Starting phenix.real_space_refine on Thu Mar 5 03:57:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nba_12258/03_2026/7nba_12258.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nba_12258/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7nba_12258/03_2026/7nba_12258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nba_12258/03_2026/7nba_12258.map" model { file = "/net/cci-nas-00/data/ceres_data/7nba_12258/03_2026/7nba_12258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nba_12258/03_2026/7nba_12258.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 3.20, per 1000 atoms: 0.17 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: 1.79 Conformation dependent library (CDL) restraints added in 527.6 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: 0.52 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: 3.94 Time building geometry restraints manager: 2.46 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: 8737 34.76 - 69.51: 203 69.51 - 104.27: 12 104.27 - 139.02: 0 139.02 - 173.78: 4 Dihedral angle restraints: 8956 sinusoidal: 4921 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 8953 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: 0.010 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: 0.080 Extract box with map and model: 0.190 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.930 Find NCS groups from input model: 0.070 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6107 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 : 12.712 173.780 3632 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 covalent geometry : bond 0.01923 ( 9666) covalent geometry : angle 1.90397 (13093) hydrogen bonds : bond 0.16971 ( 503) hydrogen bonds : angle 7.89796 ( 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 : 0.520 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: A 24 TYR cc_start: 0.6821 (m-80) cc_final: 0.5792 (m-10) REVERT: A 198 SER cc_start: 0.7519 (m) cc_final: 0.7296 (p) REVERT: A 301 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7307 (mm-40) REVERT: A 352 LYS cc_start: 0.6796 (tptt) cc_final: 0.6239 (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: 0.7189 (tmm) REVERT: A 386 GLU cc_start: 0.8655 (tt0) cc_final: 0.8346 (tt0) REVERT: B 24 ILE cc_start: 0.8113 (mm) cc_final: 0.7903 (mm) REVERT: B 101 TRP cc_start: 0.6314 (t60) cc_final: 0.5961 (t60) REVERT: B 150 LEU cc_start: 0.7364 (tp) cc_final: 0.7149 (tt) REVERT: B 212 PHE cc_start: 0.6690 (t80) cc_final: 0.6488 (t80) REVERT: B 232 THR cc_start: 0.6464 (m) cc_final: 0.6122 (m) REVERT: B 299 MET cc_start: 0.5736 (mmp) cc_final: 0.5342 (mmp) REVERT: B 300 MET cc_start: 0.8077 (mpp) cc_final: 0.7773 (mtt) outliers start: 0 outliers final: 0 residues processed: 515 average time/residue: 0.2767 time to fit residues: 184.9817 Evaluate side-chains 296 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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: 9.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN B 8 GLN B 334 GLN B 347 ASN K 262 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.111084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.089384 restraints weight = 63858.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.093537 restraints weight = 24073.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.095944 restraints weight = 11934.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.097410 restraints weight = 7422.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.097961 restraints weight = 5565.407| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9666 Z= 0.224 Angle : 0.711 6.469 13093 Z= 0.395 Chirality : 0.046 0.164 1458 Planarity : 0.006 0.064 1680 Dihedral : 12.028 177.260 1364 Min Nonbonded Distance : 1.638 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.08 % Allowed : 12.12 % Favored : 84.81 % 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: 0.55 (0.24), residues: 1165 helix: 0.99 (0.22), residues: 505 sheet: 0.31 (0.35), residues: 203 loop : -0.17 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 422 TYR 0.026 0.002 TYR A 210 PHE 0.021 0.002 PHE A 255 TRP 0.010 0.002 TRP B 397 HIS 0.008 0.002 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 9666) covalent geometry : angle 0.71124 (13093) hydrogen bonds : bond 0.06665 ( 503) hydrogen bonds : angle 6.11457 ( 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 318 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 286 time to evaluate : 0.443 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: A 203 MET cc_start: 0.5952 (mtp) cc_final: 0.5604 (mtt) REVERT: A 301 GLN cc_start: 0.8255 (mm-40) cc_final: 0.7958 (mt0) REVERT: A 313 MET cc_start: 0.7280 (mtp) cc_final: 0.7019 (mmm) REVERT: A 332 ILE cc_start: 0.8724 (mm) cc_final: 0.8274 (pt) REVERT: A 341 ILE cc_start: 0.6703 (mm) cc_final: 0.6448 (mt) REVERT: A 352 LYS cc_start: 0.7404 (tptt) cc_final: 0.6481 (mptt) REVERT: A 377 MET cc_start: 0.7742 (tmm) cc_final: 0.7309 (tmm) REVERT: B 24 ILE cc_start: 0.7545 (mm) cc_final: 0.7223 (mm) REVERT: B 69 GLU cc_start: 0.7734 (tt0) cc_final: 0.7451 (tt0) REVERT: B 123 GLU cc_start: 0.8781 (tp30) cc_final: 0.8534 (tp30) REVERT: B 134 GLN cc_start: 0.7006 (mt0) cc_final: 0.6774 (mt0) REVERT: B 198 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6452 (pt0) REVERT: B 229 VAL cc_start: 0.7413 (t) cc_final: 0.7196 (p) REVERT: B 257 MET cc_start: 0.8199 (mmp) cc_final: 0.7970 (mmt) REVERT: B 299 MET cc_start: 0.6007 (mmp) cc_final: 0.5616 (mmp) REVERT: B 300 MET cc_start: 0.8098 (mpp) cc_final: 0.7760 (mtt) REVERT: B 363 MET cc_start: 0.8053 (mtt) cc_final: 0.7703 (mtp) REVERT: K 199 GLU cc_start: 0.6969 (tp30) cc_final: 0.6579 (tp30) REVERT: K 380 GLU cc_start: 0.7913 (mp0) cc_final: 0.7705 (mp0) outliers start: 32 outliers final: 22 residues processed: 309 average time/residue: 0.2248 time to fit residues: 94.9963 Evaluate side-chains 252 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 229 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 151 SER 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 332 ASN 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 10.0000 chunk 90 optimal weight: 30.0000 chunk 38 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 100 optimal weight: 30.0000 chunk 99 optimal weight: 5.9990 chunk 106 optimal weight: 40.0000 chunk 83 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS A 192 HIS B 424 GLN K 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.104149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.082871 restraints weight = 65672.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.086698 restraints weight = 24753.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.088948 restraints weight = 12341.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.090271 restraints weight = 7769.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.090780 restraints weight = 5921.008| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.7186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9666 Z= 0.179 Angle : 0.632 7.435 13093 Z= 0.346 Chirality : 0.043 0.148 1458 Planarity : 0.005 0.054 1680 Dihedral : 11.369 178.142 1364 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.98 % Allowed : 14.23 % Favored : 82.79 % 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: 0.88 (0.22), residues: 508 sheet: 0.27 (0.36), residues: 196 loop : -0.46 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 77 TYR 0.014 0.002 TYR B 281 PHE 0.015 0.002 PHE A 255 TRP 0.020 0.002 TRP B 397 HIS 0.009 0.002 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 9666) covalent geometry : angle 0.63156 (13093) hydrogen bonds : bond 0.05545 ( 503) hydrogen bonds : angle 5.64686 ( 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 274 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 243 time to evaluate : 0.328 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: A 53 PHE cc_start: 0.7690 (m-80) cc_final: 0.7146 (m-80) REVERT: A 161 TYR cc_start: 0.7832 (m-80) cc_final: 0.7509 (m-80) REVERT: A 253 THR cc_start: 0.7604 (p) cc_final: 0.7366 (t) REVERT: A 313 MET cc_start: 0.7328 (mtp) cc_final: 0.7013 (mmm) REVERT: A 352 LYS cc_start: 0.7660 (tptt) cc_final: 0.6706 (mptt) REVERT: A 424 ASP cc_start: 0.7779 (m-30) cc_final: 0.7534 (m-30) REVERT: A 425 MET cc_start: 0.8359 (tpp) cc_final: 0.7666 (tpp) REVERT: B 198 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6665 (pt0) REVERT: B 233 MET cc_start: 0.7507 (mtm) cc_final: 0.6966 (mtm) REVERT: B 257 MET cc_start: 0.8302 (mmp) cc_final: 0.8001 (mmt) REVERT: B 299 MET cc_start: 0.6690 (mmp) cc_final: 0.6139 (mmp) REVERT: K 191 ILE cc_start: 0.8506 (mp) cc_final: 0.8199 (mm) REVERT: K 215 ARG cc_start: 0.8012 (mmp80) cc_final: 0.7775 (mmp80) outliers start: 31 outliers final: 21 residues processed: 257 average time/residue: 0.2247 time to fit residues: 79.2152 Evaluate side-chains 230 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 208 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER 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 11 GLN Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 147 MET 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 276 LEU Chi-restraints excluded: chain K residue 298 ASP Chi-restraints excluded: chain K residue 313 LEU 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: 10.0000 chunk 106 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 chunk 93 optimal weight: 30.0000 chunk 52 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 89 optimal weight: 50.0000 chunk 1 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 112 optimal weight: 20.0000 overall best weight: 9.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN B 423 GLN K 40 ASN K 48 ASN ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.096512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.075199 restraints weight = 67168.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.078507 restraints weight = 26055.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.080443 restraints weight = 13434.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.081647 restraints weight = 8819.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.082138 restraints weight = 6857.368| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.8447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9666 Z= 0.238 Angle : 0.677 7.250 13093 Z= 0.372 Chirality : 0.044 0.160 1458 Planarity : 0.005 0.054 1680 Dihedral : 11.335 176.333 1364 Min Nonbonded Distance : 1.631 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.13 % Allowed : 15.48 % Favored : 80.38 % 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: -0.31 (0.23), residues: 1165 helix: 0.47 (0.21), residues: 521 sheet: 0.04 (0.36), residues: 186 loop : -1.00 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 390 TYR 0.018 0.002 TYR B 310 PHE 0.019 0.002 PHE A 141 TRP 0.035 0.003 TRP B 397 HIS 0.013 0.003 HIS B 396 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 9666) covalent geometry : angle 0.67651 (13093) hydrogen bonds : bond 0.05728 ( 503) hydrogen bonds : angle 5.60722 ( 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 259 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 216 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: A 53 PHE cc_start: 0.7395 (m-80) cc_final: 0.7186 (m-80) REVERT: A 302 MET cc_start: 0.7601 (mmm) cc_final: 0.7074 (ttm) REVERT: A 313 MET cc_start: 0.7342 (mtp) cc_final: 0.7036 (mmm) REVERT: B 198 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.7023 (pt0) REVERT: B 215 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7590 (tp) REVERT: B 257 MET cc_start: 0.8098 (mmp) cc_final: 0.7853 (mmt) REVERT: B 299 MET cc_start: 0.7684 (mmp) cc_final: 0.7407 (mmp) REVERT: B 355 ASP cc_start: 0.6934 (m-30) cc_final: 0.5849 (t0) REVERT: B 362 LYS cc_start: 0.9040 (mmmt) cc_final: 0.8760 (mmmt) REVERT: B 363 MET cc_start: 0.8045 (mtp) cc_final: 0.7807 (mtp) REVERT: B 384 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7104 (mt0) REVERT: K 215 ARG cc_start: 0.8000 (mmp80) cc_final: 0.7741 (mmp80) outliers start: 43 outliers final: 33 residues processed: 240 average time/residue: 0.2281 time to fit residues: 75.6178 Evaluate side-chains 229 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 110 ILE 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 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 181 GLU Chi-restraints excluded: chain B residue 198 GLU 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 381 ILE Chi-restraints excluded: chain B residue 384 GLN Chi-restraints excluded: chain B residue 403 MET 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 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 319 GLU 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: 40.0000 chunk 89 optimal weight: 40.0000 chunk 50 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 56 optimal weight: 30.0000 chunk 108 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 115 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 overall best weight: 6.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 188 ASN ** 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 = 0.3805 r_free = 0.3805 target = 0.096732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.075634 restraints weight = 66138.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.078895 restraints weight = 25500.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.080811 restraints weight = 13136.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.081987 restraints weight = 8572.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.082458 restraints weight = 6701.231| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.8829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9666 Z= 0.168 Angle : 0.594 5.936 13093 Z= 0.322 Chirality : 0.042 0.149 1458 Planarity : 0.005 0.090 1680 Dihedral : 11.072 175.909 1364 Min Nonbonded Distance : 1.687 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.46 % Allowed : 18.65 % 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: -0.16 (0.24), residues: 1165 helix: 0.67 (0.22), residues: 523 sheet: -0.14 (0.35), residues: 188 loop : -0.90 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 276 TYR 0.016 0.001 TYR B 310 PHE 0.014 0.002 PHE K 166 TRP 0.009 0.001 TRP B 397 HIS 0.008 0.002 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9666) covalent geometry : angle 0.59380 (13093) hydrogen bonds : bond 0.05040 ( 503) hydrogen bonds : angle 5.32294 ( 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 239 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 0.540 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 302 MET cc_start: 0.7551 (mmm) cc_final: 0.7168 (ttm) REVERT: B 198 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.7009 (pt0) REVERT: B 215 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7486 (tp) REVERT: B 293 MET cc_start: 0.8138 (mtp) cc_final: 0.7757 (mtp) REVERT: B 299 MET cc_start: 0.7850 (mmp) cc_final: 0.7616 (mmp) REVERT: B 362 LYS cc_start: 0.9013 (mmmt) cc_final: 0.8781 (mmmt) REVERT: B 363 MET cc_start: 0.7883 (mtp) cc_final: 0.7673 (mtp) REVERT: K 215 ARG cc_start: 0.7817 (mmp80) cc_final: 0.7561 (mmp80) outliers start: 36 outliers final: 27 residues processed: 222 average time/residue: 0.2451 time to fit residues: 74.1344 Evaluate side-chains 222 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 165 SER 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 391 LEU Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 11 GLN 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 332 ASN Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain K residue 28 CYS Chi-restraints excluded: chain K residue 88 TYR Chi-restraints excluded: chain K residue 103 PHE Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 298 ASP Chi-restraints excluded: chain K residue 302 SER Chi-restraints excluded: chain K residue 313 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 23 optimal weight: 9.9990 chunk 33 optimal weight: 0.0570 chunk 10 optimal weight: 0.8980 chunk 100 optimal weight: 30.0000 chunk 5 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 overall best weight: 3.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 337 ASN ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.097791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.076565 restraints weight = 65163.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.079936 restraints weight = 24898.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.081909 restraints weight = 12704.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.083105 restraints weight = 8224.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.083592 restraints weight = 6409.928| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.9052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9666 Z= 0.127 Angle : 0.564 6.295 13093 Z= 0.299 Chirality : 0.042 0.149 1458 Planarity : 0.004 0.060 1680 Dihedral : 10.701 174.998 1364 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.69 % Allowed : 19.62 % Favored : 77.69 % 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: 0.22 (0.24), residues: 1165 helix: 1.12 (0.22), residues: 517 sheet: -0.17 (0.35), residues: 197 loop : -0.77 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 276 TYR 0.010 0.001 TYR B 310 PHE 0.014 0.001 PHE K 166 TRP 0.009 0.001 TRP A 21 HIS 0.008 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9666) covalent geometry : angle 0.56354 (13093) hydrogen bonds : bond 0.04436 ( 503) hydrogen bonds : angle 5.08166 ( 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 244 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 0.492 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 302 MET cc_start: 0.7501 (mmm) cc_final: 0.7170 (ttm) REVERT: A 334 THR cc_start: 0.8729 (m) cc_final: 0.8484 (p) REVERT: A 386 GLU cc_start: 0.8403 (tt0) cc_final: 0.7739 (tm-30) REVERT: B 198 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6697 (pt0) REVERT: B 293 MET cc_start: 0.8135 (mtp) cc_final: 0.7716 (mtp) REVERT: B 299 MET cc_start: 0.7867 (mmp) cc_final: 0.7640 (mmp) REVERT: B 323 MET cc_start: 0.8080 (mmm) cc_final: 0.7843 (mmm) REVERT: B 327 ASP cc_start: 0.8267 (t0) cc_final: 0.7988 (t0) REVERT: B 362 LYS cc_start: 0.9022 (mmmt) cc_final: 0.8762 (mmmt) REVERT: B 363 MET cc_start: 0.7832 (mtp) cc_final: 0.7628 (mtp) REVERT: K 191 ILE cc_start: 0.8646 (mp) cc_final: 0.8303 (mm) outliers start: 28 outliers final: 22 residues processed: 232 average time/residue: 0.2420 time to fit residues: 77.1882 Evaluate side-chains 219 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 157 LEU 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 316 CYS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain B residue 3 GLU 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 178 THR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 370 ASN 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 298 ASP Chi-restraints excluded: chain K residue 302 SER Chi-restraints excluded: chain K residue 313 LEU 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: 3.9990 chunk 115 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 116 optimal weight: 40.0000 chunk 9 optimal weight: 20.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 188 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.093976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.073052 restraints weight = 67352.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.076194 restraints weight = 26844.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.078053 restraints weight = 13973.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.079136 restraints weight = 9225.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.079869 restraints weight = 7305.786| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.9498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9666 Z= 0.197 Angle : 0.611 6.261 13093 Z= 0.332 Chirality : 0.043 0.147 1458 Planarity : 0.005 0.090 1680 Dihedral : 10.727 172.525 1364 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.75 % Allowed : 19.33 % Favored : 76.92 % 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: -0.07 (0.24), residues: 1165 helix: 0.88 (0.22), residues: 522 sheet: -0.18 (0.36), residues: 193 loop : -1.00 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 276 TYR 0.016 0.002 TYR B 310 PHE 0.021 0.002 PHE A 141 TRP 0.018 0.002 TRP B 397 HIS 0.008 0.002 HIS B 396 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 9666) covalent geometry : angle 0.61144 (13093) hydrogen bonds : bond 0.05008 ( 503) hydrogen bonds : angle 5.17597 ( 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 240 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 0.497 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: A 302 MET cc_start: 0.7697 (mmm) cc_final: 0.7371 (ttm) REVERT: A 334 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8643 (p) REVERT: A 425 MET cc_start: 0.8186 (tpp) cc_final: 0.7228 (tpp) REVERT: B 263 LEU cc_start: 0.8192 (mp) cc_final: 0.7988 (mp) REVERT: B 299 MET cc_start: 0.8116 (mmp) cc_final: 0.7906 (mmp) REVERT: B 323 MET cc_start: 0.8080 (mmm) cc_final: 0.7865 (mmm) REVERT: B 327 ASP cc_start: 0.8306 (t0) cc_final: 0.8010 (t0) REVERT: B 362 LYS cc_start: 0.9057 (mmmt) cc_final: 0.8799 (mmmt) REVERT: B 363 MET cc_start: 0.7582 (mtp) cc_final: 0.7379 (mtp) REVERT: B 384 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7354 (mt0) REVERT: K 191 ILE cc_start: 0.8473 (mp) cc_final: 0.8253 (mp) outliers start: 39 outliers final: 28 residues processed: 223 average time/residue: 0.2336 time to fit residues: 72.3304 Evaluate side-chains 221 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 165 SER 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 316 CYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 391 LEU 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 181 GLU Chi-restraints excluded: chain B residue 270 PHE 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 28 CYS Chi-restraints excluded: chain K residue 93 GLU Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 188 ASN 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 319 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 28 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 99 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 103 optimal weight: 30.0000 chunk 104 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 93 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.093353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.072161 restraints weight = 67248.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.075361 restraints weight = 25959.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.077239 restraints weight = 13414.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.078399 restraints weight = 8826.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.078868 restraints weight = 6946.391| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.9784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9666 Z= 0.175 Angle : 0.596 8.753 13093 Z= 0.320 Chirality : 0.042 0.169 1458 Planarity : 0.005 0.082 1680 Dihedral : 10.711 171.196 1364 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.98 % Allowed : 20.96 % 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: 0.02 (0.25), residues: 1165 helix: 1.01 (0.22), residues: 516 sheet: -0.31 (0.36), residues: 204 loop : -0.92 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 276 TYR 0.016 0.001 TYR B 310 PHE 0.025 0.002 PHE K 187 TRP 0.013 0.002 TRP B 397 HIS 0.006 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 9666) covalent geometry : angle 0.59645 (13093) hydrogen bonds : bond 0.04802 ( 503) hydrogen bonds : angle 5.08277 ( 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 225 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 194 time to evaluate : 0.566 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: A 203 MET cc_start: 0.8455 (mmp) cc_final: 0.8230 (mmp) REVERT: A 302 MET cc_start: 0.7700 (mmm) cc_final: 0.7381 (ttm) REVERT: A 334 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8646 (p) REVERT: A 425 MET cc_start: 0.8064 (tpp) cc_final: 0.7116 (tpp) REVERT: B 179 VAL cc_start: 0.7592 (m) cc_final: 0.7350 (p) REVERT: B 181 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: B 267 MET cc_start: 0.8320 (ptp) cc_final: 0.7746 (ptp) REVERT: B 323 MET cc_start: 0.8015 (mmm) cc_final: 0.7777 (mmm) REVERT: B 327 ASP cc_start: 0.8400 (t0) cc_final: 0.8096 (t0) REVERT: B 362 LYS cc_start: 0.9038 (mmmt) cc_final: 0.8788 (mmmt) REVERT: B 384 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7313 (mt0) REVERT: K 191 ILE cc_start: 0.8563 (mp) cc_final: 0.8328 (mp) REVERT: K 269 HIS cc_start: 0.9322 (m90) cc_final: 0.9089 (m170) outliers start: 31 outliers final: 23 residues processed: 215 average time/residue: 0.2381 time to fit residues: 70.9567 Evaluate side-chains 213 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 238 ILE Chi-restraints excluded: chain A residue 254 GLU 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 A residue 375 VAL Chi-restraints excluded: chain A residue 391 LEU 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 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 384 GLN 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 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 319 GLU 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: 30.0000 chunk 111 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 370 ASN K 96 GLN K 188 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.093788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.072465 restraints weight = 66740.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.075635 restraints weight = 25906.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.077550 restraints weight = 13553.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.078642 restraints weight = 8944.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.079401 restraints weight = 7113.517| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.9989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9666 Z= 0.154 Angle : 0.579 7.174 13093 Z= 0.309 Chirality : 0.042 0.156 1458 Planarity : 0.005 0.077 1680 Dihedral : 10.575 169.639 1364 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.88 % Allowed : 20.96 % Favored : 76.15 % 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 (0.25), residues: 1165 helix: 1.17 (0.22), residues: 517 sheet: -0.32 (0.36), residues: 204 loop : -0.89 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 276 TYR 0.013 0.001 TYR B 310 PHE 0.017 0.002 PHE B 92 TRP 0.011 0.001 TRP B 397 HIS 0.006 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9666) covalent geometry : angle 0.57901 (13093) hydrogen bonds : bond 0.04545 ( 503) hydrogen bonds : angle 4.96920 ( 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 222 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 0.505 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: A 205 ASP cc_start: 0.7395 (t0) cc_final: 0.6722 (m-30) REVERT: A 302 MET cc_start: 0.7659 (mmm) cc_final: 0.7416 (ttm) REVERT: A 334 THR cc_start: 0.8941 (m) cc_final: 0.8660 (p) REVERT: A 377 MET cc_start: 0.7534 (tmm) cc_final: 0.7235 (tmm) REVERT: A 425 MET cc_start: 0.8056 (tpp) cc_final: 0.7095 (tpp) REVERT: B 179 VAL cc_start: 0.7407 (m) cc_final: 0.7128 (p) REVERT: B 181 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7509 (tt0) REVERT: B 267 MET cc_start: 0.8304 (ptp) cc_final: 0.7738 (ptp) REVERT: B 293 MET cc_start: 0.8361 (mtm) cc_final: 0.7998 (mtp) REVERT: B 362 LYS cc_start: 0.9135 (mmmt) cc_final: 0.8758 (mmmt) REVERT: B 384 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7154 (mt0) REVERT: K 191 ILE cc_start: 0.8485 (mp) cc_final: 0.8266 (mp) REVERT: K 269 HIS cc_start: 0.9316 (m90) cc_final: 0.9071 (m170) outliers start: 30 outliers final: 25 residues processed: 211 average time/residue: 0.2461 time to fit residues: 71.2611 Evaluate side-chains 210 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 165 SER 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 316 CYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 391 LEU 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 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 384 GLN 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 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 319 GLU 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: 7.9990 chunk 29 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 16 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 33 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.092802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.071788 restraints weight = 66862.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.074839 restraints weight = 26550.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.076668 restraints weight = 14066.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.077700 restraints weight = 9362.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.078401 restraints weight = 7486.811| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 1.0140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9666 Z= 0.177 Angle : 0.599 6.913 13093 Z= 0.320 Chirality : 0.042 0.158 1458 Planarity : 0.004 0.052 1680 Dihedral : 10.594 169.560 1364 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.88 % Allowed : 21.44 % Favored : 75.67 % 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: 0.06 (0.25), residues: 1165 helix: 1.11 (0.22), residues: 517 sheet: -0.37 (0.37), residues: 207 loop : -0.96 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 162 TYR 0.015 0.001 TYR B 310 PHE 0.015 0.002 PHE K 166 TRP 0.014 0.002 TRP B 397 HIS 0.006 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 9666) covalent geometry : angle 0.59862 (13093) hydrogen bonds : bond 0.04703 ( 503) hydrogen bonds : angle 5.00358 ( 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 213 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.529 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: A 203 MET cc_start: 0.8752 (mmp) cc_final: 0.8283 (mmp) REVERT: A 205 ASP cc_start: 0.7285 (t0) cc_final: 0.6559 (m-30) REVERT: A 302 MET cc_start: 0.7757 (mmm) cc_final: 0.7496 (ttm) REVERT: A 313 MET cc_start: 0.7872 (ttm) cc_final: 0.7566 (ttm) REVERT: A 334 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8723 (p) REVERT: A 425 MET cc_start: 0.8085 (tpp) cc_final: 0.7150 (tpp) REVERT: B 179 VAL cc_start: 0.7463 (m) cc_final: 0.7135 (p) REVERT: B 267 MET cc_start: 0.8290 (ptp) cc_final: 0.7787 (ptp) REVERT: B 293 MET cc_start: 0.8322 (mtm) cc_final: 0.7909 (mtm) REVERT: B 362 LYS cc_start: 0.9117 (mmmt) cc_final: 0.8738 (mmmt) REVERT: B 384 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7166 (mt0) REVERT: K 191 ILE cc_start: 0.8510 (mp) cc_final: 0.8273 (mp) REVERT: K 269 HIS cc_start: 0.9286 (m90) cc_final: 0.9021 (m170) outliers start: 30 outliers final: 24 residues processed: 204 average time/residue: 0.2198 time to fit residues: 62.3526 Evaluate side-chains 203 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 334 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 391 LEU 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 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 93 GLU Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 244 TYR 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 319 GLU 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: 5.9990 chunk 105 optimal weight: 30.0000 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 20.0000 chunk 100 optimal weight: 0.5980 chunk 60 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.094209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.072960 restraints weight = 66473.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.076188 restraints weight = 25597.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.078080 restraints weight = 13179.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.079247 restraints weight = 8644.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.079724 restraints weight = 6779.025| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 1.0223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9666 Z= 0.129 Angle : 0.569 6.661 13093 Z= 0.300 Chirality : 0.042 0.141 1458 Planarity : 0.004 0.051 1680 Dihedral : 10.386 168.431 1364 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.12 % Allowed : 22.21 % Favored : 75.67 % 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: 0.32 (0.25), residues: 1165 helix: 1.35 (0.23), residues: 517 sheet: -0.28 (0.38), residues: 201 loop : -0.83 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 309 TYR 0.014 0.001 TYR B 425 PHE 0.015 0.001 PHE K 166 TRP 0.011 0.001 TRP A 21 HIS 0.006 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9666) covalent geometry : angle 0.56853 (13093) hydrogen bonds : bond 0.04293 ( 503) hydrogen bonds : angle 4.83880 ( 1428) =============================================================================== Job complete usr+sys time: 3183.61 seconds wall clock time: 55 minutes 19.35 seconds (3319.35 seconds total)