Starting phenix.real_space_refine on Fri Aug 22 18:48:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r0z_14225/08_2025/7r0z_14225.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r0z_14225/08_2025/7r0z_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 { model { file = "/net/cci-nas-00/data/ceres_data/7r0z_14225/08_2025/7r0z_14225.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r0z_14225/08_2025/7r0z_14225.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r0z_14225/08_2025/7r0z_14225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r0z_14225/08_2025/7r0z_14225.map" } 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-2.0-5787/lib/python3.9/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 dihedrals: 18 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.88, per 1000 atoms: 0.27 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: 0.66 Conformation dependent library (CDL) restraints added in 457.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.24 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: 1.00 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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: 3851 17.02 - 34.04: 350 34.04 - 51.07: 59 51.07 - 68.09: 16 68.09 - 85.11: 10 Dihedral angle restraints: 4286 sinusoidal: 1829 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 4283 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: 4.580 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.010 Find NCS groups from input model: 0.040 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 : 13.556 85.110 2684 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 aren 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 covalent geometry : bond 0.00512 ( 7075) covalent geometry : angle 0.64044 ( 9613) SS BOND : bond 0.00250 ( 8) SS BOND : angle 0.96235 ( 16) hydrogen bonds : bond 0.16272 ( 310) hydrogen bonds : angle 5.75073 ( 879) metal coordination : bond 0.00288 ( 2) link_NAG-ASN : bond 0.01070 ( 8) link_NAG-ASN : angle 5.53804 ( 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 : 0.159 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: 0.0565 time to fit residues: 7.9277 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 : 0.168 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: D 401 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.189407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.172837 restraints weight = 7734.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.160209 restraints weight = 13776.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.158092 restraints weight = 10634.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.158454 restraints weight = 10091.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.158567 restraints weight = 7948.622| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7093 Z= 0.106 Angle : 0.562 16.643 9653 Z= 0.274 Chirality : 0.041 0.196 1042 Planarity : 0.004 0.035 1231 Dihedral : 6.446 56.710 1076 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.41 % Allowed : 6.50 % Favored : 93.10 % 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 aren not related in a simple way. whole: 0.78 (0.28), residues: 831 helix: 1.48 (0.27), residues: 374 sheet: 1.14 (0.59), residues: 70 loop : -0.54 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 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 covalent geometry : bond 0.00217 ( 7075) covalent geometry : angle 0.50957 ( 9613) SS BOND : bond 0.00163 ( 8) SS BOND : angle 0.58340 ( 16) hydrogen bonds : bond 0.04601 ( 310) hydrogen bonds : angle 4.51279 ( 879) metal coordination : bond 0.00029 ( 2) link_NAG-ASN : bond 0.00673 ( 8) link_NAG-ASN : angle 4.79295 ( 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 : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 438 SER cc_start: 0.8900 (t) cc_final: 0.8521 (t) outliers start: 3 outliers final: 2 residues processed: 85 average time/residue: 0.0606 time to fit residues: 7.7735 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 : 0.296 ------------------------------------------------------------------------------- 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: 0.5980 chunk 62 optimal weight: 0.1980 chunk 42 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.184818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.167051 restraints weight = 7803.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.155949 restraints weight = 14303.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.153267 restraints weight = 10154.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.153816 restraints weight = 9546.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.154215 restraints weight = 8104.295| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7093 Z= 0.169 Angle : 0.589 15.239 9653 Z= 0.293 Chirality : 0.043 0.192 1042 Planarity : 0.004 0.036 1231 Dihedral : 6.382 59.912 1076 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.35 % Allowed : 9.47 % Favored : 89.17 % 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 aren not related in a simple way. whole: 0.70 (0.28), residues: 831 helix: 1.44 (0.27), residues: 368 sheet: 1.16 (0.58), residues: 71 loop : -0.61 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 328 TYR 0.016 0.002 TYR A 495 PHE 0.022 0.002 PHE D 327 TRP 0.011 0.001 TRP A 436 HIS 0.008 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 7075) covalent geometry : angle 0.54564 ( 9613) SS BOND : bond 0.00223 ( 8) SS BOND : angle 0.70067 ( 16) hydrogen bonds : bond 0.05393 ( 310) hydrogen bonds : angle 4.52421 ( 879) metal coordination : bond 0.00139 ( 2) link_NAG-ASN : bond 0.00677 ( 8) link_NAG-ASN : angle 4.45611 ( 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: 10 poor density : 76 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 471 ASP cc_start: 0.7684 (t0) cc_final: 0.7246 (t0) REVERT: A 358 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8066 (mt) REVERT: A 438 SER cc_start: 0.9024 (t) cc_final: 0.8615 (t) outliers start: 10 outliers final: 6 residues processed: 82 average time/residue: 0.0649 time to fit residues: 7.9775 Evaluate side-chains 79 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 52 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.159238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.125556 restraints weight = 7919.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.125075 restraints weight = 8241.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.125494 restraints weight = 9546.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.125977 restraints weight = 7065.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.126589 restraints weight = 6101.764| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7093 Z= 0.181 Angle : 0.597 14.710 9653 Z= 0.297 Chirality : 0.044 0.193 1042 Planarity : 0.004 0.037 1231 Dihedral : 6.378 59.491 1076 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.76 % Allowed : 10.28 % Favored : 87.96 % 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 aren not related in a simple way. whole: 0.54 (0.28), residues: 831 helix: 1.31 (0.27), residues: 369 sheet: 1.10 (0.59), residues: 69 loop : -0.69 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 357 TYR 0.014 0.002 TYR D 183 PHE 0.024 0.002 PHE D 369 TRP 0.013 0.001 TRP A 436 HIS 0.007 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 7075) covalent geometry : angle 0.55621 ( 9613) SS BOND : bond 0.00216 ( 8) SS BOND : angle 0.72353 ( 16) hydrogen bonds : bond 0.05370 ( 310) hydrogen bonds : angle 4.55072 ( 879) metal coordination : bond 0.00169 ( 2) link_NAG-ASN : bond 0.00667 ( 8) link_NAG-ASN : angle 4.37077 ( 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: 13 poor density : 76 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: D 78 THR cc_start: 0.8065 (m) cc_final: 0.7714 (m) REVERT: D 471 ASP cc_start: 0.7617 (t0) cc_final: 0.7106 (t0) REVERT: A 358 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8018 (mt) REVERT: A 420 ASP cc_start: 0.8264 (m-30) cc_final: 0.7845 (m-30) REVERT: A 438 SER cc_start: 0.9023 (t) cc_final: 0.8613 (t) outliers start: 13 outliers final: 9 residues processed: 84 average time/residue: 0.0636 time to fit residues: 7.8235 Evaluate side-chains 82 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 5 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 31 optimal weight: 0.3980 chunk 60 optimal weight: 0.1980 chunk 76 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.160163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.125165 restraints weight = 7975.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.124390 restraints weight = 7947.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.125123 restraints weight = 6963.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.125870 restraints weight = 6259.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.126177 restraints weight = 5450.686| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7093 Z= 0.144 Angle : 0.560 14.763 9653 Z= 0.276 Chirality : 0.042 0.193 1042 Planarity : 0.004 0.037 1231 Dihedral : 6.224 58.678 1076 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.17 % Allowed : 10.55 % Favored : 87.28 % 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 aren not related in a simple way. whole: 0.59 (0.28), residues: 831 helix: 1.39 (0.27), residues: 369 sheet: 1.04 (0.59), residues: 69 loop : -0.68 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 328 TYR 0.013 0.001 TYR D 183 PHE 0.020 0.001 PHE D 369 TRP 0.012 0.001 TRP A 436 HIS 0.006 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 7075) covalent geometry : angle 0.51729 ( 9613) SS BOND : bond 0.00175 ( 8) SS BOND : angle 0.61507 ( 16) hydrogen bonds : bond 0.04853 ( 310) hydrogen bonds : angle 4.45690 ( 879) metal coordination : bond 0.00110 ( 2) link_NAG-ASN : bond 0.00710 ( 8) link_NAG-ASN : angle 4.34058 ( 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: 16 poor density : 73 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: D 78 THR cc_start: 0.7977 (m) cc_final: 0.7627 (m) REVERT: D 471 ASP cc_start: 0.7622 (t0) cc_final: 0.7074 (t0) REVERT: A 358 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8050 (mt) REVERT: A 438 SER cc_start: 0.8988 (t) cc_final: 0.8571 (t) outliers start: 16 outliers final: 7 residues processed: 84 average time/residue: 0.0542 time to fit residues: 7.1366 Evaluate side-chains 80 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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: 0.0270 chunk 13 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 75 optimal weight: 0.0980 chunk 44 optimal weight: 0.9990 chunk 66 optimal weight: 0.2980 chunk 78 optimal weight: 1.9990 overall best weight: 0.3438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.162342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.127764 restraints weight = 7945.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.126718 restraints weight = 7904.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.127337 restraints weight = 7114.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.128065 restraints weight = 6521.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.128442 restraints weight = 5716.173| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7093 Z= 0.115 Angle : 0.535 14.292 9653 Z= 0.263 Chirality : 0.041 0.192 1042 Planarity : 0.003 0.036 1231 Dihedral : 6.030 56.347 1076 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.35 % Allowed : 11.50 % 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 aren not related in a simple way. whole: 0.79 (0.29), residues: 831 helix: 1.55 (0.27), residues: 369 sheet: 1.17 (0.58), residues: 71 loop : -0.59 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 328 TYR 0.013 0.001 TYR D 183 PHE 0.015 0.001 PHE D 369 TRP 0.011 0.001 TRP A 436 HIS 0.003 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 7075) covalent geometry : angle 0.49357 ( 9613) SS BOND : bond 0.00140 ( 8) SS BOND : angle 0.54600 ( 16) hydrogen bonds : bond 0.04267 ( 310) hydrogen bonds : angle 4.35025 ( 879) metal coordination : bond 0.00087 ( 2) link_NAG-ASN : bond 0.00669 ( 8) link_NAG-ASN : angle 4.18851 ( 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 86 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: D 78 THR cc_start: 0.7938 (m) cc_final: 0.7600 (m) REVERT: D 471 ASP cc_start: 0.7668 (t0) cc_final: 0.7124 (t0) REVERT: A 358 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.7955 (mt) REVERT: A 438 SER cc_start: 0.8950 (t) cc_final: 0.8520 (t) outliers start: 10 outliers final: 5 residues processed: 84 average time/residue: 0.0548 time to fit residues: 7.0529 Evaluate side-chains 81 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 A residue 336 CYS Chi-restraints excluded: chain A residue 358 ILE 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: 0.1980 chunk 24 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 chunk 27 optimal weight: 0.0470 chunk 56 optimal weight: 0.4980 chunk 55 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 overall best weight: 0.2878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.163849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.126897 restraints weight = 7849.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.129663 restraints weight = 6002.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.130587 restraints weight = 4911.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.131259 restraints weight = 4319.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.131542 restraints weight = 4030.371| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1659 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= 0.105 Angle : 0.526 13.569 9653 Z= 0.255 Chirality : 0.040 0.190 1042 Planarity : 0.003 0.035 1231 Dihedral : 5.892 55.959 1076 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.22 % Allowed : 12.04 % Favored : 86.74 % 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 aren not related in a simple way. whole: 0.90 (0.29), residues: 831 helix: 1.69 (0.28), residues: 368 sheet: 1.15 (0.58), residues: 71 loop : -0.55 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 328 TYR 0.023 0.001 TYR D 279 PHE 0.014 0.001 PHE D 369 TRP 0.010 0.001 TRP A 436 HIS 0.003 0.000 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 7075) covalent geometry : angle 0.48789 ( 9613) SS BOND : bond 0.00143 ( 8) SS BOND : angle 0.52108 ( 16) hydrogen bonds : bond 0.03937 ( 310) hydrogen bonds : angle 4.25500 ( 879) metal coordination : bond 0.00088 ( 2) link_NAG-ASN : bond 0.00621 ( 8) link_NAG-ASN : angle 3.99440 ( 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 91 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.252 Fit side-chains REVERT: D 78 THR cc_start: 0.7837 (m) cc_final: 0.7499 (m) REVERT: D 383 MET cc_start: 0.8971 (mtt) cc_final: 0.8721 (mtp) REVERT: D 406 GLU cc_start: 0.8259 (tp30) cc_final: 0.7903 (tp30) REVERT: D 471 ASP cc_start: 0.7696 (t0) cc_final: 0.7126 (t0) REVERT: D 584 LEU cc_start: 0.8442 (tt) cc_final: 0.8213 (tt) REVERT: A 358 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.7907 (mt) REVERT: A 438 SER cc_start: 0.8989 (t) cc_final: 0.8540 (t) outliers start: 9 outliers final: 6 residues processed: 87 average time/residue: 0.0622 time to fit residues: 8.1292 Evaluate side-chains 86 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.175 ------------------------------------------------------------------------------- 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 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 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: 0.2980 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 75 optimal weight: 0.3980 chunk 66 optimal weight: 0.4980 chunk 25 optimal weight: 0.0020 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 overall best weight: 0.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.163533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.129665 restraints weight = 7953.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.129042 restraints weight = 8113.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.129439 restraints weight = 9101.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.131361 restraints weight = 7306.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.131262 restraints weight = 6081.306| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7093 Z= 0.109 Angle : 0.526 13.277 9653 Z= 0.256 Chirality : 0.040 0.191 1042 Planarity : 0.003 0.035 1231 Dihedral : 5.887 56.075 1076 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % 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 aren not related in a simple way. whole: 0.94 (0.29), residues: 831 helix: 1.73 (0.28), residues: 368 sheet: 1.17 (0.59), residues: 71 loop : -0.55 (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 0.015 0.001 PHE D 369 TRP 0.009 0.001 TRP A 436 HIS 0.003 0.000 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 7075) covalent geometry : angle 0.48852 ( 9613) SS BOND : bond 0.00241 ( 8) SS BOND : angle 0.62759 ( 16) hydrogen bonds : bond 0.03982 ( 310) hydrogen bonds : angle 4.23506 ( 879) metal coordination : bond 0.00085 ( 2) link_NAG-ASN : bond 0.00584 ( 8) link_NAG-ASN : angle 3.91775 ( 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 88 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.170 Fit side-chains REVERT: D 78 THR cc_start: 0.7894 (m) cc_final: 0.7568 (m) REVERT: D 406 GLU cc_start: 0.8266 (tp30) cc_final: 0.7960 (tp30) REVERT: D 471 ASP cc_start: 0.7690 (t0) cc_final: 0.7113 (t0) REVERT: D 584 LEU cc_start: 0.8544 (tt) cc_final: 0.8307 (tt) REVERT: A 358 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.7913 (mt) REVERT: A 438 SER cc_start: 0.8968 (t) cc_final: 0.8514 (t) outliers start: 8 outliers final: 7 residues processed: 85 average time/residue: 0.0536 time to fit residues: 7.0438 Evaluate side-chains 89 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 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 440 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 26 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 41 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 42 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.161102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.127416 restraints weight = 7949.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.126889 restraints weight = 8863.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.128428 restraints weight = 8788.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.128644 restraints weight = 6195.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.128809 restraints weight = 5821.120| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7093 Z= 0.147 Angle : 0.566 13.353 9653 Z= 0.277 Chirality : 0.042 0.191 1042 Planarity : 0.004 0.036 1231 Dihedral : 6.052 58.119 1076 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.62 % Allowed : 12.72 % Favored : 85.66 % 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 aren not related in a simple way. whole: 0.89 (0.29), residues: 831 helix: 1.72 (0.28), residues: 362 sheet: 1.22 (0.58), residues: 68 loop : -0.57 (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 0.020 0.001 PHE D 369 TRP 0.009 0.001 TRP D 165 HIS 0.004 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 7075) covalent geometry : angle 0.53027 ( 9613) SS BOND : bond 0.00151 ( 8) SS BOND : angle 0.78202 ( 16) hydrogen bonds : bond 0.04626 ( 310) hydrogen bonds : angle 4.34083 ( 879) metal coordination : bond 0.00115 ( 2) link_NAG-ASN : bond 0.00580 ( 8) link_NAG-ASN : angle 3.99379 ( 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 93 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.285 Fit side-chains REVERT: D 78 THR cc_start: 0.7928 (m) cc_final: 0.7611 (m) REVERT: D 406 GLU cc_start: 0.8301 (tp30) cc_final: 0.7976 (tp30) REVERT: D 471 ASP cc_start: 0.7704 (t0) cc_final: 0.7139 (t0) REVERT: A 358 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.7922 (mt) REVERT: A 438 SER cc_start: 0.9032 (t) cc_final: 0.8582 (t) outliers start: 12 outliers final: 9 residues processed: 88 average time/residue: 0.0518 time to fit residues: 7.0195 Evaluate side-chains 88 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 78 optimal weight: 0.9990 chunk 29 optimal weight: 0.0980 chunk 66 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.160137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.126263 restraints weight = 7930.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.124674 restraints weight = 9889.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.126575 restraints weight = 9892.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.127047 restraints weight = 6689.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.127518 restraints weight = 5932.551| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7093 Z= 0.156 Angle : 0.574 13.452 9653 Z= 0.284 Chirality : 0.042 0.192 1042 Planarity : 0.004 0.037 1231 Dihedral : 6.146 58.800 1076 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.35 % Allowed : 12.99 % Favored : 85.66 % 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 aren not related in a simple way. whole: 0.78 (0.29), residues: 831 helix: 1.62 (0.28), residues: 363 sheet: 1.16 (0.59), residues: 66 loop : -0.62 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 357 TYR 0.027 0.002 TYR D 279 PHE 0.021 0.002 PHE D 369 TRP 0.010 0.001 TRP A 436 HIS 0.005 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 7075) covalent geometry : angle 0.53761 ( 9613) SS BOND : bond 0.00180 ( 8) SS BOND : angle 0.82919 ( 16) hydrogen bonds : bond 0.04856 ( 310) hydrogen bonds : angle 4.40373 ( 879) metal coordination : bond 0.00172 ( 2) link_NAG-ASN : bond 0.00560 ( 8) link_NAG-ASN : angle 4.04694 ( 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 87 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.258 Fit side-chains REVERT: D 78 THR cc_start: 0.7967 (m) cc_final: 0.7642 (m) REVERT: D 471 ASP cc_start: 0.7709 (t0) cc_final: 0.7138 (t0) REVERT: A 358 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8046 (mt) REVERT: A 438 SER cc_start: 0.9053 (t) cc_final: 0.8585 (t) outliers start: 10 outliers final: 9 residues processed: 82 average time/residue: 0.0587 time to fit residues: 7.2468 Evaluate side-chains 84 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 26 optimal weight: 0.0570 chunk 22 optimal weight: 0.0030 chunk 13 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 overall best weight: 0.4108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.161465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.127186 restraints weight = 7891.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.126091 restraints weight = 7956.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.126753 restraints weight = 7144.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.127384 restraints weight = 6568.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.127744 restraints weight = 5775.430| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1714 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= 0.126 Angle : 0.554 13.151 9653 Z= 0.269 Chirality : 0.041 0.195 1042 Planarity : 0.003 0.037 1231 Dihedral : 6.026 57.084 1076 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.35 % Allowed : 13.40 % 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 aren not related in a simple way. whole: 0.84 (0.29), residues: 831 helix: 1.69 (0.28), residues: 363 sheet: 1.06 (0.60), residues: 69 loop : -0.58 (0.30), residues: 399 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 covalent geometry : bond 0.00294 ( 7075) covalent geometry : angle 0.51835 ( 9613) SS BOND : bond 0.00141 ( 8) SS BOND : angle 0.69820 ( 16) hydrogen bonds : bond 0.04390 ( 310) hydrogen bonds : angle 4.33384 ( 879) metal coordination : bond 0.00103 ( 2) link_NAG-ASN : bond 0.00560 ( 8) link_NAG-ASN : angle 3.93794 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1170.24 seconds wall clock time: 20 minutes 56.37 seconds (1256.37 seconds total)