Starting phenix.real_space_refine on Thu Jul 2 03:48:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xoc_33344/07_2026/7xoc_33344.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xoc_33344/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7xoc_33344/07_2026/7xoc_33344.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xoc_33344/07_2026/7xoc_33344.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xoc_33344/07_2026/7xoc_33344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xoc_33344/07_2026/7xoc_33344.map" model { file = "/net/cci-nas-00/data/ceres_data/7xoc_33344/07_2026/7xoc_33344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xoc_33344/07_2026/7xoc_33344.cif" } 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-6108/lib/python3.11/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 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 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 chiralities: 1 Time building chain proxies: 1.10, per 1000 atoms: 0.17 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: 0.49 Conformation dependent library (CDL) restraints added in 294.7 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: 0.10 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: 0.57 Time building geometry restraints manager: 0.67 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 - 16.77: 3723 16.77 - 33.54: 120 33.54 - 50.31: 22 50.31 - 67.09: 5 67.09 - 83.86: 4 Dihedral angle restraints: 3874 sinusoidal: 1565 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=" N PHE A 371 " pdb=" C PHE A 371 " pdb=" CA PHE A 371 " pdb=" CB PHE A 371 " ideal model delta harmonic sigma weight residual 122.80 131.44 -8.64 0 2.50e+00 1.60e-01 1.19e+01 dihedral pdb=" N ASN A 370 " pdb=" C ASN A 370 " pdb=" CA ASN A 370 " pdb=" CB ASN A 370 " ideal model delta harmonic sigma weight residual 122.80 131.17 -8.37 0 2.50e+00 1.60e-01 1.12e+01 ... (remaining 3871 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: 10.210 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.550 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 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 : 8.650 83.153 2371 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/Z covalent geometry : bond 0.00226 / 0.13 ( 6611) covalent geometry : angle 0.49418 / 0.29 ( 8977) SS BOND : bond 0.07662 / 3.65 ( 7) SS BOND : angle 8.66294 / 4.26 ( 14) hydrogen bonds : bond 0.18252 / 12.37 ( 282) hydrogen bonds : angle 5.45427 / 4.15 ( 798) link_BETA1-4 : bond 0.00363 / 0.19 ( 1) link_BETA1-4 : angle 1.44785 / 0.77 ( 3) link_NAG-ASN : bond 0.00766 / 0.40 ( 3) link_NAG-ASN : angle 3.51627 / 1.81 ( 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 : 0.210 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: 0.3652 time to fit residues: 96.4061 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 : 0.225 ------------------------------------------------------------------------------- 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... 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 572 ASN 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 = 0.3658 r_free = 0.3658 target = 0.127760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.115260 restraints weight = 9362.157| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.10 r_work: 0.3372 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6622 Z= 0.143 Angle : 0.553 9.900 9003 Z= 0.275 Chirality : 0.043 0.379 942 Planarity : 0.004 0.062 1160 Dihedral : 3.363 26.259 862 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.64 % Allowed : 17.16 % Favored : 80.21 % 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: 0.63 (0.28), residues: 377 sheet: -0.45 (0.52), residues: 43 loop : -1.84 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 246 TYR 0.017 0.001 TYR A 453 PHE 0.021 0.002 PHE D 308 TRP 0.007 0.001 TRP D 302 HIS 0.007 0.001 HIS D 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 6611) covalent geometry : angle 0.53944 / 0.27 ( 8977) SS BOND : bond 0.00177 / 0.09 ( 7) SS BOND : angle 1.21377 / 0.56 ( 14) hydrogen bonds : bond 0.03846 / 2.57 ( 282) hydrogen bonds : angle 4.12048 / 2.96 ( 798) link_BETA1-4 : bond 0.00267 / 0.14 ( 1) link_BETA1-4 : angle 0.84004 / 0.47 ( 3) link_NAG-ASN : bond 0.00847 / 0.44 ( 3) link_NAG-ASN : angle 3.66137 / 1.89 ( 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 225 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 207 time to evaluate : 0.155 Fit side-chains REVERT: D 75 GLU cc_start: 0.8032 (tp30) cc_final: 0.7733 (tp30) REVERT: D 94 LYS cc_start: 0.8422 (ttmt) cc_final: 0.8214 (ttmt) REVERT: D 126 ILE cc_start: 0.8617 (mt) cc_final: 0.8404 (mt) REVERT: D 161 ARG cc_start: 0.8258 (mtp85) cc_final: 0.8014 (mtp85) REVERT: D 206 ASP cc_start: 0.7633 (t70) cc_final: 0.7307 (t0) REVERT: D 225 ASP cc_start: 0.7986 (t0) cc_final: 0.7724 (t0) REVERT: D 229 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8314 (t) REVERT: D 232 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7467 (mm-30) REVERT: D 364 VAL cc_start: 0.8512 (m) cc_final: 0.8181 (t) REVERT: D 496 THR cc_start: 0.8095 (m) cc_final: 0.7829 (t) REVERT: D 517 THR cc_start: 0.7752 (p) cc_final: 0.7500 (p) REVERT: D 539 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8298 (tt) REVERT: D 549 GLU cc_start: 0.7324 (tp30) cc_final: 0.7112 (tp30) REVERT: A 405 ASN cc_start: 0.8269 (p0) cc_final: 0.8060 (p0) REVERT: A 453 TYR cc_start: 0.7778 (p90) cc_final: 0.7409 (p90) outliers start: 18 outliers final: 4 residues processed: 216 average time/residue: 0.3845 time to fit residues: 87.9670 Evaluate side-chains 209 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 203 time to evaluate : 0.225 ------------------------------------------------------------------------------- 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 42 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 48 optimal weight: 0.0270 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: 0.4980 chunk 1 optimal weight: 0.1980 chunk 11 optimal weight: 0.2980 chunk 4 optimal weight: 0.5980 overall best weight: 0.3038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 197 ASN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.121554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.109236 restraints weight = 9326.025| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.06 r_work: 0.3278 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3746 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= 0.165 Angle : 0.582 7.765 9003 Z= 0.289 Chirality : 0.043 0.179 942 Planarity : 0.004 0.061 1160 Dihedral : 3.563 17.023 860 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.37 % Allowed : 19.50 % 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 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: -0.23 (0.30), residues: 780 helix: 0.94 (0.28), residues: 379 sheet: 0.50 (0.63), residues: 43 loop : -1.48 (0.33), residues: 358 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 0.022 0.002 PHE D 428 TRP 0.011 0.001 TRP D 478 HIS 0.005 0.001 HIS D 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 ( 6611) covalent geometry : angle 0.57637 / 0.29 ( 8977) SS BOND : bond 0.00175 / 0.09 ( 7) SS BOND : angle 1.22584 / 0.52 ( 14) hydrogen bonds : bond 0.04321 / 2.85 ( 282) hydrogen bonds : angle 4.12945 / 2.94 ( 798) link_BETA1-4 : bond 0.00546 / 0.29 ( 1) link_BETA1-4 : angle 0.58951 / 0.32 ( 3) link_NAG-ASN : bond 0.00211 / 0.10 ( 3) link_NAG-ASN : angle 2.30411 / 1.24 ( 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 213 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 22 GLU cc_start: 0.6975 (tm-30) cc_final: 0.6764 (tm-30) REVERT: D 75 GLU cc_start: 0.8095 (tp30) cc_final: 0.7833 (tp30) REVERT: D 88 ILE cc_start: 0.8192 (mp) cc_final: 0.7982 (mm) REVERT: D 152 MET cc_start: 0.8183 (mmm) cc_final: 0.7548 (mmp) REVERT: D 169 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.6067 (mtm-85) REVERT: D 206 ASP cc_start: 0.7787 (t70) cc_final: 0.7529 (t0) REVERT: D 225 ASP cc_start: 0.8156 (t0) cc_final: 0.7829 (t0) REVERT: D 229 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8334 (t) REVERT: D 232 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7748 (mm-30) REVERT: D 496 THR cc_start: 0.8260 (m) cc_final: 0.8043 (t) REVERT: D 517 THR cc_start: 0.7885 (p) cc_final: 0.7086 (t) REVERT: D 539 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8364 (tt) REVERT: D 571 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7485 (tt0) REVERT: D 577 ARG cc_start: 0.7873 (ptp-170) cc_final: 0.7557 (ptp90) REVERT: D 578 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.8030 (t0) REVERT: D 609 GLU cc_start: 0.6824 (pm20) cc_final: 0.6395 (pm20) REVERT: A 421 TYR cc_start: 0.8586 (m-10) cc_final: 0.8115 (m-80) REVERT: A 451 TYR cc_start: 0.8442 (m-80) cc_final: 0.8143 (m-80) REVERT: A 453 TYR cc_start: 0.8254 (p90) cc_final: 0.7895 (p90) REVERT: A 477 ASN cc_start: 0.8426 (m110) cc_final: 0.8155 (m110) outliers start: 23 outliers final: 3 residues processed: 198 average time/residue: 0.3936 time to fit residues: 82.1904 Evaluate side-chains 193 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 185 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 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 76 optimal weight: 0.9980 chunk 62 optimal weight: 0.0980 chunk 68 optimal weight: 0.0470 chunk 37 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 50 optimal weight: 0.0980 chunk 53 optimal weight: 0.6980 chunk 45 optimal weight: 0.1980 chunk 15 optimal weight: 0.2980 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 overall best weight: 0.1478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 586 ASN A 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.122870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.110407 restraints weight = 9189.334| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.02 r_work: 0.3297 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6622 Z= 0.113 Angle : 0.530 6.095 9003 Z= 0.260 Chirality : 0.040 0.173 942 Planarity : 0.003 0.030 1160 Dihedral : 3.407 14.244 860 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.08 % Allowed : 20.38 % Favored : 76.54 % 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: 0.24 (0.31), residues: 780 helix: 1.32 (0.28), residues: 378 sheet: 0.74 (0.64), residues: 43 loop : -1.21 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 169 TYR 0.015 0.001 TYR A 453 PHE 0.023 0.001 PHE D 428 TRP 0.011 0.001 TRP D 163 HIS 0.004 0.001 HIS D 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 6611) covalent geometry : angle 0.52609 / 0.26 ( 8977) SS BOND : bond 0.00255 / 0.13 ( 7) SS BOND : angle 0.87404 / 0.40 ( 14) hydrogen bonds : bond 0.03605 / 2.41 ( 282) hydrogen bonds : angle 4.02496 / 2.86 ( 798) link_BETA1-4 : bond 0.00197 / 0.10 ( 1) link_BETA1-4 : angle 0.85450 / 0.47 ( 3) link_NAG-ASN : bond 0.00268 / 0.14 ( 3) link_NAG-ASN : angle 1.89532 / 0.99 ( 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 214 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: D 22 GLU cc_start: 0.6889 (mm-30) cc_final: 0.6573 (tm-30) REVERT: D 38 ASP cc_start: 0.7618 (t0) cc_final: 0.7309 (t0) REVERT: D 75 GLU cc_start: 0.8169 (tp30) cc_final: 0.7903 (tp30) REVERT: D 95 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8099 (ttp-110) REVERT: D 152 MET cc_start: 0.8129 (mmm) cc_final: 0.7854 (mmp) REVERT: D 163 TRP cc_start: 0.8456 (p-90) cc_final: 0.8121 (p-90) REVERT: D 169 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.6174 (mtm-85) REVERT: D 206 ASP cc_start: 0.7816 (t70) cc_final: 0.7556 (t0) REVERT: D 364 VAL cc_start: 0.8417 (t) cc_final: 0.8018 (t) REVERT: D 406 GLU cc_start: 0.7891 (tp30) cc_final: 0.7655 (mm-30) REVERT: D 429 GLN cc_start: 0.7551 (pm20) cc_final: 0.7120 (pm20) REVERT: D 471 GLU cc_start: 0.7917 (mp0) cc_final: 0.7579 (mp0) REVERT: D 514 ARG cc_start: 0.8205 (ptm-80) cc_final: 0.7749 (ptm160) REVERT: D 517 THR cc_start: 0.7787 (p) cc_final: 0.6983 (t) REVERT: D 539 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8364 (tt) REVERT: D 578 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7926 (t160) REVERT: D 581 VAL cc_start: 0.8100 (OUTLIER) cc_final: 0.7878 (t) REVERT: D 606 TRP cc_start: 0.8458 (p90) cc_final: 0.7950 (p90) REVERT: D 609 GLU cc_start: 0.6802 (pm20) cc_final: 0.6368 (pm20) REVERT: A 421 TYR cc_start: 0.8548 (m-80) cc_final: 0.8104 (m-80) REVERT: A 453 TYR cc_start: 0.8227 (p90) cc_final: 0.7910 (p90) REVERT: A 477 ASN cc_start: 0.8398 (m110) cc_final: 0.8115 (m110) outliers start: 21 outliers final: 6 residues processed: 203 average time/residue: 0.4020 time to fit residues: 86.2388 Evaluate side-chains 200 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 334 THR 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 46 optimal weight: 0.0040 chunk 4 optimal weight: 0.2980 chunk 73 optimal weight: 0.3980 chunk 54 optimal weight: 0.7980 chunk 30 optimal weight: 0.3980 chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 70 optimal weight: 0.0770 chunk 65 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.2350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 197 ASN D 586 ASN A 414 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 = 0.3567 r_free = 0.3567 target = 0.121430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.108901 restraints weight = 9265.637| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.03 r_work: 0.3276 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6622 Z= 0.137 Angle : 0.540 6.163 9003 Z= 0.268 Chirality : 0.042 0.179 942 Planarity : 0.003 0.028 1160 Dihedral : 3.529 16.727 860 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.23 % Allowed : 20.82 % Favored : 75.95 % 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: 0.44 (0.31), residues: 780 helix: 1.44 (0.28), residues: 381 sheet: 0.99 (0.67), residues: 43 loop : -1.09 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 340 TYR 0.016 0.001 TYR A 453 PHE 0.024 0.001 PHE D 428 TRP 0.011 0.001 TRP D 163 HIS 0.003 0.001 HIS D 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 6611) covalent geometry : angle 0.53546 / 0.27 ( 8977) SS BOND : bond 0.00246 / 0.12 ( 7) SS BOND : angle 1.05534 / 0.47 ( 14) hydrogen bonds : bond 0.03934 / 2.60 ( 282) hydrogen bonds : angle 4.04912 / 2.87 ( 798) link_BETA1-4 : bond 0.00341 / 0.18 ( 1) link_BETA1-4 : angle 0.95054 / 0.54 ( 3) link_NAG-ASN : bond 0.00232 / 0.12 ( 3) link_NAG-ASN : angle 1.84784 / 0.96 ( 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 214 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: D 22 GLU cc_start: 0.7061 (mm-30) cc_final: 0.6793 (tp30) REVERT: D 38 ASP cc_start: 0.7643 (t0) cc_final: 0.7323 (t0) REVERT: D 75 GLU cc_start: 0.8173 (tp30) cc_final: 0.7916 (tp30) REVERT: D 95 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8092 (ttp-110) REVERT: D 98 GLN cc_start: 0.8291 (tt0) cc_final: 0.8015 (mt0) REVERT: D 152 MET cc_start: 0.8032 (mmm) cc_final: 0.7828 (mmt) REVERT: D 197 ASN cc_start: 0.7848 (t0) cc_final: 0.7414 (t0) REVERT: D 206 ASP cc_start: 0.7913 (t70) cc_final: 0.7658 (t0) REVERT: D 364 VAL cc_start: 0.8423 (OUTLIER) cc_final: 0.7990 (t) REVERT: D 429 GLN cc_start: 0.7536 (pm20) cc_final: 0.7125 (pm20) REVERT: D 471 GLU cc_start: 0.8027 (mp0) cc_final: 0.7683 (mp0) REVERT: D 510 TYR cc_start: 0.8018 (m-10) cc_final: 0.7674 (m-10) REVERT: D 517 THR cc_start: 0.7851 (p) cc_final: 0.6993 (t) REVERT: D 539 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8405 (tt) REVERT: D 562 ASN cc_start: 0.8326 (t0) cc_final: 0.8058 (t160) REVERT: D 581 VAL cc_start: 0.8196 (OUTLIER) cc_final: 0.7961 (t) REVERT: D 606 TRP cc_start: 0.8519 (p90) cc_final: 0.7998 (p90) REVERT: D 609 GLU cc_start: 0.6853 (pm20) cc_final: 0.6410 (pm20) REVERT: A 350 VAL cc_start: 0.8205 (p) cc_final: 0.7831 (t) REVERT: A 421 TYR cc_start: 0.8619 (m-80) cc_final: 0.8222 (m-80) REVERT: A 453 TYR cc_start: 0.8242 (p90) cc_final: 0.7868 (p90) REVERT: A 477 ASN cc_start: 0.8357 (m110) cc_final: 0.8085 (m110) outliers start: 22 outliers final: 9 residues processed: 202 average time/residue: 0.4069 time to fit residues: 86.8685 Evaluate side-chains 197 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 223 ILE Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 390 LEU 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: 0.0470 chunk 59 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 35 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 239 HIS D 374 HIS D 378 HIS 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 = 0.3528 r_free = 0.3528 target = 0.118875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.106758 restraints weight = 9243.773| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.99 r_work: 0.3241 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6622 Z= 0.193 Angle : 0.597 6.713 9003 Z= 0.296 Chirality : 0.044 0.195 942 Planarity : 0.004 0.061 1160 Dihedral : 3.827 17.294 860 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.64 % Allowed : 23.46 % 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: 0.57 (0.31), residues: 780 helix: 1.49 (0.28), residues: 379 sheet: 1.16 (0.71), residues: 43 loop : -0.95 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 577 TYR 0.020 0.002 TYR A 453 PHE 0.026 0.002 PHE D 428 TRP 0.025 0.002 TRP D 163 HIS 0.004 0.001 HIS D 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 ( 6611) covalent geometry : angle 0.59277 / 0.29 ( 8977) SS BOND : bond 0.00245 / 0.13 ( 7) SS BOND : angle 1.11747 / 0.52 ( 14) hydrogen bonds : bond 0.04405 / 2.93 ( 282) hydrogen bonds : angle 4.15547 / 2.94 ( 798) link_BETA1-4 : bond 0.00265 / 0.14 ( 1) link_BETA1-4 : angle 0.78635 / 0.45 ( 3) link_NAG-ASN : bond 0.00169 / 0.08 ( 3) link_NAG-ASN : angle 2.06897 / 1.07 ( 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 200 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 22 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6783 (tm-30) REVERT: D 38 ASP cc_start: 0.7638 (t0) cc_final: 0.7303 (t0) REVERT: D 75 GLU cc_start: 0.8181 (tp30) cc_final: 0.7937 (tp30) REVERT: D 88 ILE cc_start: 0.8246 (mp) cc_final: 0.8039 (mm) REVERT: D 95 ARG cc_start: 0.8364 (ttp-170) cc_final: 0.8107 (ttm110) REVERT: D 197 ASN cc_start: 0.7963 (t0) cc_final: 0.7496 (t0) REVERT: D 206 ASP cc_start: 0.8002 (t70) cc_final: 0.7592 (t0) REVERT: D 249 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7581 (mtt) REVERT: D 406 GLU cc_start: 0.7923 (tp30) cc_final: 0.7663 (mm-30) REVERT: D 471 GLU cc_start: 0.8054 (mp0) cc_final: 0.7702 (mp0) REVERT: D 510 TYR cc_start: 0.8090 (m-10) cc_final: 0.7741 (m-10) REVERT: D 536 ASN cc_start: 0.7035 (m110) cc_final: 0.6648 (p0) REVERT: D 562 ASN cc_start: 0.8415 (t0) cc_final: 0.8167 (t160) REVERT: D 581 VAL cc_start: 0.8164 (OUTLIER) cc_final: 0.7831 (t) REVERT: A 350 VAL cc_start: 0.8251 (p) cc_final: 0.7875 (t) REVERT: A 477 ASN cc_start: 0.8347 (m110) cc_final: 0.8089 (m110) outliers start: 18 outliers final: 6 residues processed: 190 average time/residue: 0.4339 time to fit residues: 87.0685 Evaluate side-chains 175 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 167 time to evaluate : 0.135 ------------------------------------------------------------------------------- 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 223 ILE 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 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 35 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 64 optimal weight: 0.3980 chunk 20 optimal weight: 0.3980 chunk 49 optimal weight: 0.3980 chunk 28 optimal weight: 0.0980 chunk 13 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 51 optimal weight: 0.2980 chunk 1 optimal weight: 0.2980 overall best weight: 0.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 378 HIS 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 = 0.3536 r_free = 0.3536 target = 0.119325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.107167 restraints weight = 9151.167| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.99 r_work: 0.3246 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6622 Z= 0.160 Angle : 0.598 11.627 9003 Z= 0.290 Chirality : 0.043 0.229 942 Planarity : 0.003 0.029 1160 Dihedral : 3.760 15.226 860 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.35 % Allowed : 23.61 % 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: 0.68 (0.31), residues: 780 helix: 1.64 (0.28), residues: 378 sheet: 1.23 (0.72), residues: 43 loop : -0.97 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 577 TYR 0.018 0.002 TYR A 453 PHE 0.027 0.001 PHE D 428 TRP 0.023 0.001 TRP D 163 HIS 0.004 0.001 HIS D 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 6611) covalent geometry : angle 0.59398 / 0.29 ( 8977) SS BOND : bond 0.00281 / 0.14 ( 7) SS BOND : angle 1.15712 / 0.52 ( 14) hydrogen bonds : bond 0.04140 / 2.74 ( 282) hydrogen bonds : angle 4.17266 / 2.96 ( 798) link_BETA1-4 : bond 0.00405 / 0.21 ( 1) link_BETA1-4 : angle 0.78629 / 0.44 ( 3) link_NAG-ASN : bond 0.00136 / 0.07 ( 3) link_NAG-ASN : angle 1.94215 / 1.00 ( 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 186 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: D 22 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6813 (tp30) REVERT: D 35 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7627 (mm-30) REVERT: D 38 ASP cc_start: 0.7604 (t0) cc_final: 0.7266 (t0) REVERT: D 75 GLU cc_start: 0.8177 (tp30) cc_final: 0.7947 (tp30) REVERT: D 88 ILE cc_start: 0.8255 (mp) cc_final: 0.7892 (mm) REVERT: D 95 ARG cc_start: 0.8290 (ttp-170) cc_final: 0.8056 (ttm110) REVERT: D 206 ASP cc_start: 0.7861 (t70) cc_final: 0.6472 (t0) REVERT: D 249 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7567 (mtt) REVERT: D 292 ASP cc_start: 0.7595 (p0) cc_final: 0.7327 (p0) REVERT: D 398 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7515 (mp0) REVERT: D 406 GLU cc_start: 0.7870 (tp30) cc_final: 0.7634 (mm-30) REVERT: D 421 ILE cc_start: 0.8725 (mm) cc_final: 0.8446 (mt) REVERT: D 471 GLU cc_start: 0.8050 (mp0) cc_final: 0.7725 (mp0) REVERT: D 510 TYR cc_start: 0.8089 (m-10) cc_final: 0.7744 (m-10) REVERT: D 534 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8208 (mmtp) REVERT: D 536 ASN cc_start: 0.7050 (m110) cc_final: 0.6776 (p0) REVERT: D 562 ASN cc_start: 0.8380 (t0) cc_final: 0.8092 (t160) REVERT: D 581 VAL cc_start: 0.8100 (OUTLIER) cc_final: 0.7859 (t) REVERT: D 606 TRP cc_start: 0.8514 (p90) cc_final: 0.8063 (p90) REVERT: A 350 VAL cc_start: 0.8228 (p) cc_final: 0.7840 (t) REVERT: A 477 ASN cc_start: 0.8335 (m110) cc_final: 0.8083 (m110) outliers start: 16 outliers final: 6 residues processed: 174 average time/residue: 0.4420 time to fit residues: 80.9553 Evaluate side-chains 177 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 168 time to evaluate : 0.225 ------------------------------------------------------------------------------- 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 491 LEU Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 534 LYS Chi-restraints excluded: chain D residue 581 VAL 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: 0.9980 chunk 59 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 72 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 32 optimal weight: 0.0980 chunk 40 optimal weight: 0.6980 chunk 45 optimal weight: 0.2980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 522 GLN 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 = 0.3505 r_free = 0.3505 target = 0.116413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.104523 restraints weight = 9239.885| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.99 r_work: 0.3215 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6622 Z= 0.197 Angle : 0.634 11.545 9003 Z= 0.310 Chirality : 0.045 0.238 942 Planarity : 0.004 0.034 1160 Dihedral : 3.945 18.645 860 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.76 % Allowed : 24.49 % Favored : 73.75 % 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: 0.69 (0.31), residues: 780 helix: 1.64 (0.28), residues: 378 sheet: 1.23 (0.74), residues: 43 loop : -0.96 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 169 TYR 0.020 0.002 TYR A 453 PHE 0.028 0.002 PHE D 428 TRP 0.027 0.002 TRP D 163 HIS 0.004 0.001 HIS D 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 ( 6611) covalent geometry : angle 0.63045 / 0.31 ( 8977) SS BOND : bond 0.00313 / 0.16 ( 7) SS BOND : angle 1.22962 / 0.59 ( 14) hydrogen bonds : bond 0.04509 / 2.99 ( 282) hydrogen bonds : angle 4.23579 / 3.01 ( 798) link_BETA1-4 : bond 0.00380 / 0.20 ( 1) link_BETA1-4 : angle 0.73197 / 0.42 ( 3) link_NAG-ASN : bond 0.00101 / 0.05 ( 3) link_NAG-ASN : angle 1.89917 / 0.98 ( 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 180 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 75 GLU cc_start: 0.8035 (tp30) cc_final: 0.7820 (tp30) REVERT: D 78 LYS cc_start: 0.8584 (ttmm) cc_final: 0.8321 (mtpp) REVERT: D 95 ARG cc_start: 0.8231 (ttp-170) cc_final: 0.8002 (ttm110) REVERT: D 206 ASP cc_start: 0.7878 (t70) cc_final: 0.7361 (t0) REVERT: D 249 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7528 (mtt) REVERT: D 292 ASP cc_start: 0.7687 (p0) cc_final: 0.7426 (p0) REVERT: D 398 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7685 (mp0) REVERT: D 406 GLU cc_start: 0.7874 (tp30) cc_final: 0.7650 (mm-30) REVERT: D 471 GLU cc_start: 0.8033 (mp0) cc_final: 0.7695 (mp0) REVERT: D 510 TYR cc_start: 0.8032 (m-10) cc_final: 0.7726 (m-10) REVERT: D 534 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8264 (mmtm) REVERT: D 562 ASN cc_start: 0.8418 (t0) cc_final: 0.8109 (t160) REVERT: D 574 VAL cc_start: 0.8473 (m) cc_final: 0.8084 (p) REVERT: D 581 VAL cc_start: 0.8086 (OUTLIER) cc_final: 0.7837 (t) REVERT: A 350 VAL cc_start: 0.8257 (p) cc_final: 0.7879 (t) REVERT: A 477 ASN cc_start: 0.8338 (m110) cc_final: 0.8094 (m110) outliers start: 12 outliers final: 7 residues processed: 172 average time/residue: 0.4258 time to fit residues: 77.2391 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 : 0.164 ------------------------------------------------------------------------------- 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 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 581 VAL Chi-restraints excluded: chain D residue 611 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 62 optimal weight: 0.0870 chunk 44 optimal weight: 0.0980 chunk 28 optimal weight: 0.3980 chunk 30 optimal weight: 0.1980 chunk 25 optimal weight: 0.4980 chunk 56 optimal weight: 0.0970 chunk 27 optimal weight: 0.3980 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 0.1980 overall best weight: 0.1356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 299 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 = 0.3546 r_free = 0.3546 target = 0.119357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.107284 restraints weight = 9402.080| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.04 r_work: 0.3255 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6622 Z= 0.118 Angle : 0.584 10.380 9003 Z= 0.286 Chirality : 0.041 0.187 942 Planarity : 0.004 0.035 1160 Dihedral : 3.727 17.143 860 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.32 % Allowed : 25.51 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.87 (0.31), residues: 780 helix: 1.83 (0.28), residues: 377 sheet: 1.19 (0.74), residues: 43 loop : -0.90 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 246 TYR 0.013 0.001 TYR A 453 PHE 0.028 0.001 PHE D 428 TRP 0.024 0.001 TRP D 163 HIS 0.002 0.001 HIS D 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 6611) covalent geometry : angle 0.58058 / 0.29 ( 8977) SS BOND : bond 0.00263 / 0.14 ( 7) SS BOND : angle 1.01861 / 0.50 ( 14) hydrogen bonds : bond 0.03682 / 2.45 ( 282) hydrogen bonds : angle 4.11343 / 2.93 ( 798) link_BETA1-4 : bond 0.00406 / 0.21 ( 1) link_BETA1-4 : angle 0.90000 / 0.48 ( 3) link_NAG-ASN : bond 0.00232 / 0.12 ( 3) link_NAG-ASN : angle 1.60916 / 0.83 ( 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 185 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 176 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 22 GLU cc_start: 0.7099 (tm-30) cc_final: 0.6714 (tp30) REVERT: D 38 ASP cc_start: 0.7588 (t0) cc_final: 0.7254 (t0) REVERT: D 75 GLU cc_start: 0.8031 (tp30) cc_final: 0.7803 (tp30) REVERT: D 88 ILE cc_start: 0.8195 (mm) cc_final: 0.7916 (mm) REVERT: D 95 ARG cc_start: 0.8200 (ttp-170) cc_final: 0.7966 (ttm110) REVERT: D 206 ASP cc_start: 0.7829 (t70) cc_final: 0.7347 (t0) REVERT: D 249 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7399 (mtt) REVERT: D 292 ASP cc_start: 0.7628 (p0) cc_final: 0.7375 (p0) REVERT: D 398 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7664 (mp0) REVERT: D 400 PHE cc_start: 0.8380 (m-80) cc_final: 0.7979 (m-80) REVERT: D 406 GLU cc_start: 0.7877 (tp30) cc_final: 0.7644 (mm-30) REVERT: D 471 GLU cc_start: 0.7977 (mp0) cc_final: 0.7646 (mp0) REVERT: D 510 TYR cc_start: 0.8017 (m-10) cc_final: 0.7688 (m-10) REVERT: D 514 ARG cc_start: 0.8030 (ptm-80) cc_final: 0.7814 (ptm160) REVERT: D 517 THR cc_start: 0.7710 (p) cc_final: 0.6810 (t) REVERT: D 534 LYS cc_start: 0.8484 (ptpp) cc_final: 0.8205 (mmtp) REVERT: D 562 ASN cc_start: 0.8312 (t0) cc_final: 0.7949 (t160) REVERT: D 579 MET cc_start: 0.8644 (mtm) cc_final: 0.8255 (mtp) REVERT: D 581 VAL cc_start: 0.7958 (OUTLIER) cc_final: 0.7694 (t) REVERT: A 420 ASP cc_start: 0.7468 (OUTLIER) cc_final: 0.7015 (m-30) REVERT: A 477 ASN cc_start: 0.8331 (m110) cc_final: 0.8063 (m110) outliers start: 9 outliers final: 7 residues processed: 179 average time/residue: 0.4717 time to fit residues: 89.1340 Evaluate side-chains 175 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 165 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 421 ILE 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 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: 0.0060 chunk 39 optimal weight: 0.2980 chunk 63 optimal weight: 0.1980 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 0.0270 chunk 64 optimal weight: 0.0050 chunk 77 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 13 optimal weight: 0.6980 chunk 6 optimal weight: 0.1980 chunk 48 optimal weight: 0.7980 overall best weight: 0.0868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 522 GLN D 536 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 = 0.3566 r_free = 0.3566 target = 0.120872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.108724 restraints weight = 9206.637| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.04 r_work: 0.3274 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6622 Z= 0.111 Angle : 0.584 10.611 9003 Z= 0.284 Chirality : 0.041 0.178 942 Planarity : 0.003 0.031 1160 Dihedral : 3.590 17.895 860 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.32 % Allowed : 26.10 % Favored : 72.58 % 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: 0.87 (0.31), residues: 780 helix: 1.78 (0.28), residues: 385 sheet: 1.16 (0.72), residues: 43 loop : -0.88 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 246 TYR 0.012 0.001 TYR A 453 PHE 0.029 0.001 PHE D 428 TRP 0.028 0.001 TRP D 163 HIS 0.002 0.001 HIS D 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 6611) covalent geometry : angle 0.58141 / 0.28 ( 8977) SS BOND : bond 0.00181 / 0.09 ( 7) SS BOND : angle 0.96149 / 0.47 ( 14) hydrogen bonds : bond 0.03516 / 2.35 ( 282) hydrogen bonds : angle 4.06796 / 2.90 ( 798) link_BETA1-4 : bond 0.00262 / 0.14 ( 1) link_BETA1-4 : angle 0.78418 / 0.43 ( 3) link_NAG-ASN : bond 0.00265 / 0.14 ( 3) link_NAG-ASN : angle 1.43316 / 0.74 ( 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 185 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 176 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 22 GLU cc_start: 0.6976 (tm-30) cc_final: 0.6721 (tp30) REVERT: D 38 ASP cc_start: 0.7556 (t0) cc_final: 0.7222 (t0) REVERT: D 75 GLU cc_start: 0.8092 (tp30) cc_final: 0.7863 (tp30) REVERT: D 88 ILE cc_start: 0.8221 (mm) cc_final: 0.8001 (mp) REVERT: D 98 GLN cc_start: 0.8197 (tt0) cc_final: 0.7972 (mt0) REVERT: D 163 TRP cc_start: 0.8463 (p-90) cc_final: 0.8077 (p-90) REVERT: D 206 ASP cc_start: 0.7875 (t70) cc_final: 0.7645 (t0) REVERT: D 249 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7321 (mtt) REVERT: D 292 ASP cc_start: 0.7511 (p0) cc_final: 0.7284 (p0) REVERT: D 315 PHE cc_start: 0.8531 (m-80) cc_final: 0.8304 (m-80) REVERT: D 406 GLU cc_start: 0.7884 (tp30) cc_final: 0.7667 (mm-30) REVERT: D 471 GLU cc_start: 0.7979 (mp0) cc_final: 0.7619 (mp0) REVERT: D 510 TYR cc_start: 0.7968 (m-10) cc_final: 0.7693 (m-10) REVERT: D 517 THR cc_start: 0.7644 (p) cc_final: 0.6719 (t) REVERT: D 534 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8195 (mmtp) REVERT: D 536 ASN cc_start: 0.7448 (OUTLIER) cc_final: 0.7105 (p0) REVERT: D 562 ASN cc_start: 0.8282 (t0) cc_final: 0.7927 (t160) REVERT: D 581 VAL cc_start: 0.7931 (OUTLIER) cc_final: 0.7685 (t) REVERT: A 350 VAL cc_start: 0.8277 (p) cc_final: 0.7877 (t) REVERT: A 477 ASN cc_start: 0.8332 (m110) cc_final: 0.8084 (m110) outliers start: 9 outliers final: 4 residues processed: 178 average time/residue: 0.4297 time to fit residues: 80.7956 Evaluate side-chains 179 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 171 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 534 LYS Chi-restraints excluded: chain D residue 536 ASN Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain A residue 405 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 63 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 40 optimal weight: 0.0050 chunk 12 optimal weight: 0.0050 chunk 68 optimal weight: 0.0470 chunk 57 optimal weight: 0.7980 overall best weight: 0.1906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 536 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 = 0.3565 r_free = 0.3565 target = 0.120882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.108728 restraints weight = 9212.609| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.00 r_work: 0.3274 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.133 6622 Z= 0.214 Angle : 1.019 59.195 9003 Z= 0.589 Chirality : 0.054 1.008 942 Planarity : 0.004 0.040 1160 Dihedral : 3.828 39.468 860 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.88 % Allowed : 26.98 % Favored : 72.14 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.87 (0.31), residues: 780 helix: 1.79 (0.28), residues: 385 sheet: 1.14 (0.71), residues: 43 loop : -0.89 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 577 TYR 0.011 0.001 TYR A 453 PHE 0.027 0.001 PHE D 428 TRP 0.025 0.001 TRP D 163 HIS 0.002 0.001 HIS D 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.21 ( 6611) covalent geometry : angle 1.01906 / 0.59 ( 8977) SS BOND : bond 0.00196 / 0.10 ( 7) SS BOND : angle 0.92721 / 0.45 ( 14) hydrogen bonds : bond 0.03539 / 2.37 ( 282) hydrogen bonds : angle 4.06866 / 2.91 ( 798) link_BETA1-4 : bond 0.00122 / 0.06 ( 1) link_BETA1-4 : angle 0.67525 / 0.37 ( 3) link_NAG-ASN : bond 0.00233 / 0.12 ( 3) link_NAG-ASN : angle 1.44364 / 0.75 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2380.18 seconds wall clock time: 41 minutes 16.96 seconds (2476.96 seconds total)