Starting phenix.real_space_refine on Thu Jul 2 05:40:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7r0z_14225/07_2026/7r0z_14225.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r0z_14225/07_2026/7r0z_14225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7r0z_14225/07_2026/7r0z_14225.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7r0z_14225/07_2026/7r0z_14225.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r0z_14225/07_2026/7r0z_14225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r0z_14225/07_2026/7r0z_14225.map" model { file = "/net/cci-nas-00/data/ceres_data/7r0z_14225/07_2026/7r0z_14225.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r0z_14225/07_2026/7r0z_14225.cif" } resolution = 3.5 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= 0.002 sd= 0.074 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 39 5.16 5 C 4404 2.51 5 N 1131 2.21 5 O 1316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 6891 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 4801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4801 Classifications: {'peptide': 588} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 562} Chain breaks: 1 Chain: "A" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1977 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 14, 'TRANS': 236} Chain breaks: 1 Chain: "D" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 85 Unusual residues: {' ZN': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "A" 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 Time building chain proxies: 1.61, per 1000 atoms: 0.23 Number of scatterers: 6891 At special positions: 0 Unit cell: (72.226, 99.176, 140.14, 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 39 16.00 O 1316 8.00 N 1131 7.00 C 4404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, 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=2.03 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 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " 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 NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG D 902 " - " ASN D 53 " " NAG D 903 " - " ASN D 90 " " NAG D 904 " - " ASN D 322 " " NAG D 905 " - " ASN D 432 " " NAG D 906 " - " ASN D 546 " " NAG D 907 " - " ASN D 103 " Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 411.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 901 " pdb="ZN ZN D 901 " - pdb=" NE2 HIS D 378 " pdb="ZN ZN D 901 " - pdb=" NE2 HIS D 374 " 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1578 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 7 sheets defined 51.1% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.845A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLU D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 3.804A pdb=" N VAL D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.678A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 146 through 155 removed outlier: 3.756A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 173 Processing helix chain 'D' and resid 176 through 194 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 218 through 223 removed outlier: 3.706A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 218 through 223' Processing helix chain 'D' and resid 226 through 233 Processing helix chain 'D' and resid 233 through 249 Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 281 removed outlier: 4.042A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 301 Processing helix chain 'D' and resid 305 through 319 removed outlier: 3.526A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 removed outlier: 4.183A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.800A pdb=" N ALA D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.505A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.627A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 4.061A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 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 removed outlier: 3.521A pdb=" N SER D 507 " --> pdb=" O LEU D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 533 removed outlier: 4.234A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.652A 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 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.982A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.185A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.741A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.162A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 347 through 352 removed outlier: 5.999A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.952A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A 584 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.780A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 392 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 474 310 hydrogen bonds defined for protein. 879 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: 0.87 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2194 1.34 - 1.46: 1764 1.46 - 1.58: 3057 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 7075 Sorted by residual: bond pdb=" C1 NAG D 907 " pdb=" O5 NAG D 907 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.19e+00 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" C1 NAG D 904 " pdb=" O5 NAG D 904 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.47e+00 bond pdb=" C1 NAG D 906 " pdb=" O5 NAG D 906 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.44e+00 bond pdb=" CB CYS D 530 " pdb=" SG CYS D 530 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.42e+00 ... (remaining 7070 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 9332 1.64 - 3.27: 237 3.27 - 4.91: 34 4.91 - 6.54: 6 6.54 - 8.18: 4 Bond angle restraints: 9613 Sorted by residual: angle pdb=" C ILE D 233 " pdb=" CA ILE D 233 " pdb=" CB ILE D 233 " ideal model delta sigma weight residual 111.29 104.99 6.30 1.64e+00 3.72e-01 1.48e+01 angle pdb=" C HIS D 34 " pdb=" N GLU D 35 " pdb=" CA GLU D 35 " ideal model delta sigma weight residual 121.54 126.81 -5.27 1.91e+00 2.74e-01 7.62e+00 angle pdb=" N GLU D 224 " pdb=" CA GLU D 224 " pdb=" C GLU D 224 " ideal model delta sigma weight residual 109.86 106.08 3.78 1.55e+00 4.16e-01 5.94e+00 angle pdb=" N HIS D 401 " pdb=" CA HIS D 401 " pdb=" C HIS D 401 " ideal model delta sigma weight residual 113.12 110.21 2.91 1.25e+00 6.40e-01 5.42e+00 angle pdb=" N ILE D 233 " pdb=" CA ILE D 233 " pdb=" CB ILE D 233 " ideal model delta sigma weight residual 111.23 114.94 -3.71 1.65e+00 3.67e-01 5.06e+00 ... (remaining 9608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 3704 17.02 - 34.04: 339 34.04 - 51.07: 57 51.07 - 68.09: 8 68.09 - 85.11: 10 Dihedral angle restraints: 4118 sinusoidal: 1661 harmonic: 2457 Sorted by residual: dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 31.45 61.55 1 1.00e+01 1.00e-02 5.03e+01 dihedral pdb=" CB CYS D 530 " pdb=" SG CYS D 530 " pdb=" SG CYS D 542 " pdb=" CB CYS D 542 " ideal model delta sinusoidal sigma weight residual 93.00 129.07 -36.07 1 1.00e+01 1.00e-02 1.84e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -119.29 33.29 1 1.00e+01 1.00e-02 1.58e+01 ... (remaining 4115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 910 0.067 - 0.135: 125 0.135 - 0.202: 5 0.202 - 0.269: 1 0.269 - 0.336: 1 Chirality restraints: 1042 Sorted by residual: chirality pdb=" C1 NAG D 907 " pdb=" ND2 ASN D 103 " pdb=" C2 NAG D 907 " pdb=" O5 NAG D 907 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.51e-01 ... (remaining 1039 not shown) Planarity restraints: 1239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 35 " 0.019 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C GLU D 35 " -0.064 2.00e-02 2.50e+03 pdb=" O GLU D 35 " 0.023 2.00e-02 2.50e+03 pdb=" N ALA D 36 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 145 " 0.040 5.00e-02 4.00e+02 6.08e-02 5.91e+00 pdb=" N PRO D 146 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 146 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 146 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 103 " 0.004 2.00e-02 2.50e+03 2.13e-02 5.66e+00 pdb=" CG ASN D 103 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN D 103 " 0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN D 103 " -0.024 2.00e-02 2.50e+03 pdb=" C1 NAG D 907 " 0.021 2.00e-02 2.50e+03 ... (remaining 1236 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 709 2.74 - 3.28: 6443 3.28 - 3.82: 10488 3.82 - 4.36: 12373 4.36 - 4.90: 22418 Nonbonded interactions: 52431 Sorted by model distance: nonbonded pdb=" OD1 ASN D 103 " pdb=" OG SER D 106 " model vdw 2.203 3.040 nonbonded pdb=" NH2 ARG A 454 " pdb=" O SER A 469 " model vdw 2.245 3.120 nonbonded pdb=" OE1 GLU D 402 " pdb="ZN ZN D 901 " model vdw 2.255 2.230 nonbonded pdb=" NH1 ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 2.291 3.120 nonbonded pdb=" OE1 GLU A 406 " pdb=" OH TYR A 495 " model vdw 2.393 3.040 ... (remaining 52426 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 group one per residue 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: 4.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.900 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7093 Z= 0.218 Angle : 0.697 18.235 9653 Z= 0.344 Chirality : 0.047 0.336 1042 Planarity : 0.005 0.061 1231 Dihedral : 13.435 85.110 2516 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.47 (0.28), residues: 831 helix: 1.31 (0.28), residues: 356 sheet: 0.93 (0.58), residues: 70 loop : -0.70 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 328 TYR 0.020 0.002 TYR A 495 PHE 0.027 0.002 PHE D 369 TRP 0.012 0.001 TRP D 165 HIS 0.009 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.22 ( 7075) covalent geometry : angle 0.64044 / 0.33 ( 9613) SS BOND : bond 0.00250 / 0.16 ( 8) SS BOND : angle 0.96235 / 0.56 ( 16) hydrogen bonds : bond 0.16272 / 10.56 ( 310) hydrogen bonds : angle 5.75073 / 4.13 ( 879) metal coordination : bond 0.00288 / 0.14 ( 2) link_NAG-ASN : bond 0.01070 / 0.55 ( 8) link_NAG-ASN : angle 5.53804 / 3.21 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 438 SER cc_start: 0.8988 (t) cc_final: 0.8701 (t) REVERT: A 574 ASP cc_start: 0.6738 (m-30) cc_final: 0.6344 (t0) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.0616 time to fit residues: 8.6862 Evaluate side-chains 71 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 0.0980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.0970 chunk 51 optimal weight: 0.0370 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.1856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 401 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.189465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.174436 restraints weight = 7733.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.161427 restraints weight = 13730.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.159538 restraints weight = 12442.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.160692 restraints weight = 10316.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.160537 restraints weight = 8571.767| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7093 Z= 0.106 Angle : 0.560 16.901 9653 Z= 0.272 Chirality : 0.041 0.187 1042 Planarity : 0.004 0.035 1231 Dihedral : 4.334 17.950 908 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.41 % Allowed : 6.63 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.78 (0.28), residues: 831 helix: 1.47 (0.27), residues: 374 sheet: 1.15 (0.59), residues: 70 loop : -0.53 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 328 TYR 0.017 0.001 TYR D 183 PHE 0.013 0.001 PHE D 369 TRP 0.009 0.001 TRP D 165 HIS 0.003 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 ( 7075) covalent geometry : angle 0.50750 / 0.26 ( 9613) SS BOND : bond 0.00159 / 0.09 ( 8) SS BOND : angle 0.56969 / 0.35 ( 16) hydrogen bonds : bond 0.04646 / 3.04 ( 310) hydrogen bonds : angle 4.51205 / 3.23 ( 879) metal coordination : bond 0.00032 / 0.02 ( 2) link_NAG-ASN : bond 0.00745 / 0.39 ( 8) link_NAG-ASN : angle 4.77662 / 2.75 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 438 SER cc_start: 0.8887 (t) cc_final: 0.8500 (t) outliers start: 3 outliers final: 2 residues processed: 85 average time/residue: 0.0605 time to fit residues: 7.6793 Evaluate side-chains 78 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain A residue 390 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 57 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.158666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.125061 restraints weight = 7944.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.124935 restraints weight = 8440.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.125467 restraints weight = 9347.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.126314 restraints weight = 6815.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.126657 restraints weight = 5905.382| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7093 Z= 0.207 Angle : 0.626 15.176 9653 Z= 0.314 Chirality : 0.045 0.201 1042 Planarity : 0.004 0.040 1231 Dihedral : 4.555 19.701 908 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.49 % Allowed : 9.47 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.53 (0.28), residues: 831 helix: 1.28 (0.27), residues: 369 sheet: 1.09 (0.59), residues: 69 loop : -0.66 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 357 TYR 0.016 0.002 TYR D 587 PHE 0.026 0.002 PHE D 369 TRP 0.013 0.001 TRP A 436 HIS 0.009 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 ( 7075) covalent geometry : angle 0.58582 / 0.31 ( 9613) SS BOND : bond 0.00268 / 0.17 ( 8) SS BOND : angle 0.79427 / 0.48 ( 16) hydrogen bonds : bond 0.05909 / 3.86 ( 310) hydrogen bonds : angle 4.62434 / 3.29 ( 879) metal coordination : bond 0.00197 / 0.09 ( 2) link_NAG-ASN : bond 0.00699 / 0.36 ( 8) link_NAG-ASN : angle 4.43368 / 2.55 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 471 ASP cc_start: 0.7687 (t0) cc_final: 0.7249 (t0) REVERT: A 358 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8088 (mt) REVERT: A 438 SER cc_start: 0.9019 (t) cc_final: 0.8621 (t) outliers start: 11 outliers final: 7 residues processed: 82 average time/residue: 0.0594 time to fit residues: 7.2846 Evaluate side-chains 78 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 28 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 0.0980 chunk 82 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.159594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.125114 restraints weight = 7908.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.126054 restraints weight = 8838.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.127040 restraints weight = 8008.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.126470 restraints weight = 6995.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.127087 restraints weight = 5588.906| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7093 Z= 0.164 Angle : 0.585 14.327 9653 Z= 0.290 Chirality : 0.043 0.185 1042 Planarity : 0.004 0.038 1231 Dihedral : 4.480 18.809 908 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.03 % Allowed : 10.42 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.53 (0.28), residues: 831 helix: 1.31 (0.27), residues: 369 sheet: 1.06 (0.59), residues: 69 loop : -0.69 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 328 TYR 0.014 0.002 TYR D 183 PHE 0.022 0.002 PHE D 369 TRP 0.012 0.001 TRP A 436 HIS 0.006 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 ( 7075) covalent geometry : angle 0.54616 / 0.28 ( 9613) SS BOND : bond 0.00200 / 0.12 ( 8) SS BOND : angle 0.66355 / 0.40 ( 16) hydrogen bonds : bond 0.05204 / 3.39 ( 310) hydrogen bonds : angle 4.53182 / 3.21 ( 879) metal coordination : bond 0.00144 / 0.07 ( 2) link_NAG-ASN : bond 0.00668 / 0.34 ( 8) link_NAG-ASN : angle 4.19993 / 2.40 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: D 78 THR cc_start: 0.8053 (m) cc_final: 0.7689 (m) REVERT: D 471 ASP cc_start: 0.7595 (t0) cc_final: 0.7074 (t0) REVERT: A 358 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8064 (mt) REVERT: A 420 ASP cc_start: 0.8269 (m-30) cc_final: 0.7852 (m-30) REVERT: A 438 SER cc_start: 0.9016 (t) cc_final: 0.8584 (t) outliers start: 15 outliers final: 10 residues processed: 83 average time/residue: 0.0595 time to fit residues: 7.5552 Evaluate side-chains 83 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 39 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 60 optimal weight: 0.0970 chunk 76 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.159795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.124473 restraints weight = 7978.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.123372 restraints weight = 8807.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.124415 restraints weight = 7502.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.124996 restraints weight = 6199.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.125790 restraints weight = 5646.315| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7093 Z= 0.153 Angle : 0.568 14.042 9653 Z= 0.281 Chirality : 0.042 0.182 1042 Planarity : 0.004 0.037 1231 Dihedral : 4.372 18.962 908 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.30 % Allowed : 10.55 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.56 (0.28), residues: 831 helix: 1.35 (0.27), residues: 369 sheet: 1.00 (0.59), residues: 69 loop : -0.67 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 357 TYR 0.014 0.001 TYR D 183 PHE 0.021 0.002 PHE D 369 TRP 0.012 0.001 TRP A 436 HIS 0.006 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 ( 7075) covalent geometry : angle 0.53054 / 0.27 ( 9613) SS BOND : bond 0.00186 / 0.11 ( 8) SS BOND : angle 0.63571 / 0.39 ( 16) hydrogen bonds : bond 0.04938 / 3.22 ( 310) hydrogen bonds : angle 4.47133 / 3.17 ( 879) metal coordination : bond 0.00116 / 0.06 ( 2) link_NAG-ASN : bond 0.00706 / 0.36 ( 8) link_NAG-ASN : angle 4.10642 / 2.35 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: D 78 THR cc_start: 0.8001 (m) cc_final: 0.7649 (m) REVERT: D 471 ASP cc_start: 0.7626 (t0) cc_final: 0.7081 (t0) REVERT: A 358 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8044 (mt) REVERT: A 438 SER cc_start: 0.9012 (t) cc_final: 0.8604 (t) outliers start: 17 outliers final: 7 residues processed: 83 average time/residue: 0.0655 time to fit residues: 8.2308 Evaluate side-chains 77 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 61 optimal weight: 0.3980 chunk 13 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 75 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 chunk 66 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.160129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.124725 restraints weight = 7962.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.124521 restraints weight = 8709.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.124924 restraints weight = 7700.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.126035 restraints weight = 6468.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.126260 restraints weight = 5471.071| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7093 Z= 0.142 Angle : 0.559 13.513 9653 Z= 0.276 Chirality : 0.042 0.184 1042 Planarity : 0.004 0.037 1231 Dihedral : 4.316 18.135 908 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.89 % Allowed : 11.23 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.62 (0.28), residues: 831 helix: 1.41 (0.27), residues: 369 sheet: 1.14 (0.58), residues: 66 loop : -0.66 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 357 TYR 0.013 0.001 TYR D 183 PHE 0.018 0.001 PHE D 369 TRP 0.012 0.001 TRP A 436 HIS 0.004 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 7075) covalent geometry : angle 0.52245 / 0.27 ( 9613) SS BOND : bond 0.00174 / 0.10 ( 8) SS BOND : angle 0.59486 / 0.36 ( 16) hydrogen bonds : bond 0.04744 / 3.09 ( 310) hydrogen bonds : angle 4.43425 / 3.14 ( 879) metal coordination : bond 0.00136 / 0.07 ( 2) link_NAG-ASN : bond 0.00646 / 0.34 ( 8) link_NAG-ASN : angle 4.00802 / 2.29 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: D 78 THR cc_start: 0.7949 (m) cc_final: 0.7621 (m) REVERT: D 471 ASP cc_start: 0.7663 (t0) cc_final: 0.7111 (t0) REVERT: A 358 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8046 (mt) REVERT: A 438 SER cc_start: 0.9009 (t) cc_final: 0.8585 (t) outliers start: 14 outliers final: 10 residues processed: 81 average time/residue: 0.0544 time to fit residues: 6.8081 Evaluate side-chains 84 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 522 GLN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 71 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.0470 chunk 24 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 27 optimal weight: 0.6980 chunk 56 optimal weight: 0.1980 chunk 55 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 0.0060 chunk 82 optimal weight: 3.9990 overall best weight: 0.2894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.163104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.125697 restraints weight = 7838.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.127996 restraints weight = 5845.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.129632 restraints weight = 4834.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.130524 restraints weight = 4294.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.130765 restraints weight = 3971.951| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7093 Z= 0.107 Angle : 0.528 12.436 9653 Z= 0.257 Chirality : 0.040 0.184 1042 Planarity : 0.003 0.036 1231 Dihedral : 4.107 17.002 908 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.08 % Allowed : 12.99 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.82 (0.29), residues: 831 helix: 1.60 (0.28), residues: 368 sheet: 1.11 (0.58), residues: 71 loop : -0.59 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 328 TYR 0.025 0.001 TYR D 279 PHE 0.013 0.001 PHE D 369 TRP 0.011 0.001 TRP A 436 HIS 0.002 0.000 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 7075) covalent geometry : angle 0.49623 / 0.25 ( 9613) SS BOND : bond 0.00134 / 0.08 ( 8) SS BOND : angle 0.51517 / 0.31 ( 16) hydrogen bonds : bond 0.04013 / 2.61 ( 310) hydrogen bonds : angle 4.29919 / 3.06 ( 879) metal coordination : bond 0.00111 / 0.05 ( 2) link_NAG-ASN : bond 0.00624 / 0.33 ( 8) link_NAG-ASN : angle 3.66939 / 2.10 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: D 78 THR cc_start: 0.7859 (m) cc_final: 0.7522 (m) REVERT: D 270 MET cc_start: 0.8101 (tpp) cc_final: 0.7895 (tpp) REVERT: D 406 GLU cc_start: 0.8248 (tp30) cc_final: 0.7921 (tp30) REVERT: D 471 ASP cc_start: 0.7662 (t0) cc_final: 0.7100 (t0) REVERT: D 584 LEU cc_start: 0.8479 (tt) cc_final: 0.8240 (tt) REVERT: A 358 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.7939 (mt) REVERT: A 438 SER cc_start: 0.8997 (t) cc_final: 0.8556 (t) outliers start: 8 outliers final: 4 residues processed: 84 average time/residue: 0.0572 time to fit residues: 7.2428 Evaluate side-chains 81 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 358 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 25 optimal weight: 0.0370 chunk 26 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.159966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.125796 restraints weight = 7944.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.124839 restraints weight = 9385.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.127509 restraints weight = 8296.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.127379 restraints weight = 6026.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.127443 restraints weight = 5368.701| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7093 Z= 0.150 Angle : 0.558 12.321 9653 Z= 0.276 Chirality : 0.042 0.184 1042 Planarity : 0.004 0.037 1231 Dihedral : 4.219 17.758 908 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.49 % Allowed : 12.45 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.29), residues: 831 helix: 1.51 (0.28), residues: 369 sheet: 1.09 (0.59), residues: 66 loop : -0.65 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 357 TYR 0.026 0.002 TYR D 279 PHE 0.021 0.002 PHE D 369 TRP 0.010 0.001 TRP A 436 HIS 0.004 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 7075) covalent geometry : angle 0.52743 / 0.27 ( 9613) SS BOND : bond 0.00186 / 0.12 ( 8) SS BOND : angle 0.60201 / 0.37 ( 16) hydrogen bonds : bond 0.04777 / 3.11 ( 310) hydrogen bonds : angle 4.38557 / 3.11 ( 879) metal coordination : bond 0.00157 / 0.08 ( 2) link_NAG-ASN : bond 0.00585 / 0.30 ( 8) link_NAG-ASN : angle 3.71164 / 2.12 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.230 Fit side-chains REVERT: D 78 THR cc_start: 0.7956 (m) cc_final: 0.7612 (m) REVERT: D 471 ASP cc_start: 0.7688 (t0) cc_final: 0.7131 (t0) REVERT: A 358 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.7967 (mt) REVERT: A 438 SER cc_start: 0.9034 (t) cc_final: 0.8589 (t) outliers start: 11 outliers final: 8 residues processed: 80 average time/residue: 0.0534 time to fit residues: 6.6220 Evaluate side-chains 80 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 522 GLN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 26 optimal weight: 0.0970 chunk 62 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 41 optimal weight: 0.0980 chunk 61 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 23 optimal weight: 0.0020 chunk 42 optimal weight: 0.2980 chunk 73 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.163993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.128898 restraints weight = 7917.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.128598 restraints weight = 8650.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.129354 restraints weight = 7629.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.130206 restraints weight = 6304.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.130720 restraints weight = 5350.832| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7093 Z= 0.100 Angle : 0.516 10.927 9653 Z= 0.251 Chirality : 0.040 0.185 1042 Planarity : 0.003 0.035 1231 Dihedral : 4.028 16.398 908 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.35 % Allowed : 13.13 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.90 (0.29), residues: 831 helix: 1.69 (0.27), residues: 368 sheet: 1.19 (0.59), residues: 71 loop : -0.57 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 328 TYR 0.023 0.001 TYR D 279 PHE 0.012 0.001 PHE D 369 TRP 0.011 0.001 TRP A 436 HIS 0.003 0.000 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 7075) covalent geometry : angle 0.48984 / 0.25 ( 9613) SS BOND : bond 0.00171 / 0.11 ( 8) SS BOND : angle 0.68179 / 0.40 ( 16) hydrogen bonds : bond 0.03793 / 2.47 ( 310) hydrogen bonds : angle 4.25729 / 3.03 ( 879) metal coordination : bond 0.00092 / 0.04 ( 2) link_NAG-ASN : bond 0.00574 / 0.31 ( 8) link_NAG-ASN : angle 3.29233 / 1.88 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.170 Fit side-chains REVERT: D 78 THR cc_start: 0.7833 (m) cc_final: 0.7512 (m) REVERT: D 156 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8446 (tt) REVERT: D 406 GLU cc_start: 0.8229 (tp30) cc_final: 0.7932 (tp30) REVERT: D 471 ASP cc_start: 0.7688 (t0) cc_final: 0.7065 (t0) REVERT: D 584 LEU cc_start: 0.8508 (tt) cc_final: 0.8287 (tt) REVERT: A 438 SER cc_start: 0.8940 (t) cc_final: 0.8514 (t) outliers start: 10 outliers final: 7 residues processed: 87 average time/residue: 0.0515 time to fit residues: 6.8335 Evaluate side-chains 87 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 440 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 78 optimal weight: 0.6980 chunk 29 optimal weight: 0.0980 chunk 66 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 67 optimal weight: 0.0970 chunk 27 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.162120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.128139 restraints weight = 7930.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.127356 restraints weight = 9250.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.129282 restraints weight = 8596.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.129438 restraints weight = 6117.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.129522 restraints weight = 5597.314| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7093 Z= 0.128 Angle : 0.537 10.565 9653 Z= 0.266 Chirality : 0.041 0.191 1042 Planarity : 0.003 0.036 1231 Dihedral : 4.072 16.807 908 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.22 % Allowed : 13.40 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.96 (0.29), residues: 831 helix: 1.80 (0.28), residues: 362 sheet: 1.27 (0.59), residues: 68 loop : -0.56 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 357 TYR 0.024 0.001 TYR D 279 PHE 0.017 0.001 PHE D 369 TRP 0.010 0.001 TRP A 436 HIS 0.004 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 7075) covalent geometry : angle 0.51229 / 0.26 ( 9613) SS BOND : bond 0.00161 / 0.10 ( 8) SS BOND : angle 0.74077 / 0.43 ( 16) hydrogen bonds : bond 0.04313 / 2.81 ( 310) hydrogen bonds : angle 4.28262 / 3.05 ( 879) metal coordination : bond 0.00123 / 0.06 ( 2) link_NAG-ASN : bond 0.00540 / 0.28 ( 8) link_NAG-ASN : angle 3.26064 / 1.87 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.252 Fit side-chains REVERT: D 78 THR cc_start: 0.7915 (m) cc_final: 0.7585 (m) REVERT: D 156 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8477 (tt) REVERT: D 406 GLU cc_start: 0.8272 (tp30) cc_final: 0.7958 (tp30) REVERT: D 471 ASP cc_start: 0.7693 (t0) cc_final: 0.7119 (t0) REVERT: A 358 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.7931 (mt) REVERT: A 438 SER cc_start: 0.9034 (t) cc_final: 0.8592 (t) outliers start: 9 outliers final: 7 residues processed: 83 average time/residue: 0.0474 time to fit residues: 6.0025 Evaluate side-chains 85 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 440 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 26 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 chunk 13 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 0.0770 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.161093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.127893 restraints weight = 7913.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.126884 restraints weight = 9665.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.129049 restraints weight = 8709.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.128461 restraints weight = 6252.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.128912 restraints weight = 5590.242| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7093 Z= 0.145 Angle : 0.566 10.276 9653 Z= 0.279 Chirality : 0.042 0.204 1042 Planarity : 0.004 0.036 1231 Dihedral : 4.166 16.978 908 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.49 % Allowed : 13.26 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.89 (0.29), residues: 831 helix: 1.72 (0.28), residues: 362 sheet: 1.31 (0.59), residues: 68 loop : -0.60 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 357 TYR 0.024 0.001 TYR D 279 PHE 0.019 0.001 PHE D 369 TRP 0.009 0.001 TRP D 165 HIS 0.005 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 7075) covalent geometry : angle 0.53839 / 0.27 ( 9613) SS BOND : bond 0.00275 / 0.19 ( 8) SS BOND : angle 1.83152 / 1.26 ( 16) hydrogen bonds : bond 0.04558 / 2.96 ( 310) hydrogen bonds : angle 4.41319 / 3.17 ( 879) metal coordination : bond 0.00129 / 0.06 ( 2) link_NAG-ASN : bond 0.00524 / 0.28 ( 8) link_NAG-ASN : angle 3.22775 / 1.85 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1142.18 seconds wall clock time: 20 minutes 28.46 seconds (1228.46 seconds total)