Starting phenix.real_space_refine on Tue Mar 3 15:05:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xoc_33344/03_2026/7xoc_33344.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xoc_33344/03_2026/7xoc_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 { model { file = "/net/cci-nas-00/data/ceres_data/7xoc_33344/03_2026/7xoc_33344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xoc_33344/03_2026/7xoc_33344.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xoc_33344/03_2026/7xoc_33344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xoc_33344/03_2026/7xoc_33344.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.46, per 1000 atoms: 0.23 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: 0.61 Conformation dependent library (CDL) restraints added in 221.5 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: 0.21 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: 0.76 Time building geometry restraints manager: 0.79 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: 9.140 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.090 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.630 ------------------------------------------------------------------------------- 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 : 0.003 0.203 6622 Z= 0.183 Angle : 0.611 31.317 9003 Z= 0.337 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.001 0.000 ARG D 169 TYR 0.009 0.001 TYR A 369 PHE 0.014 0.001 PHE A 371 TRP 0.005 0.000 TRP D 165 HIS 0.001 0.000 HIS D 322 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 6611) covalent geometry : angle 0.49418 ( 8977) SS BOND : bond 0.07662 ( 7) SS BOND : angle 8.66294 ( 14) hydrogen bonds : bond 0.18252 ( 282) hydrogen bonds : angle 5.45427 ( 798) link_BETA1-4 : bond 0.00363 ( 1) link_BETA1-4 : angle 1.44785 ( 3) link_NAG-ASN : bond 0.00766 ( 3) link_NAG-ASN : angle 3.51627 ( 9) *********************** 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 : 0.238 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: 0.7224 (t-100) REVERT: A 489 TYR cc_start: 0.7850 (m-80) cc_final: 0.7619 (m-80) outliers start: 0 outliers final: 1 residues processed: 249 average time/residue: 0.4587 time to fit residues: 120.7326 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 : 0.226 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.2980 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.0670 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.1980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.2980 chunk 74 optimal weight: 0.7980 overall best weight: 0.2118 ------------------------------------------------------------------------------- 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 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.127807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.115342 restraints weight = 9351.011| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.09 r_work: 0.3374 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6622 Z= 0.140 Angle : 0.575 9.930 9003 Z= 0.282 Chirality : 0.043 0.391 942 Planarity : 0.004 0.062 1160 Dihedral : 7.407 57.243 946 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.64 % Allowed : 16.72 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.30), residues: 780 helix: 0.61 (0.28), residues: 377 sheet: -0.42 (0.53), residues: 43 loop : -1.81 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 246 TYR 0.017 0.002 TYR A 453 PHE 0.035 0.002 PHE D 308 TRP 0.008 0.001 TRP A 353 HIS 0.008 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6611) covalent geometry : angle 0.56054 ( 8977) SS BOND : bond 0.00351 ( 7) SS BOND : angle 1.51545 ( 14) hydrogen bonds : bond 0.03780 ( 282) hydrogen bonds : angle 4.13474 ( 798) link_BETA1-4 : bond 0.00246 ( 1) link_BETA1-4 : angle 0.96159 ( 3) link_NAG-ASN : bond 0.00792 ( 3) link_NAG-ASN : angle 3.70090 ( 9) *********************** 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 223 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: D 75 GLU cc_start: 0.8022 (tp30) cc_final: 0.7621 (tm-30) REVERT: D 77 SER cc_start: 0.8645 (t) cc_final: 0.8321 (m) REVERT: D 126 ILE cc_start: 0.8616 (mt) cc_final: 0.8407 (mt) REVERT: D 161 ARG cc_start: 0.8238 (mtp85) cc_final: 0.8008 (mtp85) REVERT: D 206 ASP cc_start: 0.7624 (t70) cc_final: 0.7293 (t0) REVERT: D 225 ASP cc_start: 0.7977 (t0) cc_final: 0.7616 (t0) REVERT: D 229 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8288 (t) REVERT: D 232 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7459 (mm-30) REVERT: D 270 MET cc_start: 0.7793 (tpp) cc_final: 0.7556 (tpp) REVERT: D 364 VAL cc_start: 0.8519 (m) cc_final: 0.8214 (t) REVERT: D 496 THR cc_start: 0.8080 (m) cc_final: 0.7828 (t) REVERT: D 517 THR cc_start: 0.7752 (p) cc_final: 0.7507 (p) REVERT: D 539 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8322 (tt) REVERT: D 549 GLU cc_start: 0.7257 (tp30) cc_final: 0.7022 (tp30) REVERT: A 405 ASN cc_start: 0.8269 (p0) cc_final: 0.8055 (p0) REVERT: A 453 TYR cc_start: 0.7760 (p90) cc_final: 0.7399 (p90) outliers start: 18 outliers final: 5 residues processed: 213 average time/residue: 0.4497 time to fit residues: 101.2884 Evaluate side-chains 202 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 195 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 228 ARG 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 42 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 75 optimal weight: 0.1980 chunk 1 optimal weight: 0.0980 chunk 11 optimal weight: 0.0060 chunk 4 optimal weight: 0.5980 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 322 HIS D 345 HIS D 493 HIS D 572 ASN D 586 ASN A 388 ASN A 417 ASN A 450 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.121832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.109548 restraints weight = 9327.324| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.06 r_work: 0.3300 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6622 Z= 0.156 Angle : 0.600 10.118 9003 Z= 0.291 Chirality : 0.042 0.157 942 Planarity : 0.004 0.062 1160 Dihedral : 6.414 80.651 944 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.52 % Allowed : 19.50 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.31), residues: 780 helix: 0.98 (0.28), residues: 379 sheet: 0.47 (0.63), residues: 43 loop : -1.49 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 246 TYR 0.017 0.002 TYR A 453 PHE 0.021 0.002 PHE D 428 TRP 0.010 0.001 TRP D 478 HIS 0.004 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 6611) covalent geometry : angle 0.59055 ( 8977) SS BOND : bond 0.00332 ( 7) SS BOND : angle 1.03557 ( 14) hydrogen bonds : bond 0.04175 ( 282) hydrogen bonds : angle 4.08911 ( 798) link_BETA1-4 : bond 0.00838 ( 1) link_BETA1-4 : angle 1.64870 ( 3) link_NAG-ASN : bond 0.00196 ( 3) link_NAG-ASN : angle 3.18021 ( 9) *********************** 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 216 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: D 22 GLU cc_start: 0.6917 (tm-30) cc_final: 0.6668 (tm-30) REVERT: D 75 GLU cc_start: 0.8083 (tp30) cc_final: 0.7819 (tp30) REVERT: D 94 LYS cc_start: 0.8468 (ttmt) cc_final: 0.8139 (ttpp) REVERT: D 95 ARG cc_start: 0.8353 (ttp-170) cc_final: 0.8110 (ttp-110) REVERT: D 152 MET cc_start: 0.8171 (mmm) cc_final: 0.7871 (mmp) REVERT: D 169 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.6129 (mtm-85) REVERT: D 206 ASP cc_start: 0.7766 (t70) cc_final: 0.7512 (t0) REVERT: D 225 ASP cc_start: 0.8214 (t0) cc_final: 0.7894 (t0) REVERT: D 229 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8343 (t) REVERT: D 232 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7723 (mm-30) REVERT: D 335 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7164 (tm-30) REVERT: D 483 GLU cc_start: 0.7714 (tp30) cc_final: 0.7457 (tp30) REVERT: D 496 THR cc_start: 0.8257 (m) cc_final: 0.8053 (t) REVERT: D 517 THR cc_start: 0.7846 (p) cc_final: 0.7052 (t) REVERT: D 539 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8385 (tt) REVERT: D 549 GLU cc_start: 0.7294 (tp30) cc_final: 0.7012 (tp30) REVERT: D 581 VAL cc_start: 0.8202 (t) cc_final: 0.7995 (t) REVERT: D 609 GLU cc_start: 0.6768 (pm20) cc_final: 0.6347 (pm20) REVERT: A 421 TYR cc_start: 0.8544 (m-10) cc_final: 0.8111 (m-80) REVERT: A 451 TYR cc_start: 0.8409 (m-80) cc_final: 0.8160 (m-80) REVERT: A 453 TYR cc_start: 0.8219 (p90) cc_final: 0.7898 (p90) REVERT: A 477 ASN cc_start: 0.8423 (m110) cc_final: 0.8151 (m110) outliers start: 24 outliers final: 4 residues processed: 201 average time/residue: 0.4805 time to fit residues: 101.7788 Evaluate side-chains 198 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 191 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 334 THR Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 390 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 68 optimal weight: 0.0970 chunk 37 optimal weight: 0.0980 chunk 70 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 0.3980 chunk 45 optimal weight: 0.0980 chunk 15 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.2578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 197 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 = 0.3565 r_free = 0.3565 target = 0.121256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.108919 restraints weight = 9228.587| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.01 r_work: 0.3268 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6622 Z= 0.145 Angle : 0.581 8.671 9003 Z= 0.279 Chirality : 0.042 0.287 942 Planarity : 0.004 0.061 1160 Dihedral : 5.758 73.014 944 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.23 % Allowed : 20.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.31), residues: 780 helix: 1.28 (0.28), residues: 380 sheet: 0.77 (0.65), residues: 43 loop : -1.26 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 246 TYR 0.017 0.002 TYR A 453 PHE 0.023 0.002 PHE D 428 TRP 0.014 0.001 TRP D 163 HIS 0.004 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6611) covalent geometry : angle 0.56977 ( 8977) SS BOND : bond 0.00559 ( 7) SS BOND : angle 0.95195 ( 14) hydrogen bonds : bond 0.03960 ( 282) hydrogen bonds : angle 4.10463 ( 798) link_BETA1-4 : bond 0.00423 ( 1) link_BETA1-4 : angle 1.76790 ( 3) link_NAG-ASN : bond 0.00292 ( 3) link_NAG-ASN : angle 3.43759 ( 9) *********************** 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 210 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: D 22 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6640 (tm-30) REVERT: D 38 ASP cc_start: 0.7621 (t0) cc_final: 0.7321 (t0) REVERT: D 75 GLU cc_start: 0.8174 (tp30) cc_final: 0.7912 (tp30) REVERT: D 88 ILE cc_start: 0.8219 (mp) cc_final: 0.7926 (mm) REVERT: D 95 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.8113 (ttp-110) REVERT: D 152 MET cc_start: 0.8191 (mmm) cc_final: 0.7895 (mmp) REVERT: D 169 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.6202 (mtm-85) REVERT: D 197 ASN cc_start: 0.7862 (t0) cc_final: 0.7607 (t0) REVERT: D 206 ASP cc_start: 0.7823 (t70) cc_final: 0.7395 (t0) REVERT: D 364 VAL cc_start: 0.8443 (t) cc_final: 0.8037 (t) REVERT: D 429 GLN cc_start: 0.7599 (pm20) cc_final: 0.7157 (pm20) REVERT: D 471 GLU cc_start: 0.7958 (mp0) cc_final: 0.7590 (mp0) REVERT: D 496 THR cc_start: 0.8234 (m) cc_final: 0.8002 (t) REVERT: D 517 THR cc_start: 0.7853 (p) cc_final: 0.7052 (t) REVERT: D 562 ASN cc_start: 0.8286 (t0) cc_final: 0.7939 (t160) REVERT: D 578 ASN cc_start: 0.8241 (OUTLIER) cc_final: 0.7996 (t160) REVERT: D 609 GLU cc_start: 0.6823 (pm20) cc_final: 0.6385 (pm20) REVERT: A 350 VAL cc_start: 0.8264 (p) cc_final: 0.7914 (t) REVERT: A 421 TYR cc_start: 0.8617 (m-80) cc_final: 0.8194 (m-80) REVERT: A 451 TYR cc_start: 0.8467 (m-80) cc_final: 0.8250 (m-80) REVERT: A 453 TYR cc_start: 0.8319 (p90) cc_final: 0.7970 (p90) REVERT: A 477 ASN cc_start: 0.8407 (m110) cc_final: 0.8134 (m110) outliers start: 22 outliers final: 6 residues processed: 197 average time/residue: 0.4892 time to fit residues: 101.4600 Evaluate side-chains 189 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 180 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 169 ARG Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 534 LYS Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 390 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 46 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 22 optimal weight: 0.2980 chunk 44 optimal weight: 0.0020 chunk 32 optimal weight: 0.6980 chunk 70 optimal weight: 0.2980 chunk 65 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 overall best weight: 0.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 586 ASN A 414 GLN A 450 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.106448 restraints weight = 9549.966| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.07 r_work: 0.3245 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6622 Z= 0.152 Angle : 0.598 8.919 9003 Z= 0.287 Chirality : 0.042 0.268 942 Planarity : 0.004 0.061 1160 Dihedral : 5.510 67.120 944 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.37 % Allowed : 21.41 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.31), residues: 780 helix: 1.45 (0.28), residues: 380 sheet: 1.00 (0.68), residues: 43 loop : -1.17 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 577 TYR 0.017 0.002 TYR A 453 PHE 0.026 0.002 PHE D 428 TRP 0.026 0.001 TRP D 163 HIS 0.004 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 6611) covalent geometry : angle 0.58703 ( 8977) SS BOND : bond 0.00231 ( 7) SS BOND : angle 0.98516 ( 14) hydrogen bonds : bond 0.04072 ( 282) hydrogen bonds : angle 4.09525 ( 798) link_BETA1-4 : bond 0.00722 ( 1) link_BETA1-4 : angle 1.45183 ( 3) link_NAG-ASN : bond 0.00206 ( 3) link_NAG-ASN : angle 3.44918 ( 9) *********************** 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 209 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 22 GLU cc_start: 0.7039 (mm-30) cc_final: 0.6710 (tm-30) REVERT: D 38 ASP cc_start: 0.7607 (t0) cc_final: 0.7291 (t0) REVERT: D 75 GLU cc_start: 0.8079 (tp30) cc_final: 0.7825 (tp30) REVERT: D 95 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.8123 (ttm110) REVERT: D 152 MET cc_start: 0.7952 (mmm) cc_final: 0.7739 (mmt) REVERT: D 169 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.6178 (mtm-85) REVERT: D 206 ASP cc_start: 0.7734 (t70) cc_final: 0.7488 (t0) REVERT: D 364 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.8010 (t) REVERT: D 429 GLN cc_start: 0.7557 (pm20) cc_final: 0.7119 (pm20) REVERT: D 483 GLU cc_start: 0.7691 (tp30) cc_final: 0.7350 (tp30) REVERT: D 496 THR cc_start: 0.8217 (m) cc_final: 0.7934 (t) REVERT: D 510 TYR cc_start: 0.8028 (m-10) cc_final: 0.7645 (m-10) REVERT: D 536 ASN cc_start: 0.7021 (m110) cc_final: 0.6519 (p0) REVERT: D 562 ASN cc_start: 0.8370 (t0) cc_final: 0.8043 (t160) REVERT: D 585 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7594 (mp) REVERT: A 350 VAL cc_start: 0.8285 (p) cc_final: 0.7948 (t) REVERT: A 421 TYR cc_start: 0.8641 (m-80) cc_final: 0.8172 (m-80) REVERT: A 453 TYR cc_start: 0.8394 (p90) cc_final: 0.7948 (p90) REVERT: A 477 ASN cc_start: 0.8381 (m110) cc_final: 0.8118 (m110) outliers start: 23 outliers final: 9 residues processed: 195 average time/residue: 0.5016 time to fit residues: 102.8578 Evaluate side-chains 185 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 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 364 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 534 LYS Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 10 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 74 optimal weight: 0.3980 chunk 29 optimal weight: 0.2980 chunk 22 optimal weight: 0.3980 chunk 35 optimal weight: 0.0980 chunk 9 optimal weight: 0.9990 chunk 72 optimal weight: 0.3980 chunk 14 optimal weight: 0.7980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 239 HIS D 374 HIS D 552 GLN D 578 ASN D 586 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 = 0.3521 r_free = 0.3521 target = 0.117437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.105390 restraints weight = 9460.340| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.04 r_work: 0.3227 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6622 Z= 0.167 Angle : 0.611 8.776 9003 Z= 0.295 Chirality : 0.043 0.265 942 Planarity : 0.004 0.060 1160 Dihedral : 5.318 58.276 944 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.20 % Allowed : 22.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.31), residues: 780 helix: 1.53 (0.28), residues: 380 sheet: 1.20 (0.71), residues: 43 loop : -1.11 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 177 TYR 0.017 0.002 TYR A 453 PHE 0.026 0.002 PHE D 428 TRP 0.025 0.001 TRP D 163 HIS 0.004 0.001 HIS D 540 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 6611) covalent geometry : angle 0.59821 ( 8977) SS BOND : bond 0.00281 ( 7) SS BOND : angle 1.18193 ( 14) hydrogen bonds : bond 0.04217 ( 282) hydrogen bonds : angle 4.17552 ( 798) link_BETA1-4 : bond 0.00592 ( 1) link_BETA1-4 : angle 1.46305 ( 3) link_NAG-ASN : bond 0.00155 ( 3) link_NAG-ASN : angle 3.73613 ( 9) *********************** 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 191 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 22 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6742 (tp30) REVERT: D 38 ASP cc_start: 0.7572 (t0) cc_final: 0.7246 (t0) REVERT: D 75 GLU cc_start: 0.8057 (tp30) cc_final: 0.7828 (tp30) REVERT: D 88 ILE cc_start: 0.8279 (mm) cc_final: 0.8014 (mp) REVERT: D 89 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7802 (mm-40) REVERT: D 169 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.6185 (mtm-85) REVERT: D 206 ASP cc_start: 0.7836 (t70) cc_final: 0.7348 (t0) REVERT: D 249 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7501 (mtp) REVERT: D 398 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7676 (mp0) REVERT: D 471 GLU cc_start: 0.8038 (mp0) cc_final: 0.7653 (mp0) REVERT: D 496 THR cc_start: 0.8245 (m) cc_final: 0.7997 (t) REVERT: D 510 TYR cc_start: 0.8043 (m-10) cc_final: 0.7667 (m-10) REVERT: D 536 ASN cc_start: 0.7016 (m110) cc_final: 0.6687 (p0) REVERT: D 548 THR cc_start: 0.8153 (t) cc_final: 0.7943 (m) REVERT: D 562 ASN cc_start: 0.8368 (t0) cc_final: 0.8064 (t160) REVERT: D 585 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7517 (mp) REVERT: A 350 VAL cc_start: 0.8319 (p) cc_final: 0.7967 (t) REVERT: A 477 ASN cc_start: 0.8359 (m110) cc_final: 0.8105 (m110) outliers start: 15 outliers final: 9 residues processed: 183 average time/residue: 0.4993 time to fit residues: 96.0583 Evaluate side-chains 181 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 0.158 ------------------------------------------------------------------------------- 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 491 LEU Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 534 LYS Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 405 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 0.2980 chunk 65 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 chunk 49 optimal weight: 0.0970 chunk 28 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 chunk 51 optimal weight: 0.7980 chunk 1 optimal weight: 0.3980 overall best weight: 0.2378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 378 HIS D 578 ASN 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 = 0.3529 r_free = 0.3529 target = 0.117858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.105853 restraints weight = 9357.311| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.04 r_work: 0.3235 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6622 Z= 0.142 Angle : 0.612 8.452 9003 Z= 0.293 Chirality : 0.042 0.264 942 Planarity : 0.003 0.029 1160 Dihedral : 5.209 55.369 944 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.05 % Allowed : 23.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.31), residues: 780 helix: 1.67 (0.28), residues: 380 sheet: 1.23 (0.71), residues: 43 loop : -1.07 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 246 TYR 0.016 0.001 TYR A 453 PHE 0.027 0.001 PHE D 428 TRP 0.024 0.001 TRP D 163 HIS 0.003 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 6611) covalent geometry : angle 0.60098 ( 8977) SS BOND : bond 0.00245 ( 7) SS BOND : angle 1.00856 ( 14) hydrogen bonds : bond 0.04001 ( 282) hydrogen bonds : angle 4.17477 ( 798) link_BETA1-4 : bond 0.00602 ( 1) link_BETA1-4 : angle 1.43094 ( 3) link_NAG-ASN : bond 0.00181 ( 3) link_NAG-ASN : angle 3.55118 ( 9) *********************** 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 189 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 22 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6910 (tp30) REVERT: D 35 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7481 (mm-30) REVERT: D 38 ASP cc_start: 0.7573 (t0) cc_final: 0.7241 (t0) REVERT: D 75 GLU cc_start: 0.8052 (tp30) cc_final: 0.7817 (tp30) REVERT: D 88 ILE cc_start: 0.8292 (mm) cc_final: 0.7947 (mp) REVERT: D 89 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7829 (mm110) REVERT: D 169 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.6331 (mtm-85) REVERT: D 206 ASP cc_start: 0.7825 (t70) cc_final: 0.7337 (t0) REVERT: D 249 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7421 (mtt) REVERT: D 292 ASP cc_start: 0.7618 (p0) cc_final: 0.7355 (p0) REVERT: D 398 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7682 (mp0) REVERT: D 471 GLU cc_start: 0.7987 (mp0) cc_final: 0.7613 (mp0) REVERT: D 496 THR cc_start: 0.8214 (m) cc_final: 0.7966 (t) REVERT: D 510 TYR cc_start: 0.8052 (m-10) cc_final: 0.7678 (m-10) REVERT: D 534 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8154 (mmtp) REVERT: D 536 ASN cc_start: 0.7007 (m110) cc_final: 0.6721 (p0) REVERT: D 562 ASN cc_start: 0.8365 (t0) cc_final: 0.7986 (t160) REVERT: D 577 ARG cc_start: 0.8056 (ttp-170) cc_final: 0.7510 (ttm-80) REVERT: D 585 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7429 (mt) REVERT: A 350 VAL cc_start: 0.8306 (p) cc_final: 0.7957 (t) REVERT: A 477 ASN cc_start: 0.8347 (m110) cc_final: 0.8094 (m110) outliers start: 14 outliers final: 6 residues processed: 178 average time/residue: 0.5257 time to fit residues: 98.3170 Evaluate side-chains 181 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 171 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 491 LEU Chi-restraints excluded: chain D residue 534 LYS 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 22 optimal weight: 0.3980 chunk 37 optimal weight: 0.4980 chunk 59 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 chunk 72 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 44 optimal weight: 0.1980 chunk 32 optimal weight: 0.8980 chunk 40 optimal weight: 0.2980 chunk 45 optimal weight: 0.3980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 378 HIS D 522 GLN A 450 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.116681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.104733 restraints weight = 9300.668| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.01 r_work: 0.3220 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6622 Z= 0.175 Angle : 0.628 8.167 9003 Z= 0.303 Chirality : 0.044 0.274 942 Planarity : 0.004 0.034 1160 Dihedral : 5.109 47.467 944 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.05 % Allowed : 23.17 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.31), residues: 780 helix: 1.72 (0.28), residues: 377 sheet: 1.33 (0.73), residues: 43 loop : -1.00 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 246 TYR 0.018 0.002 TYR A 453 PHE 0.027 0.002 PHE D 428 TRP 0.028 0.001 TRP D 163 HIS 0.005 0.001 HIS D 322 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 6611) covalent geometry : angle 0.61570 ( 8977) SS BOND : bond 0.00445 ( 7) SS BOND : angle 1.15636 ( 14) hydrogen bonds : bond 0.04358 ( 282) hydrogen bonds : angle 4.21597 ( 798) link_BETA1-4 : bond 0.00839 ( 1) link_BETA1-4 : angle 1.73443 ( 3) link_NAG-ASN : bond 0.00124 ( 3) link_NAG-ASN : angle 3.71967 ( 9) *********************** 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 181 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 22 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6850 (tp30) REVERT: D 35 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7583 (mm-30) REVERT: D 75 GLU cc_start: 0.8036 (tp30) cc_final: 0.7811 (tp30) REVERT: D 78 LYS cc_start: 0.8579 (ttmm) cc_final: 0.8262 (mtpp) REVERT: D 88 ILE cc_start: 0.8299 (mm) cc_final: 0.7938 (mp) REVERT: D 89 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7796 (mm110) REVERT: D 169 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.6232 (mtm-85) REVERT: D 206 ASP cc_start: 0.7894 (t70) cc_final: 0.7516 (t0) REVERT: D 249 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7506 (mtt) REVERT: D 292 ASP cc_start: 0.7638 (p0) cc_final: 0.7389 (p0) REVERT: D 398 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7737 (mt-10) REVERT: D 471 GLU cc_start: 0.8047 (mp0) cc_final: 0.7679 (mp0) REVERT: D 496 THR cc_start: 0.8219 (m) cc_final: 0.7939 (t) REVERT: D 510 TYR cc_start: 0.8044 (m-10) cc_final: 0.7696 (m-10) REVERT: D 534 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8216 (mmtp) REVERT: D 562 ASN cc_start: 0.8427 (t0) cc_final: 0.8141 (t160) REVERT: D 574 VAL cc_start: 0.8479 (m) cc_final: 0.8087 (p) REVERT: D 585 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7560 (mp) REVERT: A 350 VAL cc_start: 0.8333 (p) cc_final: 0.7984 (t) REVERT: A 420 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.7048 (m-30) REVERT: A 477 ASN cc_start: 0.8346 (m110) cc_final: 0.8099 (m110) outliers start: 14 outliers final: 9 residues processed: 174 average time/residue: 0.4962 time to fit residues: 90.9572 Evaluate side-chains 179 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 376 MET Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 534 LYS Chi-restraints excluded: chain D residue 544 ILE 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 420 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 0.3980 chunk 35 optimal weight: 0.5980 chunk 62 optimal weight: 0.0980 chunk 44 optimal weight: 0.0570 chunk 28 optimal weight: 0.1980 chunk 30 optimal weight: 0.1980 chunk 25 optimal weight: 0.6980 chunk 56 optimal weight: 0.1980 chunk 27 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 29 optimal weight: 0.3980 overall best weight: 0.1498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 299 ASN D 522 GLN A 450 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.118827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.106727 restraints weight = 9481.178| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.07 r_work: 0.3244 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6622 Z= 0.121 Angle : 0.610 8.160 9003 Z= 0.295 Chirality : 0.041 0.251 942 Planarity : 0.004 0.036 1160 Dihedral : 4.950 47.651 944 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.91 % Allowed : 24.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.31), residues: 780 helix: 1.84 (0.28), residues: 379 sheet: 1.30 (0.73), residues: 43 loop : -1.03 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 246 TYR 0.013 0.001 TYR A 453 PHE 0.028 0.001 PHE D 428 TRP 0.027 0.001 TRP D 163 HIS 0.003 0.001 HIS D 540 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 6611) covalent geometry : angle 0.59932 ( 8977) SS BOND : bond 0.00219 ( 7) SS BOND : angle 0.95240 ( 14) hydrogen bonds : bond 0.03719 ( 282) hydrogen bonds : angle 4.14304 ( 798) link_BETA1-4 : bond 0.00776 ( 1) link_BETA1-4 : angle 1.36039 ( 3) link_NAG-ASN : bond 0.00186 ( 3) link_NAG-ASN : angle 3.48221 ( 9) *********************** 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 188 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 22 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6754 (tp30) REVERT: D 38 ASP cc_start: 0.7556 (t0) cc_final: 0.7233 (t0) REVERT: D 75 GLU cc_start: 0.8071 (tp30) cc_final: 0.7834 (tp30) REVERT: D 88 ILE cc_start: 0.8261 (mm) cc_final: 0.7863 (mp) REVERT: D 89 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7814 (mm110) REVERT: D 169 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.6194 (mtm-85) REVERT: D 206 ASP cc_start: 0.7853 (t70) cc_final: 0.7364 (t0) REVERT: D 249 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7387 (mtt) REVERT: D 292 ASP cc_start: 0.7661 (p0) cc_final: 0.7413 (p0) REVERT: D 398 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7634 (mp0) REVERT: D 471 GLU cc_start: 0.7982 (mp0) cc_final: 0.7624 (mp0) REVERT: D 483 GLU cc_start: 0.7654 (tp30) cc_final: 0.7423 (mt-10) REVERT: D 496 THR cc_start: 0.8221 (m) cc_final: 0.7919 (t) REVERT: D 510 TYR cc_start: 0.8016 (m-10) cc_final: 0.7652 (m-10) REVERT: D 514 ARG cc_start: 0.8043 (ptm-80) cc_final: 0.7828 (ptm160) REVERT: D 517 THR cc_start: 0.7721 (p) cc_final: 0.6842 (t) REVERT: D 534 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8203 (mmtp) REVERT: D 562 ASN cc_start: 0.8361 (t0) cc_final: 0.8009 (t160) REVERT: D 585 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7321 (mt) REVERT: A 350 VAL cc_start: 0.8304 (p) cc_final: 0.7942 (t) REVERT: A 420 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7051 (m-30) REVERT: A 477 ASN cc_start: 0.8344 (m110) cc_final: 0.8087 (m110) outliers start: 13 outliers final: 9 residues processed: 179 average time/residue: 0.5068 time to fit residues: 95.4680 Evaluate side-chains 188 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 53 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 229 THR Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 534 LYS Chi-restraints excluded: chain D residue 544 ILE 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 420 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 0.1980 chunk 63 optimal weight: 0.1980 chunk 59 optimal weight: 0.1980 chunk 23 optimal weight: 0.0030 chunk 64 optimal weight: 0.0020 chunk 77 optimal weight: 0.6980 chunk 1 optimal weight: 0.0980 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 chunk 48 optimal weight: 0.9990 overall best weight: 0.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN A 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.119949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.107932 restraints weight = 9262.030| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.04 r_work: 0.3274 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6622 Z= 0.112 Angle : 0.597 7.868 9003 Z= 0.286 Chirality : 0.041 0.240 942 Planarity : 0.003 0.034 1160 Dihedral : 4.846 46.624 944 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.05 % Allowed : 24.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.31), residues: 780 helix: 1.99 (0.28), residues: 373 sheet: 1.25 (0.73), residues: 43 loop : -0.86 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 246 TYR 0.012 0.001 TYR A 380 PHE 0.029 0.001 PHE D 428 TRP 0.029 0.001 TRP D 163 HIS 0.004 0.001 HIS D 322 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 6611) covalent geometry : angle 0.58686 ( 8977) SS BOND : bond 0.00197 ( 7) SS BOND : angle 0.91237 ( 14) hydrogen bonds : bond 0.03553 ( 282) hydrogen bonds : angle 4.08287 ( 798) link_BETA1-4 : bond 0.00739 ( 1) link_BETA1-4 : angle 1.36674 ( 3) link_NAG-ASN : bond 0.00193 ( 3) link_NAG-ASN : angle 3.38104 ( 9) ********************** 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 183 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 38 ASP cc_start: 0.7524 (t0) cc_final: 0.7203 (t0) REVERT: D 75 GLU cc_start: 0.8093 (tp30) cc_final: 0.7845 (tp30) REVERT: D 88 ILE cc_start: 0.8276 (mm) cc_final: 0.7843 (mp) REVERT: D 89 GLN cc_start: 0.8085 (mm-40) cc_final: 0.7846 (mm110) REVERT: D 98 GLN cc_start: 0.8227 (tt0) cc_final: 0.8013 (mt0) REVERT: D 169 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.6269 (mtm-85) REVERT: D 206 ASP cc_start: 0.7887 (t70) cc_final: 0.7393 (t0) REVERT: D 249 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7381 (mtt) REVERT: D 292 ASP cc_start: 0.7652 (p0) cc_final: 0.7393 (p0) REVERT: D 398 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7620 (mp0) REVERT: D 471 GLU cc_start: 0.7997 (mp0) cc_final: 0.7598 (mp0) REVERT: D 483 GLU cc_start: 0.7628 (tp30) cc_final: 0.7405 (mt-10) REVERT: D 496 THR cc_start: 0.8263 (m) cc_final: 0.8022 (t) REVERT: D 510 TYR cc_start: 0.7972 (m-10) cc_final: 0.7664 (m-10) REVERT: D 517 THR cc_start: 0.7669 (p) cc_final: 0.6774 (t) REVERT: D 534 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8204 (mmtp) REVERT: D 536 ASN cc_start: 0.7336 (p0) cc_final: 0.7048 (p0) REVERT: D 562 ASN cc_start: 0.8339 (t0) cc_final: 0.7981 (t160) REVERT: D 577 ARG cc_start: 0.8101 (ttm-80) cc_final: 0.7107 (ttm-80) REVERT: D 585 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7338 (mm) REVERT: A 350 VAL cc_start: 0.8311 (p) cc_final: 0.7937 (t) REVERT: A 420 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.6967 (m-30) REVERT: A 477 ASN cc_start: 0.8329 (m110) cc_final: 0.8069 (m110) outliers start: 14 outliers final: 10 residues processed: 174 average time/residue: 0.4774 time to fit residues: 87.5089 Evaluate side-chains 179 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 53 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 229 THR Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 534 LYS Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 585 LEU 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 65 optimal weight: 0.9990 chunk 61 optimal weight: 0.3980 chunk 43 optimal weight: 0.1980 chunk 37 optimal weight: 0.3980 chunk 63 optimal weight: 0.5980 chunk 11 optimal weight: 0.0040 chunk 28 optimal weight: 0.2980 chunk 40 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 overall best weight: 0.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 216 ASN D 522 GLN 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 = 0.3534 r_free = 0.3534 target = 0.118652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.106680 restraints weight = 9279.912| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.04 r_work: 0.3252 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6622 Z= 0.151 Angle : 0.661 11.708 9003 Z= 0.313 Chirality : 0.043 0.264 942 Planarity : 0.004 0.032 1160 Dihedral : 4.902 45.256 944 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.91 % Allowed : 24.78 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.31), residues: 780 helix: 1.93 (0.28), residues: 373 sheet: 1.04 (0.72), residues: 44 loop : -0.84 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 246 TYR 0.014 0.001 TYR A 453 PHE 0.030 0.002 PHE D 428 TRP 0.030 0.001 TRP D 163 HIS 0.005 0.001 HIS D 322 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 6611) covalent geometry : angle 0.65004 ( 8977) SS BOND : bond 0.00260 ( 7) SS BOND : angle 1.15235 ( 14) hydrogen bonds : bond 0.03896 ( 282) hydrogen bonds : angle 4.11555 ( 798) link_BETA1-4 : bond 0.00726 ( 1) link_BETA1-4 : angle 1.41658 ( 3) link_NAG-ASN : bond 0.00165 ( 3) link_NAG-ASN : angle 3.51405 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2640.47 seconds wall clock time: 45 minutes 37.44 seconds (2737.44 seconds total)