Starting phenix.real_space_refine on Tue Aug 4 13:33:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v3t_64756/08_2026/9v3t_64756.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v3t_64756/08_2026/9v3t_64756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v3t_64756/08_2026/9v3t_64756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v3t_64756/08_2026/9v3t_64756.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v3t_64756/08_2026/9v3t_64756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v3t_64756/08_2026/9v3t_64756.map" } resolution = 3.73 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= -0.003 sd= 0.042 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: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 2221 2.51 5 N 527 2.21 5 O 569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3340 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3326 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 22, 'TRANS': 401} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.02, per 1000 atoms: 0.31 Number of scatterers: 3340 At special positions: 0 Unit cell: (75.53, 68.89, 73.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 569 8.00 N 527 7.00 C 2221 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 329 " 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 A 501 " - " ASN A 174 " Time building additional restraints: 0.27 Conformation dependent library (CDL) restraints added in 125.0 milliseconds 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 0 sheets defined 77.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 48 through 60 removed outlier: 4.152A pdb=" N GLY A 59 " --> pdb=" O HIS A 55 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASN A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 67 removed outlier: 3.636A pdb=" N LEU A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 78 through 108 removed outlier: 3.885A pdb=" N ILE A 82 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE A 105 " --> pdb=" O CYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 126 removed outlier: 3.999A pdb=" N VAL A 120 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET A 121 " --> pdb=" O GLY A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 removed outlier: 4.461A pdb=" N HIS A 137 " --> pdb=" O ASN A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 161 removed outlier: 3.637A pdb=" N VAL A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 148 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N CYS A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 160 " --> pdb=" O CYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 172 removed outlier: 4.151A pdb=" N LYS A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE A 170 " --> pdb=" O PHE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 201 through 210 removed outlier: 4.380A pdb=" N LEU A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A 210 " --> pdb=" O VAL A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 240 removed outlier: 3.556A pdb=" N ASN A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 232 " --> pdb=" O MET A 228 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 269 removed outlier: 3.989A pdb=" N THR A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 281 removed outlier: 3.990A pdb=" N LEU A 278 " --> pdb=" O MET A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 287 through 315 removed outlier: 4.121A pdb=" N ILE A 291 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A 300 " --> pdb=" O MET A 296 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.533A pdb=" N LEU A 326 " --> pdb=" O THR A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 364 removed outlier: 3.996A pdb=" N SER A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA A 348 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Proline residue: A 354 - end of helix removed outlier: 3.708A pdb=" N ILE A 357 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 374 through 393 removed outlier: 3.773A pdb=" N ARG A 379 " --> pdb=" O ASP A 375 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N THR A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL A 383 " --> pdb=" O ARG A 379 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 407 removed outlier: 4.100A pdb=" N ILE A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER A 401 " --> pdb=" O ASP A 397 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'A' and resid 414 through 424 removed outlier: 3.607A pdb=" N GLU A 420 " --> pdb=" O PRO A 416 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A 421 " --> pdb=" O PRO A 417 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 424 " --> pdb=" O GLU A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 461 removed outlier: 3.614A pdb=" N ILE A 434 " --> pdb=" O SER A 430 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER A 441 " --> pdb=" O ASP A 437 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR A 452 " --> pdb=" O PHE A 448 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA A 455 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 456 " --> pdb=" O THR A 452 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) 171 hydrogen bonds defined for protein. 507 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: 0.54 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 575 1.33 - 1.45: 872 1.45 - 1.57: 1945 1.57 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 3426 Sorted by residual: bond pdb=" CA ILE A 272 " pdb=" C ILE A 272 " ideal model delta sigma weight residual 1.523 1.466 0.057 1.27e-02 6.20e+03 2.02e+01 bond pdb=" C LEU A 276 " pdb=" N PRO A 277 " ideal model delta sigma weight residual 1.336 1.382 -0.046 1.23e-02 6.61e+03 1.40e+01 bond pdb=" N MET A 274 " pdb=" CA MET A 274 " ideal model delta sigma weight residual 1.455 1.419 0.036 1.25e-02 6.40e+03 8.48e+00 bond pdb=" CA MET A 274 " pdb=" C MET A 274 " ideal model delta sigma weight residual 1.524 1.477 0.048 1.66e-02 3.63e+03 8.31e+00 bond pdb=" C ILE A 272 " pdb=" O ILE A 272 " ideal model delta sigma weight residual 1.236 1.207 0.029 1.19e-02 7.06e+03 5.89e+00 ... (remaining 3421 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 4453 2.03 - 4.05: 171 4.05 - 6.08: 30 6.08 - 8.10: 12 8.10 - 10.13: 8 Bond angle restraints: 4674 Sorted by residual: angle pdb=" N GLU A 270 " pdb=" CA GLU A 270 " pdb=" C GLU A 270 " ideal model delta sigma weight residual 114.12 122.38 -8.26 1.39e+00 5.18e-01 3.54e+01 angle pdb=" N ILE A 148 " pdb=" CA ILE A 148 " pdb=" C ILE A 148 " ideal model delta sigma weight residual 111.90 108.02 3.88 8.10e-01 1.52e+00 2.30e+01 angle pdb=" N VAL A 421 " pdb=" CA VAL A 421 " pdb=" C VAL A 421 " ideal model delta sigma weight residual 111.81 107.73 4.08 8.60e-01 1.35e+00 2.25e+01 angle pdb=" C SER A 247 " pdb=" N HIS A 248 " pdb=" CA HIS A 248 " ideal model delta sigma weight residual 121.54 129.81 -8.27 1.91e+00 2.74e-01 1.87e+01 angle pdb=" N MET A 274 " pdb=" CA MET A 274 " pdb=" C MET A 274 " ideal model delta sigma weight residual 112.93 108.13 4.80 1.12e+00 7.97e-01 1.84e+01 ... (remaining 4669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.39: 1884 14.39 - 28.78: 103 28.78 - 43.17: 28 43.17 - 57.57: 2 57.57 - 71.96: 2 Dihedral angle restraints: 2019 sinusoidal: 788 harmonic: 1231 Sorted by residual: dihedral pdb=" CA CYS A 329 " pdb=" C CYS A 329 " pdb=" N TRP A 330 " pdb=" CA TRP A 330 " ideal model delta harmonic sigma weight residual -180.00 -154.81 -25.19 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA LEU A 205 " pdb=" C LEU A 205 " pdb=" N VAL A 206 " pdb=" CA VAL A 206 " ideal model delta harmonic sigma weight residual 180.00 160.59 19.41 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA PRO A 416 " pdb=" C PRO A 416 " pdb=" N PRO A 417 " pdb=" CA PRO A 417 " ideal model delta harmonic sigma weight residual 180.00 161.63 18.37 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 2016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 276 0.032 - 0.063: 178 0.063 - 0.095: 76 0.095 - 0.126: 23 0.126 - 0.158: 14 Chirality restraints: 567 Sorted by residual: chirality pdb=" CA GLU A 270 " pdb=" N GLU A 270 " pdb=" C GLU A 270 " pdb=" CB GLU A 270 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" C1 NAG A 501 " pdb=" ND2 ASN A 174 " pdb=" C2 NAG A 501 " pdb=" O5 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" CA LEU A 68 " pdb=" N LEU A 68 " pdb=" C LEU A 68 " pdb=" CB LEU A 68 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.77e-01 ... (remaining 564 not shown) Planarity restraints: 571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 268 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C SER A 268 " -0.062 2.00e-02 2.50e+03 pdb=" O SER A 268 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE A 269 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 416 " 0.054 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO A 417 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 417 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 417 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 258 " -0.040 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO A 259 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 259 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 259 " -0.034 5.00e-02 4.00e+02 ... (remaining 568 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.46: 19 2.46 - 3.07: 1929 3.07 - 3.68: 5141 3.68 - 4.29: 7369 4.29 - 4.90: 11801 Nonbonded interactions: 26259 Sorted by model distance: nonbonded pdb=" CD1 PHE A 113 " pdb=" OD1 ASN A 280 " model vdw 1.844 3.340 nonbonded pdb=" CE1 PHE A 113 " pdb=" ND2 ASN A 280 " model vdw 1.914 3.420 nonbonded pdb=" CD1 PHE A 314 " pdb=" ND2 ASN A 325 " model vdw 2.083 3.420 nonbonded pdb=" CD1 PHE A 113 " pdb=" ND2 ASN A 280 " model vdw 2.106 3.420 nonbonded pdb=" CZ PHE A 113 " pdb=" ND2 ASN A 280 " model vdw 2.106 3.420 ... (remaining 26254 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.370 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 0.057 3428 Z= 0.276 Angle : 1.050 10.131 4679 Z= 0.576 Chirality : 0.051 0.158 567 Planarity : 0.009 0.081 570 Dihedral : 10.151 71.957 1224 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.98 % Favored : 94.79 % Rotamer: Outliers : 0.27 % Allowed : 2.94 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.65 (0.29), residues: 422 helix: -4.20 (0.14), residues: 282 sheet: None (None), residues: 0 loop : -2.17 (0.53), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 286 TYR 0.023 0.002 TYR A 116 PHE 0.021 0.002 PHE A 269 TRP 0.008 0.001 TRP A 330 HIS 0.002 0.000 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.28 ( 3426) covalent geometry : angle 1.04937 / 0.58 ( 4674) SS BOND : bond 0.00205 / 0.13 ( 1) SS BOND : angle 0.49480 / 0.21 ( 2) hydrogen bonds : bond 0.31688 / 20.72 ( 171) hydrogen bonds : angle 11.25975 / 8.18 ( 507) link_NAG-ASN : bond 0.00119 / 0.07 ( 1) link_NAG-ASN : angle 1.62737 / 0.57 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 HIS cc_start: 0.8584 (m-70) cc_final: 0.8161 (m90) REVERT: A 61 ILE cc_start: 0.8448 (pt) cc_final: 0.8221 (tp) REVERT: A 89 ILE cc_start: 0.8452 (mm) cc_final: 0.7947 (mt) REVERT: A 118 ASP cc_start: 0.7941 (m-30) cc_final: 0.7168 (m-30) REVERT: A 168 GLN cc_start: 0.8375 (tt0) cc_final: 0.7925 (tt0) REVERT: A 435 PHE cc_start: 0.8578 (t80) cc_final: 0.8230 (t80) REVERT: A 453 TYR cc_start: 0.7910 (t80) cc_final: 0.7658 (t80) REVERT: A 454 GLU cc_start: 0.7689 (mt-10) cc_final: 0.6960 (mt-10) REVERT: A 458 GLU cc_start: 0.7424 (mp0) cc_final: 0.6637 (mp0) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.0622 time to fit residues: 11.4534 Evaluate side-chains 121 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN A 181 HIS ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.141017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.113675 restraints weight = 5467.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.117898 restraints weight = 2889.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.120873 restraints weight = 1897.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.122469 restraints weight = 1430.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.124188 restraints weight = 1206.445| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3428 Z= 0.154 Angle : 0.727 8.208 4679 Z= 0.366 Chirality : 0.044 0.139 567 Planarity : 0.007 0.071 570 Dihedral : 6.280 42.224 473 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.14 % Allowed : 16.04 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.64 (0.36), residues: 422 helix: -2.57 (0.23), residues: 290 sheet: None (None), residues: 0 loop : -1.48 (0.59), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 108 TYR 0.012 0.002 TYR A 339 PHE 0.014 0.002 PHE A 210 TRP 0.009 0.001 TRP A 138 HIS 0.005 0.001 HIS A 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 3426) covalent geometry : angle 0.72684 / 0.37 ( 4674) SS BOND : bond 0.00221 / 0.14 ( 1) SS BOND : angle 1.07574 / 0.40 ( 2) hydrogen bonds : bond 0.05169 / 3.22 ( 171) hydrogen bonds : angle 5.47698 / 3.82 ( 507) link_NAG-ASN : bond 0.00130 / 0.08 ( 1) link_NAG-ASN : angle 1.13409 / 0.44 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 HIS cc_start: 0.8389 (m-70) cc_final: 0.7773 (m90) REVERT: A 61 ILE cc_start: 0.8543 (pt) cc_final: 0.8305 (tp) REVERT: A 239 ILE cc_start: 0.8621 (mm) cc_final: 0.8292 (mt) REVERT: A 281 LYS cc_start: 0.8524 (mtpt) cc_final: 0.8167 (mtpt) REVERT: A 435 PHE cc_start: 0.8534 (t80) cc_final: 0.8278 (t80) outliers start: 8 outliers final: 4 residues processed: 126 average time/residue: 0.0318 time to fit residues: 5.1596 Evaluate side-chains 110 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 408 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 0.2980 chunk 3 optimal weight: 0.3980 chunk 7 optimal weight: 0.0970 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN A 213 ASN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.141278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.113276 restraints weight = 5367.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.117497 restraints weight = 2830.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.120420 restraints weight = 1866.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.122272 restraints weight = 1417.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.123646 restraints weight = 1188.244| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3428 Z= 0.128 Angle : 0.667 7.531 4679 Z= 0.330 Chirality : 0.043 0.156 567 Planarity : 0.006 0.062 570 Dihedral : 5.457 24.580 473 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.21 % Allowed : 16.58 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.39), residues: 422 helix: -1.56 (0.27), residues: 286 sheet: None (None), residues: 0 loop : -1.19 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 108 TYR 0.014 0.002 TYR A 457 PHE 0.025 0.001 PHE A 210 TRP 0.014 0.001 TRP A 49 HIS 0.013 0.002 HIS A 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 3426) covalent geometry : angle 0.66667 / 0.33 ( 4674) SS BOND : bond 0.00063 / 0.04 ( 1) SS BOND : angle 0.98476 / 0.45 ( 2) hydrogen bonds : bond 0.04229 / 2.66 ( 171) hydrogen bonds : angle 4.82893 / 3.34 ( 507) link_NAG-ASN : bond 0.00300 / 0.19 ( 1) link_NAG-ASN : angle 0.74830 / 0.29 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ARG cc_start: 0.8320 (ttm110) cc_final: 0.7916 (ttm110) REVERT: A 221 SER cc_start: 0.8322 (m) cc_final: 0.7703 (p) REVERT: A 239 ILE cc_start: 0.8584 (mm) cc_final: 0.8319 (mt) REVERT: A 435 PHE cc_start: 0.8538 (t80) cc_final: 0.8270 (t80) outliers start: 12 outliers final: 8 residues processed: 122 average time/residue: 0.0471 time to fit residues: 7.2005 Evaluate side-chains 111 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 369 HIS Chi-restraints excluded: chain A residue 421 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 31 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 11 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 52.752 > 50:) chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.140645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111939 restraints weight = 5255.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.116052 restraints weight = 2823.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.119012 restraints weight = 1893.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.120993 restraints weight = 1453.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.122243 restraints weight = 1216.186| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3428 Z= 0.127 Angle : 0.685 8.892 4679 Z= 0.326 Chirality : 0.043 0.147 567 Planarity : 0.006 0.058 570 Dihedral : 4.912 17.960 473 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.67 % Allowed : 20.86 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.42), residues: 422 helix: -0.97 (0.30), residues: 290 sheet: None (None), residues: 0 loop : -0.79 (0.64), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 108 TYR 0.012 0.002 TYR A 457 PHE 0.022 0.001 PHE A 210 TRP 0.015 0.001 TRP A 49 HIS 0.008 0.002 HIS A 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 3426) covalent geometry : angle 0.68474 / 0.33 ( 4674) SS BOND : bond 0.00102 / 0.06 ( 1) SS BOND : angle 0.81355 / 0.32 ( 2) hydrogen bonds : bond 0.03746 / 2.39 ( 171) hydrogen bonds : angle 4.65099 / 3.20 ( 507) link_NAG-ASN : bond 0.00247 / 0.15 ( 1) link_NAG-ASN : angle 0.73387 / 0.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 PHE cc_start: 0.8374 (t80) cc_final: 0.8142 (t80) REVERT: A 108 ARG cc_start: 0.8331 (ttm110) cc_final: 0.7921 (ttm110) REVERT: A 140 ARG cc_start: 0.6886 (ttt180) cc_final: 0.6528 (ttt180) REVERT: A 239 ILE cc_start: 0.8572 (mm) cc_final: 0.8301 (mt) REVERT: A 333 GLN cc_start: 0.8552 (mm110) cc_final: 0.8199 (mp10) REVERT: A 356 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8108 (mp0) REVERT: A 417 PRO cc_start: 0.8909 (Cg_exo) cc_final: 0.8633 (Cg_endo) REVERT: A 435 PHE cc_start: 0.8559 (t80) cc_final: 0.8340 (t80) REVERT: A 458 GLU cc_start: 0.7733 (mp0) cc_final: 0.7217 (mp0) outliers start: 10 outliers final: 9 residues processed: 115 average time/residue: 0.0420 time to fit residues: 6.3720 Evaluate side-chains 117 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 439 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 0.2980 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.140240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.112256 restraints weight = 5232.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.116309 restraints weight = 2865.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.119154 restraints weight = 1941.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.120778 restraints weight = 1503.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.122377 restraints weight = 1282.213| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3428 Z= 0.130 Angle : 0.700 12.111 4679 Z= 0.329 Chirality : 0.043 0.147 567 Planarity : 0.005 0.055 570 Dihedral : 4.763 15.976 473 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.21 % Allowed : 21.39 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.42), residues: 422 helix: -0.76 (0.30), residues: 293 sheet: None (None), residues: 0 loop : -1.07 (0.63), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 107 TYR 0.011 0.001 TYR A 258 PHE 0.017 0.001 PHE A 448 TRP 0.007 0.001 TRP A 49 HIS 0.004 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 3426) covalent geometry : angle 0.69998 / 0.33 ( 4674) SS BOND : bond 0.01360 / 0.85 ( 1) SS BOND : angle 1.21063 / 0.44 ( 2) hydrogen bonds : bond 0.03499 / 2.22 ( 171) hydrogen bonds : angle 4.55732 / 3.14 ( 507) link_NAG-ASN : bond 0.00221 / 0.14 ( 1) link_NAG-ASN : angle 0.78620 / 0.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ASP cc_start: 0.7557 (m-30) cc_final: 0.7205 (m-30) REVERT: A 140 ARG cc_start: 0.6705 (ttt180) cc_final: 0.6331 (ttt180) REVERT: A 239 ILE cc_start: 0.8514 (mm) cc_final: 0.8250 (mt) REVERT: A 329 CYS cc_start: 0.5610 (p) cc_final: 0.5397 (p) REVERT: A 356 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8137 (mp0) REVERT: A 417 PRO cc_start: 0.8905 (Cg_exo) cc_final: 0.8661 (Cg_endo) REVERT: A 435 PHE cc_start: 0.8502 (t80) cc_final: 0.8218 (t80) REVERT: A 454 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6603 (mt-10) REVERT: A 458 GLU cc_start: 0.7628 (mp0) cc_final: 0.7292 (mp0) outliers start: 12 outliers final: 8 residues processed: 114 average time/residue: 0.0352 time to fit residues: 5.2712 Evaluate side-chains 112 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 369 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.140908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.112704 restraints weight = 5337.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.116794 restraints weight = 2923.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.119706 restraints weight = 1971.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.121251 restraints weight = 1522.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.122908 restraints weight = 1305.577| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3428 Z= 0.126 Angle : 0.690 12.801 4679 Z= 0.325 Chirality : 0.043 0.145 567 Planarity : 0.005 0.054 570 Dihedral : 4.653 17.573 473 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.74 % Allowed : 23.53 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.42), residues: 422 helix: -0.64 (0.30), residues: 293 sheet: None (None), residues: 0 loop : -1.08 (0.61), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 107 TYR 0.010 0.001 TYR A 258 PHE 0.022 0.001 PHE A 445 TRP 0.005 0.000 TRP A 49 HIS 0.002 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 3426) covalent geometry : angle 0.68969 / 0.32 ( 4674) SS BOND : bond 0.00443 / 0.28 ( 1) SS BOND : angle 1.60355 / 0.58 ( 2) hydrogen bonds : bond 0.03293 / 2.09 ( 171) hydrogen bonds : angle 4.55500 / 3.15 ( 507) link_NAG-ASN : bond 0.00219 / 0.14 ( 1) link_NAG-ASN : angle 0.83412 / 0.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ASP cc_start: 0.7561 (m-30) cc_final: 0.7182 (m-30) REVERT: A 140 ARG cc_start: 0.6645 (ttt180) cc_final: 0.6433 (ttt180) REVERT: A 278 LEU cc_start: 0.8965 (mp) cc_final: 0.8659 (tp) REVERT: A 329 CYS cc_start: 0.5592 (p) cc_final: 0.5371 (p) REVERT: A 417 PRO cc_start: 0.8894 (Cg_exo) cc_final: 0.8659 (Cg_endo) REVERT: A 435 PHE cc_start: 0.8518 (t80) cc_final: 0.8235 (t80) REVERT: A 454 GLU cc_start: 0.7384 (mt-10) cc_final: 0.6681 (mt-10) REVERT: A 458 GLU cc_start: 0.7612 (mp0) cc_final: 0.7384 (mp0) outliers start: 14 outliers final: 11 residues processed: 118 average time/residue: 0.0435 time to fit residues: 6.7804 Evaluate side-chains 116 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 369 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 0.0980 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.141103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.112974 restraints weight = 5326.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.117118 restraints weight = 2886.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.120026 restraints weight = 1942.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.121703 restraints weight = 1495.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.123312 restraints weight = 1272.628| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3428 Z= 0.124 Angle : 0.694 12.598 4679 Z= 0.327 Chirality : 0.043 0.145 567 Planarity : 0.005 0.052 570 Dihedral : 4.584 17.682 473 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.55 % Allowed : 22.46 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.41), residues: 422 helix: -0.52 (0.30), residues: 296 sheet: None (None), residues: 0 loop : -1.09 (0.61), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 107 TYR 0.009 0.001 TYR A 258 PHE 0.021 0.001 PHE A 238 TRP 0.009 0.001 TRP A 49 HIS 0.003 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 3426) covalent geometry : angle 0.69364 / 0.33 ( 4674) SS BOND : bond 0.00361 / 0.23 ( 1) SS BOND : angle 1.27144 / 0.46 ( 2) hydrogen bonds : bond 0.03283 / 2.05 ( 171) hydrogen bonds : angle 4.54874 / 3.15 ( 507) link_NAG-ASN : bond 0.00224 / 0.14 ( 1) link_NAG-ASN : angle 0.84196 / 0.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ASP cc_start: 0.7516 (m-30) cc_final: 0.7120 (m-30) REVERT: A 239 ILE cc_start: 0.8500 (mm) cc_final: 0.8197 (mt) REVERT: A 329 CYS cc_start: 0.5540 (p) cc_final: 0.5161 (p) REVERT: A 339 TYR cc_start: 0.8029 (t80) cc_final: 0.6850 (t80) REVERT: A 340 SER cc_start: 0.8326 (m) cc_final: 0.8099 (m) REVERT: A 417 PRO cc_start: 0.8862 (Cg_exo) cc_final: 0.8643 (Cg_endo) REVERT: A 435 PHE cc_start: 0.8501 (t80) cc_final: 0.8239 (t80) REVERT: A 448 PHE cc_start: 0.8033 (t80) cc_final: 0.7806 (t80) REVERT: A 454 GLU cc_start: 0.7388 (mt-10) cc_final: 0.6648 (mt-10) outliers start: 17 outliers final: 14 residues processed: 119 average time/residue: 0.0459 time to fit residues: 7.0501 Evaluate side-chains 118 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 369 HIS Chi-restraints excluded: chain A residue 439 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 0.0070 chunk 38 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.148596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.120832 restraints weight = 5275.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.125030 restraints weight = 2884.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.127832 restraints weight = 1937.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.129763 restraints weight = 1505.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.131268 restraints weight = 1262.264| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3428 Z= 0.132 Angle : 0.730 12.566 4679 Z= 0.344 Chirality : 0.043 0.144 567 Planarity : 0.005 0.052 570 Dihedral : 4.553 17.731 473 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.01 % Allowed : 23.26 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.41), residues: 422 helix: -0.52 (0.30), residues: 301 sheet: None (None), residues: 0 loop : -1.03 (0.61), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 140 TYR 0.014 0.002 TYR A 457 PHE 0.025 0.001 PHE A 445 TRP 0.004 0.000 TRP A 49 HIS 0.003 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 ( 3426) covalent geometry : angle 0.72989 / 0.34 ( 4674) SS BOND : bond 0.00213 / 0.13 ( 1) SS BOND : angle 1.19068 / 0.44 ( 2) hydrogen bonds : bond 0.03313 / 2.06 ( 171) hydrogen bonds : angle 4.63597 / 3.23 ( 507) link_NAG-ASN : bond 0.00224 / 0.14 ( 1) link_NAG-ASN : angle 0.84933 / 0.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 HIS cc_start: 0.7931 (m90) cc_final: 0.7590 (m90) REVERT: A 118 ASP cc_start: 0.7467 (m-30) cc_final: 0.6974 (m-30) REVERT: A 165 ASN cc_start: 0.8944 (m-40) cc_final: 0.8669 (m110) REVERT: A 228 MET cc_start: 0.8262 (mmm) cc_final: 0.7706 (tpt) REVERT: A 239 ILE cc_start: 0.8445 (mm) cc_final: 0.8156 (mt) REVERT: A 278 LEU cc_start: 0.9059 (tp) cc_final: 0.8767 (tp) REVERT: A 281 LYS cc_start: 0.8481 (mmtt) cc_final: 0.7821 (tptm) REVERT: A 339 TYR cc_start: 0.7857 (t80) cc_final: 0.6682 (t80) REVERT: A 340 SER cc_start: 0.8399 (m) cc_final: 0.8102 (m) REVERT: A 417 PRO cc_start: 0.8882 (Cg_exo) cc_final: 0.8660 (Cg_endo) REVERT: A 435 PHE cc_start: 0.8495 (t80) cc_final: 0.8245 (t80) REVERT: A 448 PHE cc_start: 0.8003 (t80) cc_final: 0.7772 (t80) outliers start: 15 outliers final: 15 residues processed: 116 average time/residue: 0.0362 time to fit residues: 5.4749 Evaluate side-chains 117 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 369 HIS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 439 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.145460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.117914 restraints weight = 5271.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.122002 restraints weight = 2903.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.124875 restraints weight = 1961.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.126793 restraints weight = 1512.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.128010 restraints weight = 1273.337| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3428 Z= 0.148 Angle : 0.752 12.620 4679 Z= 0.360 Chirality : 0.045 0.167 567 Planarity : 0.006 0.054 570 Dihedral : 4.601 18.601 473 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.28 % Allowed : 23.80 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.41), residues: 422 helix: -0.51 (0.29), residues: 301 sheet: None (None), residues: 0 loop : -1.05 (0.61), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 140 TYR 0.016 0.002 TYR A 457 PHE 0.025 0.002 PHE A 238 TRP 0.003 0.000 TRP A 49 HIS 0.003 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 3426) covalent geometry : angle 0.75145 / 0.36 ( 4674) SS BOND : bond 0.00644 / 0.40 ( 1) SS BOND : angle 1.33603 / 0.47 ( 2) hydrogen bonds : bond 0.03521 / 2.21 ( 171) hydrogen bonds : angle 4.71170 / 3.29 ( 507) link_NAG-ASN : bond 0.00216 / 0.13 ( 1) link_NAG-ASN : angle 0.89997 / 0.33 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ASP cc_start: 0.7873 (m-30) cc_final: 0.7527 (m-30) REVERT: A 165 ASN cc_start: 0.8906 (m-40) cc_final: 0.8648 (m110) REVERT: A 228 MET cc_start: 0.8328 (mmm) cc_final: 0.7735 (tpt) REVERT: A 239 ILE cc_start: 0.8495 (mm) cc_final: 0.8209 (mt) REVERT: A 281 LYS cc_start: 0.8450 (mmtt) cc_final: 0.8180 (mmmm) REVERT: A 339 TYR cc_start: 0.7953 (t80) cc_final: 0.6689 (t80) REVERT: A 340 SER cc_start: 0.8443 (m) cc_final: 0.8152 (m) REVERT: A 417 PRO cc_start: 0.8899 (Cg_exo) cc_final: 0.8671 (Cg_endo) REVERT: A 435 PHE cc_start: 0.8495 (t80) cc_final: 0.8280 (t80) outliers start: 16 outliers final: 14 residues processed: 117 average time/residue: 0.0363 time to fit residues: 5.4606 Evaluate side-chains 118 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 369 HIS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 439 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 40 optimal weight: 0.0770 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.0570 chunk 32 optimal weight: 0.5980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.146948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.118368 restraints weight = 5204.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.122761 restraints weight = 2789.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.125745 restraints weight = 1862.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.127933 restraints weight = 1436.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.129263 restraints weight = 1197.129| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3428 Z= 0.132 Angle : 0.771 12.426 4679 Z= 0.369 Chirality : 0.044 0.163 567 Planarity : 0.006 0.051 570 Dihedral : 4.549 19.112 473 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.74 % Allowed : 24.33 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.41), residues: 422 helix: -0.31 (0.30), residues: 297 sheet: None (None), residues: 0 loop : -0.98 (0.62), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 140 TYR 0.014 0.002 TYR A 457 PHE 0.028 0.001 PHE A 445 TRP 0.009 0.001 TRP A 49 HIS 0.006 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 3426) covalent geometry : angle 0.77035 / 0.37 ( 4674) SS BOND : bond 0.00150 / 0.09 ( 1) SS BOND : angle 1.10755 / 0.38 ( 2) hydrogen bonds : bond 0.03573 / 2.22 ( 171) hydrogen bonds : angle 4.73388 / 3.30 ( 507) link_NAG-ASN : bond 0.00230 / 0.14 ( 1) link_NAG-ASN : angle 0.79575 / 0.30 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 844 Ramachandran restraints generated. 422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ARG cc_start: 0.8240 (ttm110) cc_final: 0.7748 (ttm110) REVERT: A 118 ASP cc_start: 0.7720 (m-30) cc_final: 0.7438 (m-30) REVERT: A 239 ILE cc_start: 0.8457 (mm) cc_final: 0.8147 (mt) REVERT: A 281 LYS cc_start: 0.8404 (mmtt) cc_final: 0.8138 (mmmm) REVERT: A 340 SER cc_start: 0.8366 (m) cc_final: 0.8102 (m) REVERT: A 417 PRO cc_start: 0.8873 (Cg_exo) cc_final: 0.8655 (Cg_endo) outliers start: 14 outliers final: 11 residues processed: 112 average time/residue: 0.0479 time to fit residues: 6.8403 Evaluate side-chains 113 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 369 HIS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 439 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 27 optimal weight: 0.2980 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 36 optimal weight: 0.0670 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.146566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.118762 restraints weight = 5314.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.122906 restraints weight = 2949.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.125908 restraints weight = 2010.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.127818 restraints weight = 1545.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.129219 restraints weight = 1302.089| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3428 Z= 0.136 Angle : 0.772 12.559 4679 Z= 0.369 Chirality : 0.044 0.157 567 Planarity : 0.006 0.052 570 Dihedral : 4.521 18.904 473 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.94 % Allowed : 25.67 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.42), residues: 422 helix: -0.25 (0.30), residues: 297 sheet: None (None), residues: 0 loop : -0.96 (0.63), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 140 TYR 0.013 0.002 TYR A 457 PHE 0.025 0.002 PHE A 238 TRP 0.004 0.000 TRP A 49 HIS 0.004 0.001 HIS A 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 3426) covalent geometry : angle 0.77174 / 0.37 ( 4674) SS BOND : bond 0.00027 / 0.02 ( 1) SS BOND : angle 0.98510 / 0.34 ( 2) hydrogen bonds : bond 0.03566 / 2.21 ( 171) hydrogen bonds : angle 4.74674 / 3.30 ( 507) link_NAG-ASN : bond 0.00228 / 0.14 ( 1) link_NAG-ASN : angle 0.79894 / 0.30 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 718.74 seconds wall clock time: 13 minutes 0.65 seconds (780.65 seconds total)