780 helix: 1.68 (0.28), residues: 385 sheet: 1.24 (0.73), residues: 43 loop : -1.01 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 163 HIS 0.003 0.001 HIS D 265 PHE 0.027 0.001 PHE D 428 TYR 0.014 0.001 TYR A 453 ARG 0.008 0.000 ARG D 577 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 177 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 22 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6550 (tp30) REVERT: D 38 ASP cc_start: 0.7535 (t0) cc_final: 0.7204 (t0) REVERT: D 75 GLU cc_start: 0.8077 (tp30) cc_final: 0.7844 (tp30) REVERT: D 88 ILE cc_start: 0.8241 (mp) cc_final: 0.7811 (mm) REVERT: D 95 ARG cc_start: 0.8304 (ttp-170) cc_final: 0.8085 (ttm110) REVERT: D 206 ASP cc_start: 0.7728 (t70) cc_final: 0.6396 (t0) REVERT: D 249 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7337 (mtt) REVERT: D 292 ASP cc_start: 0.7620 (p0) cc_final: 0.7382 (p0) REVERT: D 368 ASN cc_start: 0.7703 (m-40) cc_final: 0.7485 (m-40) REVERT: D 398 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7536 (mp0) REVERT: D 421 ILE cc_start: 0.8709 (mm) cc_final: 0.8506 (mp) REVERT: D 429 GLN cc_start: 0.7554 (pm20) cc_final: 0.7138 (pm20) REVERT: D 430 GLU cc_start: 0.7576 (mp0) cc_final: 0.7312 (mp0) REVERT: D 483 GLU cc_start: 0.7648 (tp30) cc_final: 0.7394 (tp30) REVERT: D 510 TYR cc_start: 0.8041 (m-10) cc_final: 0.7724 (m-10) REVERT: D 517 THR cc_start: 0.7713 (p) cc_final: 0.6827 (t) REVERT: D 536 ASN cc_start: 0.6883 (m-40) cc_final: 0.6571 (p0) REVERT: D 562 ASN cc_start: 0.8326 (t0) cc_final: 0.8008 (t160) REVERT: D 581 VAL cc_start: 0.8134 (OUTLIER) cc_final: 0.7879 (t) REVERT: D 606 TRP cc_start: 0.8441 (p90) cc_final: 0.7929 (p90) outliers start: 13 outliers final: 6 residues processed: 182 average time/residue: 1.0615 time to fit residues: 203.8742 Evaluate side-chains 183 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 175 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain A residue 405 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 56 optimal weight: 0.0980 chunk 76 optimal weight: 0.7980 chunk 54 optimal weight: 0.2980 chunk 19 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN D 374 HIS D 522 GLN D 578 ASN D 586 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.115897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.103991 restraints weight = 9265.200| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.99 r_work: 0.3207 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6611 Z= 0.346 Angle : 0.644 8.357 8977 Z= 0.317 Chirality : 0.046 0.209 942 Planarity : 0.004 0.031 1160 Dihedral : 5.232 48.841 944 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.91 % Allowed : 23.90 % Favored : 74.19 % 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: 0.71 (0.31), residues: 780 helix: 1.65 (0.28), residues: 378 sheet: 1.15 (0.75), residues: 44 loop : -0.93 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 163 HIS 0.006 0.001 HIS D 373 PHE 0.028 0.002 PHE D 428 TYR 0.021 0.002 TYR A 453 ARG 0.007 0.001 ARG D 577 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 22 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6805 (tp30) REVERT: D 75 GLU cc_start: 0.8025 (tp30) cc_final: 0.7810 (tp30) REVERT: D 78 LYS cc_start: 0.8597 (ttmm) cc_final: 0.8330 (mtpp) REVERT: D 88 ILE cc_start: 0.8244 (mp) cc_final: 0.7865 (mm) REVERT: D 163 TRP cc_start: 0.8534 (p-90) cc_final: 0.8202 (p-90) REVERT: D 249 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7489 (mtt) REVERT: D 368 ASN cc_start: 0.7857 (m-40) cc_final: 0.7635 (m-40) REVERT: D 421 ILE cc_start: 0.8699 (mm) cc_final: 0.8498 (mp) REVERT: D 430 GLU cc_start: 0.7583 (mp0) cc_final: 0.7312 (mp0) REVERT: D 471 GLU cc_start: 0.8041 (mp0) cc_final: 0.7702 (mp0) REVERT: D 510 TYR cc_start: 0.8051 (m-10) cc_final: 0.7731 (m-10) REVERT: D 536 ASN cc_start: 0.7026 (m-40) cc_final: 0.6790 (p0) REVERT: D 562 ASN cc_start: 0.8454 (t0) cc_final: 0.8191 (t160) REVERT: D 581 VAL cc_start: 0.8114 (OUTLIER) cc_final: 0.7863 (t) REVERT: A 409 GLN cc_start: 0.8680 (mt0) cc_final: 0.8467 (mt0) outliers start: 13 outliers final: 8 residues processed: 171 average time/residue: 1.1932 time to fit residues: 215.4307 Evaluate side-chains 167 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 32 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 11 optimal weight: 0.0870 chunk 22 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 75 optimal weight: 0.0980 chunk 19 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 59 optimal weight: 0.4980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 586 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.116840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.104905 restraints weight = 9385.162| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.02 r_work: 0.3226 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6611 Z= 0.270 Angle : 0.617 8.180 8977 Z= 0.300 Chirality : 0.044 0.189 942 Planarity : 0.004 0.032 1160 Dihedral : 5.125 47.160 944 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.61 % Allowed : 24.49 % Favored : 73.90 % 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: 0.65 (0.31), residues: 780 helix: 1.68 (0.28), residues: 379 sheet: 1.22 (0.74), residues: 43 loop : -1.08 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 163 HIS 0.005 0.001 HIS D 374 PHE 0.028 0.002 PHE D 428 TYR 0.017 0.002 TYR A 453 ARG 0.008 0.000 ARG D 246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: D 22 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6747 (tp30) REVERT: D 75 GLU cc_start: 0.8038 (tp30) cc_final: 0.7823 (tp30) REVERT: D 78 LYS cc_start: 0.8562 (ttmm) cc_final: 0.8285 (mtpp) REVERT: D 88 ILE cc_start: 0.8215 (mp) cc_final: 0.7891 (mm) REVERT: D 249 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7497 (mtt) REVERT: D 292 ASP cc_start: 0.7699 (p0) cc_final: 0.7459 (p0) REVERT: D 318 VAL cc_start: 0.8476 (t) cc_final: 0.8144 (p) REVERT: D 406 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7633 (mm-30) REVERT: D 421 ILE cc_start: 0.8688 (mm) cc_final: 0.8478 (mp) REVERT: D 430 GLU cc_start: 0.7597 (mp0) cc_final: 0.7335 (mp0) REVERT: D 471 GLU cc_start: 0.7988 (mp0) cc_final: 0.7633 (mp0) REVERT: D 474 MET cc_start: 0.8373 (mmt) cc_final: 0.8165 (tpp) REVERT: D 483 GLU cc_start: 0.7655 (tp30) cc_final: 0.7453 (mt-10) REVERT: D 510 TYR cc_start: 0.8074 (m-10) cc_final: 0.7638 (m-10) REVERT: D 514 ARG cc_start: 0.8034 (ptm-80) cc_final: 0.7788 (ptm160) REVERT: D 562 ASN cc_start: 0.8425 (t0) cc_final: 0.8050 (t160) REVERT: D 581 VAL cc_start: 0.8110 (OUTLIER) cc_final: 0.7800 (t) REVERT: A 420 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7027 (m-30) outliers start: 11 outliers final: 7 residues processed: 169 average time/residue: 1.1869 time to fit residues: 210.9467 Evaluate side-chains 171 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 161 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain A residue 420 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 18 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 68 optimal weight: 0.1980 chunk 70 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 5 optimal weight: 0.1980 chunk 28 optimal weight: 0.5980 chunk 77 optimal weight: 0.4980 chunk 50 optimal weight: 0.2980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 197 ASN D 368 ASN D 586 ASN A 409 GLN A 450 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.116120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.104235 restraints weight = 9364.035| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.02 r_work: 0.3217 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6611 Z= 0.289 Angle : 0.643 8.167 8977 Z= 0.316 Chirality : 0.045 0.238 942 Planarity : 0.004 0.033 1160 Dihedral : 5.108 45.067 944 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.17 % Allowed : 24.78 % Favored : 74.05 % 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: 0.57 (0.31), residues: 780 helix: 1.62 (0.28), residues: 387 sheet: 1.20 (0.75), residues: 43 loop : -1.21 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 163 HIS 0.005 0.001 HIS D 374 PHE 0.029 0.002 PHE D 428 TYR 0.018 0.002 TYR A 453 ARG 0.010 0.000 ARG D 246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: D 22 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6798 (tp30) REVERT: D 75 GLU cc_start: 0.8055 (tp30) cc_final: 0.7837 (tp30) REVERT: D 78 LYS cc_start: 0.8551 (ttmm) cc_final: 0.8273 (mtpp) REVERT: D 88 ILE cc_start: 0.8185 (mp) cc_final: 0.7878 (mm) REVERT: D 249 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7493 (mtt) REVERT: D 292 ASP cc_start: 0.7710 (p0) cc_final: 0.7463 (p0) REVERT: D 318 VAL cc_start: 0.8478 (t) cc_final: 0.8140 (p) REVERT: D 406 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7653 (mm-30) REVERT: D 421 ILE cc_start: 0.8691 (mm) cc_final: 0.8473 (mp) REVERT: D 471 GLU cc_start: 0.8010 (mp0) cc_final: 0.7663 (mp0) REVERT: D 483 GLU cc_start: 0.7651 (tp30) cc_final: 0.7394 (mt-10) REVERT: D 487 VAL cc_start: 0.8207 (t) cc_final: 0.7784 (m) REVERT: D 510 TYR cc_start: 0.8046 (m-10) cc_final: 0.7710 (m-10) REVERT: D 562 ASN cc_start: 0.8435 (t0) cc_final: 0.8064 (t160) REVERT: D 581 VAL cc_start: 0.8065 (OUTLIER) cc_final: 0.7808 (t) REVERT: D 606 TRP cc_start: 0.8484 (p90) cc_final: 0.8082 (p90) REVERT: A 420 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7028 (m-30) outliers start: 8 outliers final: 6 residues processed: 161 average time/residue: 1.2064 time to fit residues: 204.2268 Evaluate side-chains 165 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain A residue 420 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 31 optimal weight: 0.4980 chunk 50 optimal weight: 0.3980 chunk 3 optimal weight: 0.7980 chunk 40 optimal weight: 0.0070 chunk 30 optimal weight: 0.2980 chunk 55 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 chunk 6 optimal weight: 0.0270 overall best weight: 0.2456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 536 ASN D 586 ASN A 409 GLN A 450 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.117449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.105401 restraints weight = 9445.510| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.04 r_work: 0.3233 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6611 Z= 0.229 Angle : 0.619 9.040 8977 Z= 0.301 Chirality : 0.043 0.222 942 Planarity : 0.004 0.032 1160 Dihedral : 4.997 44.177 944 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.91 % Allowed : 24.63 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.65 (0.31), residues: 780 helix: 1.74 (0.28), residues: 387 sheet: 1.10 (0.74), residues: 43 loop : -1.22 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 163 HIS 0.005 0.001 HIS D 374 PHE 0.028 0.001 PHE D 428 TYR 0.015 0.001 TYR A 453 ARG 0.009 0.000 ARG D 246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5735.62 seconds wall clock time: 102 minutes 43.23 seconds (6163.23 seconds total)