Starting phenix.real_space_refine on Sat Jul 4 06:35:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nba_12258/07_2026/7nba_12258.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nba_12258/07_2026/7nba_12258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nba_12258/07_2026/7nba_12258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nba_12258/07_2026/7nba_12258.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7nba_12258/07_2026/7nba_12258.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nba_12258/07_2026/7nba_12258.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nba_12258/07_2026/7nba_12258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nba_12258/07_2026/7nba_12258.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.008 sd= 0.022 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: 7 Type Number sf(0) Gaussians P 9 5.49 5 Mg 3 5.21 5 S 60 5.16 5 C 5957 2.51 5 N 1615 2.21 5 O 1841 1.98 5 H 9257 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18742 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 6636 Classifications: {'peptide': 428} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "B" Number of atoms: 6588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 6588 Classifications: {'peptide': 426} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "K" Number of atoms: 5420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 5420 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 4, 'TRANS': 326} Chain breaks: 6 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.39, per 1000 atoms: 0.18 Number of scatterers: 18742 At special positions: 0 Unit cell: (94.52, 109.81, 118.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 60 16.00 P 9 15.00 Mg 3 11.99 O 1841 8.00 N 1615 7.00 C 5957 6.00 H 9257 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 547.9 milliseconds 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2220 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 12 sheets defined 50.4% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 71 through 80 removed outlier: 3.969A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 128 Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.690A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.165A pdb=" N ARG A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.816A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 337 Processing helix chain 'A' and resid 384 through 401 Processing helix chain 'A' and resid 404 through 411 removed outlier: 3.749A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 437 Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 41 through 46 removed outlier: 4.070A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 69 through 78 Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 107 through 125 removed outlier: 3.986A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 Processing helix chain 'B' and resid 180 through 194 removed outlier: 4.100A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 221 through 237 Processing helix chain 'B' and resid 238 through 241 Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 276 through 282 removed outlier: 4.213A pdb=" N ARG B 282 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 295 through 299 removed outlier: 4.036A pdb=" N MET B 299 " --> pdb=" O ALA B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 374 through 390 removed outlier: 3.622A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.077A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 425 removed outlier: 4.148A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 38 Processing helix chain 'K' and resid 78 through 84 Processing helix chain 'K' and resid 85 through 97 Processing helix chain 'K' and resid 111 through 118 Processing helix chain 'K' and resid 156 through 177 Processing helix chain 'K' and resid 239 through 254 Processing helix chain 'K' and resid 304 through 309 Processing helix chain 'K' and resid 315 through 339 Processing helix chain 'K' and resid 344 through 348 removed outlier: 3.660A pdb=" N ARG K 347 " --> pdb=" O ILE K 344 " (cutoff:3.500A) Processing helix chain 'K' and resid 349 through 355 Processing helix chain 'K' and resid 374 through 376 No H-bonds generated for 'chain 'K' and resid 374 through 376' Processing helix chain 'K' and resid 377 through 392 Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.944A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N HIS A 139 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL A 9 " --> pdb=" O HIS A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 57 removed outlier: 6.857A pdb=" N LYS A 60 " --> pdb=" O THR A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 248 removed outlier: 6.336A pdb=" N ILE A 355 " --> pdb=" O ALA A 247 " (cutoff:3.500A) removed outlier: 8.896A pdb=" N LYS A 352 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N CYS A 315 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N GLY A 354 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU A 317 " --> pdb=" O GLY A 354 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ASN A 356 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR A 319 " --> pdb=" O ASN A 356 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.801A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ALA B 9 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AA6, first strand: chain 'B' and resid 269 through 271 removed outlier: 8.461A pdb=" N LYS B 350 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL B 313 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ALA B 352 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA B 315 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N CYS B 354 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N PHE B 317 " --> pdb=" O CYS B 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 20 through 21 Processing sheet with id=AA8, first strand: chain 'K' and resid 71 through 73 removed outlier: 4.167A pdb=" N CYS K 104 " --> pdb=" O VAL K 297 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 200 through 203 Processing sheet with id=AB1, first strand: chain 'K' and resid 45 through 47 Processing sheet with id=AB2, first strand: chain 'K' and resid 215 through 217 Processing sheet with id=AB3, first strand: chain 'K' and resid 256 through 257 513 hydrogen bonds defined for protein. 1428 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: 4.27 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.17: 9229 1.17 - 1.39: 3903 1.39 - 1.61: 5688 1.61 - 1.82: 95 1.82 - 2.04: 8 Bond restraints: 18923 Sorted by residual: bond pdb=" C GLU K 303 " pdb=" N ASN K 304 " ideal model delta sigma weight residual 1.331 2.041 -0.710 1.32e-02 5.74e+03 2.89e+03 bond pdb=" C LEU K 313 " pdb=" O LEU K 313 " ideal model delta sigma weight residual 1.234 1.029 0.206 1.20e-02 6.94e+03 2.94e+02 bond pdb=" C LYS K 314 " pdb=" N ILE K 315 " ideal model delta sigma weight residual 1.329 1.516 -0.187 1.44e-02 4.82e+03 1.68e+02 bond pdb=" OG1 THR K 113 " pdb=" HG1 THR K 113 " ideal model delta sigma weight residual 0.840 1.034 -0.194 2.00e-02 2.50e+03 9.40e+01 bond pdb=" N3B ANP K 700 " pdb=" PG ANP K 700 " ideal model delta sigma weight residual 1.795 1.605 0.190 2.00e-02 2.50e+03 9.05e+01 ... (remaining 18918 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.55: 33989 8.55 - 17.09: 95 17.09 - 25.64: 4 25.64 - 34.18: 2 34.18 - 42.73: 3 Bond angle restraints: 34093 Sorted by residual: angle pdb=" O LYS K 314 " pdb=" C LYS K 314 " pdb=" N ILE K 315 " ideal model delta sigma weight residual 122.59 79.86 42.73 1.33e+00 5.65e-01 1.03e+03 angle pdb=" C LYS K 314 " pdb=" N ILE K 315 " pdb=" CA ILE K 315 " ideal model delta sigma weight residual 123.08 154.61 -31.53 1.01e+00 9.80e-01 9.74e+02 angle pdb=" CA LYS K 314 " pdb=" C LYS K 314 " pdb=" N ILE K 315 " ideal model delta sigma weight residual 116.84 158.45 -41.61 1.71e+00 3.42e-01 5.92e+02 angle pdb=" O GLU K 303 " pdb=" C GLU K 303 " pdb=" N ASN K 304 " ideal model delta sigma weight residual 122.76 100.26 22.50 1.44e+00 4.82e-01 2.44e+02 angle pdb=" C LYS K 314 " pdb=" N ILE K 315 " pdb=" H ILE K 315 " ideal model delta sigma weight residual 123.61 85.10 38.51 3.00e+00 1.11e-01 1.65e+02 ... (remaining 34088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.76: 8707 34.76 - 69.51: 179 69.51 - 104.27: 10 104.27 - 139.02: 0 139.02 - 173.78: 4 Dihedral angle restraints: 8900 sinusoidal: 4865 harmonic: 4035 Sorted by residual: dihedral pdb=" CD2 HIS A 266 " pdb=" CG HIS A 266 " pdb=" ND1 HIS A 266 " pdb=" HD1 HIS A 266 " ideal model delta harmonic sigma weight residual 180.00 142.89 37.11 0 5.00e+00 4.00e-02 5.51e+01 dihedral pdb=" C5' GTP A 500 " pdb=" O5' GTP A 500 " pdb=" PA GTP A 500 " pdb=" O3A GTP A 500 " ideal model delta sinusoidal sigma weight residual 69.27 -122.53 -168.20 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C8 GTP A 500 " pdb=" C1' GTP A 500 " pdb=" N9 GTP A 500 " pdb=" O4' GTP A 500 " ideal model delta sinusoidal sigma weight residual 104.59 -51.55 156.14 1 2.00e+01 2.50e-03 4.59e+01 ... (remaining 8897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 1176 0.113 - 0.226: 259 0.226 - 0.340: 19 0.340 - 0.453: 3 0.453 - 0.566: 1 Chirality restraints: 1458 Sorted by residual: chirality pdb=" C4' ANP K 700 " pdb=" C3' ANP K 700 " pdb=" C5' ANP K 700 " pdb=" O4' ANP K 700 " both_signs ideal model delta sigma weight residual False -2.45 -3.02 0.57 2.00e-01 2.50e+01 8.01e+00 chirality pdb=" C3' G2P B 600 " pdb=" C2' G2P B 600 " pdb=" C4' G2P B 600 " pdb=" O3' G2P B 600 " both_signs ideal model delta sigma weight residual False -2.71 -2.28 -0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" CA LEU K 313 " pdb=" N LEU K 313 " pdb=" C LEU K 313 " pdb=" CB LEU K 313 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 4.08e+00 ... (remaining 1455 not shown) Planarity restraints: 2811 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 266 " 0.125 2.00e-02 2.50e+03 1.37e-01 4.20e+02 pdb=" CG HIS A 266 " 0.073 2.00e-02 2.50e+03 pdb=" ND1 HIS A 266 " 0.127 2.00e-02 2.50e+03 pdb=" CD2 HIS A 266 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 HIS A 266 " 0.070 2.00e-02 2.50e+03 pdb=" NE2 HIS A 266 " -0.033 2.00e-02 2.50e+03 pdb=" HD1 HIS A 266 " -0.319 2.00e-02 2.50e+03 pdb=" HD2 HIS A 266 " -0.109 2.00e-02 2.50e+03 pdb=" HE1 HIS A 266 " 0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU K 303 " -0.123 2.00e-02 2.50e+03 1.94e-01 3.75e+02 pdb=" C GLU K 303 " 0.332 2.00e-02 2.50e+03 pdb=" O GLU K 303 " -0.144 2.00e-02 2.50e+03 pdb=" N ASN K 304 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 264 " 0.100 2.00e-02 2.50e+03 1.15e-01 2.95e+02 pdb=" CG HIS B 264 " 0.076 2.00e-02 2.50e+03 pdb=" ND1 HIS B 264 " 0.108 2.00e-02 2.50e+03 pdb=" CD2 HIS B 264 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 HIS B 264 " 0.057 2.00e-02 2.50e+03 pdb=" NE2 HIS B 264 " -0.023 2.00e-02 2.50e+03 pdb=" HD1 HIS B 264 " -0.265 2.00e-02 2.50e+03 pdb=" HD2 HIS B 264 " -0.103 2.00e-02 2.50e+03 pdb=" HE1 HIS B 264 " 0.074 2.00e-02 2.50e+03 ... (remaining 2808 not shown) Histogram of nonbonded interaction distances: 1.27 - 1.94: 470 1.94 - 2.60: 21049 2.60 - 3.27: 59968 3.27 - 3.93: 77107 3.93 - 4.60: 119090 Nonbonded interactions: 277684 Sorted by model distance: nonbonded pdb=" H ASN K 50 " pdb=" H GLU K 51 " model vdw 1.274 2.100 nonbonded pdb=" HD2 ARG B 241 " pdb="HH11 ARG B 241 " model vdw 1.609 2.270 nonbonded pdb=" OD1 ASP A 47 " pdb=" H SER A 48 " model vdw 1.614 2.450 nonbonded pdb=" HG1 THR K 101 " pdb=" HG SER K 358 " model vdw 1.616 2.100 nonbonded pdb=" O PRO B 182 " pdb=" HG1 THR B 186 " model vdw 1.628 2.450 ... (remaining 277679 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: 0.020 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: 0.110 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.640 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5990 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 : 0.019 0.710 9666 Z= 1.103 Angle : 1.904 42.726 13093 Z= 1.242 Chirality : 0.089 0.566 1458 Planarity : 0.011 0.194 1680 Dihedral : 11.930 173.780 3576 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.75 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.17 (0.24), residues: 1163 helix: 0.19 (0.21), residues: 507 sheet: 0.72 (0.36), residues: 189 loop : -0.04 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 2 TYR 0.045 0.008 TYR A 161 PHE 0.047 0.006 PHE A 255 TRP 0.050 0.010 TRP B 101 HIS 0.007 0.002 HIS B 264 Details of bonding type rmsd/Z covalent geometry : bond 0.01923 / 1.10 ( 9666) covalent geometry : angle 1.90397 / 1.24 (13093) hydrogen bonds : bond 0.16971 / 11.11 ( 503) hydrogen bonds : angle 7.89796 / 5.55 ( 1428) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 515 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.6821 (m-80) cc_final: 0.5789 (m-10) REVERT: A 198 SER cc_start: 0.7519 (m) cc_final: 0.7277 (p) REVERT: A 301 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7297 (mm-40) REVERT: A 352 LYS cc_start: 0.6796 (tptt) cc_final: 0.6237 (mmtt) REVERT: A 357 TYR cc_start: 0.7558 (m-80) cc_final: 0.7308 (m-80) REVERT: A 377 MET cc_start: 0.7728 (tmm) cc_final: 0.7195 (tmm) REVERT: A 386 GLU cc_start: 0.8655 (tt0) cc_final: 0.8415 (tt0) REVERT: B 24 ILE cc_start: 0.8113 (mm) cc_final: 0.7887 (mm) REVERT: B 101 TRP cc_start: 0.6314 (t60) cc_final: 0.5967 (t60) REVERT: B 212 PHE cc_start: 0.6690 (t80) cc_final: 0.6486 (t80) REVERT: B 232 THR cc_start: 0.6464 (m) cc_final: 0.6115 (m) REVERT: B 266 PHE cc_start: 0.7959 (m-80) cc_final: 0.7751 (m-10) REVERT: B 299 MET cc_start: 0.5736 (mmp) cc_final: 0.5330 (mmp) REVERT: B 300 MET cc_start: 0.8077 (mpp) cc_final: 0.7768 (mtt) outliers start: 0 outliers final: 0 residues processed: 515 average time/residue: 0.2677 time to fit residues: 182.1262 Evaluate side-chains 298 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 GLN B 8 GLN B 334 GLN B 347 ASN K 96 GLN K 262 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.111601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.090105 restraints weight = 63133.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.094325 restraints weight = 23846.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.096774 restraints weight = 11720.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.098057 restraints weight = 7203.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.099040 restraints weight = 5470.353| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 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 : 0.005 0.049 9666 Z= 0.225 Angle : 0.721 6.326 13093 Z= 0.404 Chirality : 0.045 0.200 1458 Planarity : 0.006 0.063 1680 Dihedral : 10.794 176.984 1308 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.08 % Allowed : 12.31 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.24), residues: 1165 helix: 0.96 (0.22), residues: 508 sheet: 0.35 (0.35), residues: 203 loop : -0.15 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 422 TYR 0.027 0.002 TYR A 210 PHE 0.025 0.002 PHE A 255 TRP 0.009 0.002 TRP B 397 HIS 0.009 0.002 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.23 ( 9666) covalent geometry : angle 0.72082 / 0.40 (13093) hydrogen bonds : bond 0.06967 / 4.71 ( 503) hydrogen bonds : angle 6.14194 / 4.34 ( 1428) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 292 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 LYS cc_start: 0.7356 (tptt) cc_final: 0.6430 (mptt) REVERT: A 377 MET cc_start: 0.7771 (tmm) cc_final: 0.7333 (tmm) REVERT: B 69 GLU cc_start: 0.7821 (tt0) cc_final: 0.7512 (tt0) REVERT: B 123 GLU cc_start: 0.8791 (tp30) cc_final: 0.8551 (tp30) REVERT: B 198 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6466 (pt0) REVERT: B 229 VAL cc_start: 0.7389 (t) cc_final: 0.7180 (p) REVERT: B 257 MET cc_start: 0.8231 (mmp) cc_final: 0.7926 (mmt) REVERT: B 299 MET cc_start: 0.5956 (mmp) cc_final: 0.5563 (mmp) REVERT: B 300 MET cc_start: 0.8046 (mpp) cc_final: 0.7685 (mtt) REVERT: K 199 GLU cc_start: 0.6951 (tp30) cc_final: 0.6539 (tp30) REVERT: K 366 PHE cc_start: 0.8100 (m-80) cc_final: 0.7880 (m-10) outliers start: 32 outliers final: 22 residues processed: 314 average time/residue: 0.2286 time to fit residues: 98.5681 Evaluate side-chains 266 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 243 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 88 TYR Chi-restraints excluded: chain K residue 93 GLU Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 298 ASP Chi-restraints excluded: chain K residue 302 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 8.9990 chunk 90 optimal weight: 30.0000 chunk 38 optimal weight: 20.0000 chunk 110 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 chunk 99 optimal weight: 20.0000 chunk 106 optimal weight: 30.0000 chunk 83 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 HIS A 192 HIS B 57 ASN ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN K 48 ASN K 59 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.101798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.080508 restraints weight = 66657.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.084165 restraints weight = 24992.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.086369 restraints weight = 12579.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.087638 restraints weight = 7981.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.088401 restraints weight = 6139.977| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.7354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9666 Z= 0.208 Angle : 0.669 7.374 13093 Z= 0.364 Chirality : 0.044 0.153 1458 Planarity : 0.005 0.053 1680 Dihedral : 10.197 177.341 1308 Min Nonbonded Distance : 1.629 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.94 % Allowed : 14.42 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.01 (0.23), residues: 1165 helix: 0.73 (0.21), residues: 506 sheet: 0.13 (0.35), residues: 196 loop : -0.76 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 77 TYR 0.015 0.002 TYR B 281 PHE 0.017 0.002 PHE B 317 TRP 0.026 0.002 TRP B 397 HIS 0.008 0.002 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.21 ( 9666) covalent geometry : angle 0.66938 / 0.36 (13093) hydrogen bonds : bond 0.05677 / 3.77 ( 503) hydrogen bonds : angle 5.66756 / 4.06 ( 1428) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 251 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 TYR cc_start: 0.7910 (m-80) cc_final: 0.7518 (m-80) REVERT: A 253 THR cc_start: 0.7760 (p) cc_final: 0.7516 (t) REVERT: A 301 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7864 (mm-40) REVERT: A 352 LYS cc_start: 0.7737 (tptt) cc_final: 0.6697 (mptt) REVERT: A 424 ASP cc_start: 0.7875 (m-30) cc_final: 0.7528 (m-30) REVERT: A 425 MET cc_start: 0.8434 (tpp) cc_final: 0.7789 (tpp) REVERT: B 198 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6569 (pt0) REVERT: B 215 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7743 (tp) REVERT: B 257 MET cc_start: 0.8250 (mmp) cc_final: 0.7996 (mmt) REVERT: B 299 MET cc_start: 0.6627 (mmp) cc_final: 0.6248 (mmp) REVERT: K 191 ILE cc_start: 0.8388 (mp) cc_final: 0.8074 (mm) REVERT: K 215 ARG cc_start: 0.7968 (mmp80) cc_final: 0.7761 (mmp80) REVERT: K 313 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8606 (pp) REVERT: K 366 PHE cc_start: 0.8181 (m-80) cc_final: 0.7416 (m-80) outliers start: 41 outliers final: 28 residues processed: 274 average time/residue: 0.2075 time to fit residues: 79.0397 Evaluate side-chains 248 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 217 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain K residue 88 TYR Chi-restraints excluded: chain K residue 93 GLU Chi-restraints excluded: chain K residue 103 PHE Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 230 ASP Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 298 ASP Chi-restraints excluded: chain K residue 302 SER Chi-restraints excluded: chain K residue 313 LEU Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 355 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 26 optimal weight: 6.9990 chunk 106 optimal weight: 40.0000 chunk 56 optimal weight: 30.0000 chunk 93 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 88 optimal weight: 30.0000 chunk 89 optimal weight: 50.0000 chunk 1 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 112 optimal weight: 20.0000 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN K 40 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.097725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.076261 restraints weight = 66762.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.079601 restraints weight = 26037.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.081432 restraints weight = 13400.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.082762 restraints weight = 8903.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.083266 restraints weight = 6850.145| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.8319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9666 Z= 0.215 Angle : 0.641 6.195 13093 Z= 0.351 Chirality : 0.044 0.162 1458 Planarity : 0.005 0.091 1680 Dihedral : 9.983 175.545 1308 Min Nonbonded Distance : 1.649 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.94 % Allowed : 16.73 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.16 (0.24), residues: 1165 helix: 0.61 (0.22), residues: 517 sheet: -0.07 (0.35), residues: 203 loop : -0.86 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 276 TYR 0.017 0.002 TYR B 310 PHE 0.017 0.002 PHE A 141 TRP 0.027 0.002 TRP B 397 HIS 0.011 0.002 HIS B 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.22 ( 9666) covalent geometry : angle 0.64070 / 0.35 (13093) hydrogen bonds : bond 0.05446 / 3.63 ( 503) hydrogen bonds : angle 5.52581 / 3.96 ( 1428) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 223 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.7553 (m-80) cc_final: 0.7348 (m-80) REVERT: A 302 MET cc_start: 0.7649 (mmm) cc_final: 0.7021 (ttm) REVERT: B 84 ILE cc_start: 0.5886 (mt) cc_final: 0.5390 (mt) REVERT: B 198 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6754 (pt0) REVERT: B 257 MET cc_start: 0.8196 (mmp) cc_final: 0.7899 (mmt) REVERT: B 276 ARG cc_start: 0.6495 (tpt90) cc_final: 0.6192 (tpt90) REVERT: B 299 MET cc_start: 0.7598 (mmp) cc_final: 0.7338 (mmp) REVERT: B 355 ASP cc_start: 0.7221 (m-30) cc_final: 0.6308 (t0) REVERT: B 362 LYS cc_start: 0.8930 (mmmt) cc_final: 0.8488 (mtpp) REVERT: B 363 MET cc_start: 0.7912 (mtp) cc_final: 0.7523 (mtp) REVERT: K 335 ASN cc_start: 0.8645 (m-40) cc_final: 0.8406 (m-40) REVERT: K 366 PHE cc_start: 0.8160 (m-80) cc_final: 0.7380 (m-80) outliers start: 41 outliers final: 30 residues processed: 243 average time/residue: 0.2126 time to fit residues: 71.7914 Evaluate side-chains 231 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain K residue 28 CYS Chi-restraints excluded: chain K residue 93 GLU Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 230 ASP Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 298 ASP Chi-restraints excluded: chain K residue 302 SER Chi-restraints excluded: chain K residue 309 SER Chi-restraints excluded: chain K residue 313 LEU Chi-restraints excluded: chain K residue 327 LEU Chi-restraints excluded: chain K residue 338 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 54 optimal weight: 20.0000 chunk 97 optimal weight: 30.0000 chunk 89 optimal weight: 40.0000 chunk 50 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN K 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.095810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.074632 restraints weight = 67029.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.077739 restraints weight = 26668.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.079629 restraints weight = 13997.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.080550 restraints weight = 9210.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.081321 restraints weight = 7445.133| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.8915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9666 Z= 0.194 Angle : 0.619 5.980 13093 Z= 0.336 Chirality : 0.043 0.150 1458 Planarity : 0.005 0.070 1680 Dihedral : 9.725 174.507 1308 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.23 % Allowed : 17.88 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.33 (0.24), residues: 1165 helix: 0.60 (0.22), residues: 524 sheet: -0.27 (0.36), residues: 197 loop : -1.09 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 267 TYR 0.018 0.002 TYR B 310 PHE 0.017 0.002 PHE A 141 TRP 0.024 0.002 TRP B 397 HIS 0.008 0.002 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 ( 9666) covalent geometry : angle 0.61911 / 0.34 (13093) hydrogen bonds : bond 0.05189 / 3.44 ( 503) hydrogen bonds : angle 5.35702 / 3.84 ( 1428) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.7603 (m-80) cc_final: 0.7351 (m-80) REVERT: A 302 MET cc_start: 0.7616 (mmm) cc_final: 0.7220 (ttm) REVERT: A 334 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8659 (p) REVERT: B 198 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6649 (pt0) REVERT: B 215 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7462 (tp) REVERT: B 299 MET cc_start: 0.7892 (mmp) cc_final: 0.7687 (mmp) REVERT: B 362 LYS cc_start: 0.8947 (mmmt) cc_final: 0.8525 (mtpp) REVERT: B 363 MET cc_start: 0.7900 (mtp) cc_final: 0.7570 (mtp) REVERT: B 384 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7205 (mt0) REVERT: K 215 ARG cc_start: 0.7825 (mmp80) cc_final: 0.7526 (mmp80) outliers start: 44 outliers final: 33 residues processed: 236 average time/residue: 0.2175 time to fit residues: 72.3977 Evaluate side-chains 235 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 198 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 384 GLN Chi-restraints excluded: chain K residue 28 CYS Chi-restraints excluded: chain K residue 88 TYR Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 188 ASN Chi-restraints excluded: chain K residue 230 ASP Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 298 ASP Chi-restraints excluded: chain K residue 302 SER Chi-restraints excluded: chain K residue 309 SER Chi-restraints excluded: chain K residue 313 LEU Chi-restraints excluded: chain K residue 327 LEU Chi-restraints excluded: chain K residue 338 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 23 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 chunk 31 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN K 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.094556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.073224 restraints weight = 66788.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.076408 restraints weight = 26094.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.078285 restraints weight = 13572.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.079417 restraints weight = 8928.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.080088 restraints weight = 7022.547| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.9241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9666 Z= 0.193 Angle : 0.612 6.060 13093 Z= 0.333 Chirality : 0.043 0.156 1458 Planarity : 0.005 0.056 1680 Dihedral : 9.618 173.223 1308 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.52 % Allowed : 19.13 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.31 (0.24), residues: 1165 helix: 0.68 (0.22), residues: 522 sheet: -0.32 (0.35), residues: 197 loop : -1.13 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 276 TYR 0.025 0.002 TYR K 343 PHE 0.022 0.002 PHE K 187 TRP 0.023 0.002 TRP B 397 HIS 0.006 0.002 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 ( 9666) covalent geometry : angle 0.61195 / 0.33 (13093) hydrogen bonds : bond 0.05121 / 3.38 ( 503) hydrogen bonds : angle 5.26922 / 3.79 ( 1428) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 199 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.7682 (m-80) cc_final: 0.7412 (m-80) REVERT: A 302 MET cc_start: 0.7629 (mmm) cc_final: 0.7257 (ttm) REVERT: A 334 THR cc_start: 0.8976 (OUTLIER) cc_final: 0.8717 (p) REVERT: B 108 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7627 (tp30) REVERT: B 327 ASP cc_start: 0.8274 (t0) cc_final: 0.7943 (t0) REVERT: B 362 LYS cc_start: 0.8946 (mmmt) cc_final: 0.8642 (mmmt) REVERT: B 363 MET cc_start: 0.7876 (mtp) cc_final: 0.7628 (mtp) REVERT: B 384 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7156 (mt0) REVERT: K 366 PHE cc_start: 0.8069 (m-80) cc_final: 0.7295 (m-80) outliers start: 47 outliers final: 36 residues processed: 226 average time/residue: 0.2206 time to fit residues: 69.5234 Evaluate side-chains 228 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 384 GLN Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 28 CYS Chi-restraints excluded: chain K residue 88 TYR Chi-restraints excluded: chain K residue 93 GLU Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 230 ASP Chi-restraints excluded: chain K residue 244 TYR Chi-restraints excluded: chain K residue 298 ASP Chi-restraints excluded: chain K residue 302 SER Chi-restraints excluded: chain K residue 313 LEU Chi-restraints excluded: chain K residue 327 LEU Chi-restraints excluded: chain K residue 338 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 73 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 115 optimal weight: 30.0000 chunk 103 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 116 optimal weight: 30.0000 chunk 9 optimal weight: 20.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 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 = 0.093018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.071767 restraints weight = 67934.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.074901 restraints weight = 26417.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.076771 restraints weight = 13705.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.077656 restraints weight = 9012.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.078492 restraints weight = 7301.115| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.9630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9666 Z= 0.206 Angle : 0.625 6.094 13093 Z= 0.339 Chirality : 0.043 0.152 1458 Planarity : 0.005 0.086 1680 Dihedral : 9.523 170.861 1308 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.23 % Allowed : 19.71 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.38 (0.24), residues: 1165 helix: 0.69 (0.22), residues: 522 sheet: -0.59 (0.35), residues: 205 loop : -1.14 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 276 TYR 0.019 0.002 TYR B 310 PHE 0.019 0.002 PHE B 92 TRP 0.026 0.002 TRP B 397 HIS 0.006 0.002 HIS B 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.21 ( 9666) covalent geometry : angle 0.62504 / 0.34 (13093) hydrogen bonds : bond 0.05139 / 3.37 ( 503) hydrogen bonds : angle 5.25650 / 3.78 ( 1428) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 194 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.7864 (m-80) cc_final: 0.7531 (m-80) REVERT: A 205 ASP cc_start: 0.7576 (t0) cc_final: 0.6878 (m-30) REVERT: A 302 MET cc_start: 0.7705 (mmm) cc_final: 0.7448 (ttm) REVERT: A 334 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8800 (p) REVERT: A 425 MET cc_start: 0.8004 (tpp) cc_final: 0.7465 (tpp) REVERT: B 108 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7612 (tp30) REVERT: B 179 VAL cc_start: 0.7583 (m) cc_final: 0.7343 (p) REVERT: B 327 ASP cc_start: 0.8380 (t0) cc_final: 0.8093 (t0) REVERT: B 362 LYS cc_start: 0.8974 (mmmt) cc_final: 0.8609 (mmmt) REVERT: B 363 MET cc_start: 0.7932 (mtp) cc_final: 0.7706 (mtp) REVERT: B 380 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7505 (mtt90) REVERT: B 384 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7017 (mt0) REVERT: K 191 ILE cc_start: 0.8411 (mp) cc_final: 0.8035 (mm) REVERT: K 215 ARG cc_start: 0.7724 (mmp80) cc_final: 0.7433 (mmp80) REVERT: K 366 PHE cc_start: 0.7992 (m-80) cc_final: 0.7188 (m-80) outliers start: 44 outliers final: 36 residues processed: 223 average time/residue: 0.2235 time to fit residues: 70.3082 Evaluate side-chains 229 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 384 GLN Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 28 CYS Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 88 TYR Chi-restraints excluded: chain K residue 93 GLU Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 230 ASP Chi-restraints excluded: chain K residue 244 TYR Chi-restraints excluded: chain K residue 298 ASP Chi-restraints excluded: chain K residue 302 SER Chi-restraints excluded: chain K residue 313 LEU Chi-restraints excluded: chain K residue 327 LEU Chi-restraints excluded: chain K residue 338 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 28 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 99 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 103 optimal weight: 30.0000 chunk 104 optimal weight: 40.0000 chunk 52 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.092711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.071489 restraints weight = 67358.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.074600 restraints weight = 26200.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.076423 restraints weight = 13583.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.077459 restraints weight = 8971.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.077864 restraints weight = 7127.870| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.9874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9666 Z= 0.184 Angle : 0.601 6.605 13093 Z= 0.325 Chirality : 0.043 0.158 1458 Planarity : 0.005 0.091 1680 Dihedral : 9.384 170.372 1308 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.13 % Allowed : 20.48 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.25 (0.24), residues: 1165 helix: 0.85 (0.22), residues: 522 sheet: -0.57 (0.34), residues: 212 loop : -1.13 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 276 TYR 0.027 0.001 TYR K 343 PHE 0.017 0.002 PHE A 395 TRP 0.022 0.002 TRP B 397 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 ( 9666) covalent geometry : angle 0.60144 / 0.32 (13093) hydrogen bonds : bond 0.04914 / 3.24 ( 503) hydrogen bonds : angle 5.15536 / 3.70 ( 1428) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 195 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.7964 (m-80) cc_final: 0.7673 (m-80) REVERT: A 205 ASP cc_start: 0.7296 (t0) cc_final: 0.6650 (m-30) REVERT: A 302 MET cc_start: 0.7656 (mmm) cc_final: 0.7423 (ttm) REVERT: A 334 THR cc_start: 0.9113 (OUTLIER) cc_final: 0.8882 (p) REVERT: A 425 MET cc_start: 0.8026 (tpp) cc_final: 0.7470 (tpp) REVERT: B 108 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7623 (tp30) REVERT: B 179 VAL cc_start: 0.7430 (m) cc_final: 0.7118 (p) REVERT: B 362 LYS cc_start: 0.9004 (mmmt) cc_final: 0.8626 (mmmt) REVERT: B 363 MET cc_start: 0.7942 (mtp) cc_final: 0.7730 (mtp) REVERT: B 380 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.8041 (mtm180) REVERT: B 384 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7017 (mt0) REVERT: K 337 LEU cc_start: 0.9297 (mt) cc_final: 0.8996 (tp) REVERT: K 366 PHE cc_start: 0.8119 (m-80) cc_final: 0.7266 (m-80) outliers start: 43 outliers final: 31 residues processed: 225 average time/residue: 0.2265 time to fit residues: 71.4625 Evaluate side-chains 218 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 384 GLN Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 88 TYR Chi-restraints excluded: chain K residue 93 GLU Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 244 TYR Chi-restraints excluded: chain K residue 298 ASP Chi-restraints excluded: chain K residue 302 SER Chi-restraints excluded: chain K residue 327 LEU Chi-restraints excluded: chain K residue 338 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 21 optimal weight: 10.0000 chunk 94 optimal weight: 40.0000 chunk 111 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 35 optimal weight: 0.5980 chunk 74 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 329 ASN B 14 ASN 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 = 0.093725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.072418 restraints weight = 66947.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.075527 restraints weight = 25915.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.077382 restraints weight = 13488.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.078497 restraints weight = 8912.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.079002 restraints weight = 7032.449| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 1.0010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9666 Z= 0.144 Angle : 0.587 7.805 13093 Z= 0.313 Chirality : 0.042 0.156 1458 Planarity : 0.005 0.073 1680 Dihedral : 9.202 168.841 1308 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.37 % Allowed : 21.54 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.05 (0.25), residues: 1165 helix: 1.12 (0.22), residues: 523 sheet: -0.39 (0.35), residues: 212 loop : -1.01 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 390 TYR 0.023 0.001 TYR K 343 PHE 0.016 0.001 PHE B 92 TRP 0.016 0.002 TRP B 397 HIS 0.006 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 9666) covalent geometry : angle 0.58730 / 0.31 (13093) hydrogen bonds : bond 0.04534 / 2.99 ( 503) hydrogen bonds : angle 5.00289 / 3.59 ( 1428) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ASP cc_start: 0.7256 (t0) cc_final: 0.6722 (m-30) REVERT: A 334 THR cc_start: 0.9101 (OUTLIER) cc_final: 0.8863 (p) REVERT: A 425 MET cc_start: 0.8000 (tpp) cc_final: 0.7450 (tpp) REVERT: B 179 VAL cc_start: 0.7533 (m) cc_final: 0.7209 (p) REVERT: B 362 LYS cc_start: 0.8972 (mmmt) cc_final: 0.8631 (mmmt) REVERT: B 363 MET cc_start: 0.7967 (mtp) cc_final: 0.7766 (mtp) REVERT: B 384 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7191 (mt0) REVERT: K 215 ARG cc_start: 0.8114 (mmp80) cc_final: 0.7902 (mmp80) REVERT: K 337 LEU cc_start: 0.9271 (mt) cc_final: 0.8985 (tp) REVERT: K 366 PHE cc_start: 0.8093 (m-80) cc_final: 0.7260 (m-80) outliers start: 35 outliers final: 24 residues processed: 215 average time/residue: 0.2169 time to fit residues: 64.9889 Evaluate side-chains 208 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 384 GLN Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 88 TYR Chi-restraints excluded: chain K residue 93 GLU Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 244 TYR Chi-restraints excluded: chain K residue 298 ASP Chi-restraints excluded: chain K residue 302 SER Chi-restraints excluded: chain K residue 338 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 102 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 chunk 73 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 329 ASN B 329 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.092924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.071807 restraints weight = 66904.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.074910 restraints weight = 25884.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.076728 restraints weight = 13391.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.077852 restraints weight = 8847.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.078296 restraints weight = 6968.193| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 1.0171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9666 Z= 0.155 Angle : 0.591 6.934 13093 Z= 0.315 Chirality : 0.042 0.158 1458 Planarity : 0.005 0.091 1680 Dihedral : 9.121 168.019 1308 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.37 % Allowed : 21.54 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.10 (0.25), residues: 1165 helix: 1.15 (0.22), residues: 523 sheet: -0.39 (0.35), residues: 212 loop : -0.97 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 276 TYR 0.017 0.001 TYR K 343 PHE 0.018 0.002 PHE B 92 TRP 0.018 0.002 TRP B 397 HIS 0.006 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 9666) covalent geometry : angle 0.59082 / 0.32 (13093) hydrogen bonds : bond 0.04567 / 3.00 ( 503) hydrogen bonds : angle 4.99950 / 3.59 ( 1428) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.8374 (mmp) cc_final: 0.8088 (mmp) REVERT: A 205 ASP cc_start: 0.7200 (t0) cc_final: 0.6600 (m-30) REVERT: A 425 MET cc_start: 0.8129 (tpp) cc_final: 0.7437 (tpp) REVERT: B 179 VAL cc_start: 0.7566 (m) cc_final: 0.7213 (p) REVERT: B 362 LYS cc_start: 0.9122 (mmmt) cc_final: 0.8656 (mmmt) REVERT: B 363 MET cc_start: 0.7956 (mtp) cc_final: 0.7749 (mtp) REVERT: B 384 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7169 (mt0) REVERT: K 337 LEU cc_start: 0.9271 (mt) cc_final: 0.9009 (tp) REVERT: K 366 PHE cc_start: 0.8077 (m-80) cc_final: 0.7227 (m-80) outliers start: 35 outliers final: 30 residues processed: 204 average time/residue: 0.2016 time to fit residues: 58.1755 Evaluate side-chains 209 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 329 GLN Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 384 GLN Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 88 TYR Chi-restraints excluded: chain K residue 93 GLU Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 244 TYR Chi-restraints excluded: chain K residue 298 ASP Chi-restraints excluded: chain K residue 302 SER Chi-restraints excluded: chain K residue 327 LEU Chi-restraints excluded: chain K residue 338 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 37 optimal weight: 20.0000 chunk 54 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 20.0000 chunk 100 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 14 ASN B 329 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.093046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.071872 restraints weight = 67014.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.074932 restraints weight = 25930.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.076785 restraints weight = 13490.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.077896 restraints weight = 8880.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.078345 restraints weight = 6991.869| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 1.0205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.233 9666 Z= 0.220 Angle : 0.890 59.198 13093 Z= 0.524 Chirality : 0.044 0.485 1458 Planarity : 0.005 0.092 1680 Dihedral : 9.119 168.047 1308 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.27 % Allowed : 21.83 % Favored : 74.90 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.55 % 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: 0.09 (0.25), residues: 1165 helix: 1.13 (0.22), residues: 523 sheet: -0.39 (0.35), residues: 212 loop : -0.97 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 390 TYR 0.015 0.001 TYR K 343 PHE 0.016 0.002 PHE K 166 TRP 0.017 0.002 TRP B 397 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.22 ( 9666) covalent geometry : angle 0.89029 / 0.52 (13093) hydrogen bonds : bond 0.04596 / 3.01 ( 503) hydrogen bonds : angle 4.99216 / 3.59 ( 1428) =============================================================================== Job complete usr+sys time: 3079.32 seconds wall clock time: 53 minutes 25.99 seconds (3205.99 seconds total)