Starting phenix.real_space_refine on Fri Sep 11 02:20:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6e7b_8997/09_2026/6e7b_8997.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e7b_8997/09_2026/6e7b_8997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6e7b_8997/09_2026/6e7b_8997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e7b_8997/09_2026/6e7b_8997.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6e7b_8997/09_2026/6e7b_8997.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6e7b_8997/09_2026/6e7b_8997.cif" model { file = "/net/cci-nas-00/data/ceres_data/6e7b_8997/09_2026/6e7b_8997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e7b_8997/09_2026/6e7b_8997.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.204 sd= 1.216 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 4259 2.51 5 N 1155 2.21 5 O 1304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6774 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3350 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 19, 'TRANS': 406} Chain: "A" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3358 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 20, 'TRANS': 407} Chain breaks: 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: "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} Time building chain proxies: 1.11, per 1000 atoms: 0.16 Number of scatterers: 6774 At special positions: 0 Unit cell: (72, 70, 108, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 6 15.00 Mg 2 11.99 O 1304 8.00 N 1155 7.00 C 4259 6.00 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: 0.46 Conformation dependent library (CDL) restraints added in 301.8 milliseconds 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1584 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 51.4% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'B' and resid 9 through 28 removed outlier: 3.533A pdb=" N VAL B 23 " --> pdb=" O LYS B 19 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 24 " --> pdb=" O PHE B 20 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 46 removed outlier: 4.291A 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 70 through 79 removed outlier: 3.526A pdb=" N SER B 75 " --> pdb=" O GLY B 71 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) 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 106 through 127 removed outlier: 3.536A pdb=" N ALA B 110 " --> pdb=" O TYR B 106 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU B 125 " --> pdb=" O ARG B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.852A pdb=" N GLY B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 193 removed outlier: 3.552A pdb=" N HIS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 removed outlier: 3.651A pdb=" N TYR B 208 " --> pdb=" O ASN B 204 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 242 removed outlier: 3.929A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY B 235 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 removed outlier: 4.109A pdb=" N ASN B 256 " --> pdb=" O LYS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.597A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 391 removed outlier: 4.050A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 402 removed outlier: 3.898A pdb=" N GLU B 401 " --> pdb=" O TRP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 426 removed outlier: 4.038A pdb=" N THR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 71 through 80 removed outlier: 4.161A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) 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 129 removed outlier: 3.517A pdb=" N VAL A 118 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 161 Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.963A pdb=" N ILE A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.114A pdb=" N ARG A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.752A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.741A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 338 removed outlier: 4.022A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 402 removed outlier: 4.109A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.976A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 4.198A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 4 removed outlier: 7.242A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.513A pdb=" N VAL B 60 " --> pdb=" O ASN B 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 65 through 66 removed outlier: 6.683A pdb=" N LEU B 65 " --> pdb=" O ILE B 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 134 through 138 removed outlier: 7.176A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 199 through 200 removed outlier: 6.811A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 349 through 352 removed outlier: 8.542A pdb=" N LYS B 350 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL B 313 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ALA B 352 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N THR B 315 " --> pdb=" O ALA B 352 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 65 through 68 removed outlier: 3.572A pdb=" N VAL A 66 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE A 5 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE A 135 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU A 168 " --> pdb=" O CYS A 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA9, first strand: chain 'A' and resid 351 through 354 Processing sheet with id=AB1, first strand: chain 'A' and resid 351 through 354 removed outlier: 6.769A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) 282 hydrogen bonds defined for protein. 828 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.91 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2227 1.34 - 1.46: 1241 1.46 - 1.58: 3372 1.58 - 1.69: 10 1.69 - 1.81: 78 Bond restraints: 6928 Sorted by residual: bond pdb=" O3B G2P B 502 " pdb=" PG G2P B 502 " ideal model delta sigma weight residual 1.716 1.607 0.109 2.00e-02 2.50e+03 3.00e+01 bond pdb=" O1B G2P B 502 " pdb=" PB G2P B 502 " ideal model delta sigma weight residual 1.510 1.609 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" O2A G2P B 502 " pdb=" PA G2P B 502 " ideal model delta sigma weight residual 1.513 1.608 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C5 GTP A 502 " pdb=" C6 GTP A 502 " ideal model delta sigma weight residual 1.390 1.473 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C4 G2P B 502 " pdb=" C5 G2P B 502 " ideal model delta sigma weight residual 1.384 1.465 -0.081 2.00e-02 2.50e+03 1.63e+01 ... (remaining 6923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 9258 2.55 - 5.10: 117 5.10 - 7.65: 23 7.65 - 10.19: 9 10.19 - 12.74: 2 Bond angle restraints: 9409 Sorted by residual: angle pdb=" PA G2P B 502 " pdb=" C3A G2P B 502 " pdb=" PB G2P B 502 " ideal model delta sigma weight residual 120.83 108.09 12.74 3.00e+00 1.11e-01 1.80e+01 angle pdb=" N TYR B 222 " pdb=" CA TYR B 222 " pdb=" C TYR B 222 " ideal model delta sigma weight residual 111.28 107.15 4.13 1.09e+00 8.42e-01 1.44e+01 angle pdb=" C3A G2P B 502 " pdb=" PA G2P B 502 " pdb=" O5' G2P B 502 " ideal model delta sigma weight residual 99.14 109.87 -10.73 3.00e+00 1.11e-01 1.28e+01 angle pdb=" O1B GTP A 502 " pdb=" PB GTP A 502 " pdb=" O2B GTP A 502 " ideal model delta sigma weight residual 109.50 119.65 -10.15 3.00e+00 1.11e-01 1.14e+01 angle pdb=" O1A GTP A 502 " pdb=" PA GTP A 502 " pdb=" O2A GTP A 502 " ideal model delta sigma weight residual 109.50 119.32 -9.82 3.00e+00 1.11e-01 1.07e+01 ... (remaining 9404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.42: 4063 31.42 - 62.83: 38 62.83 - 94.24: 7 94.24 - 125.66: 1 125.66 - 157.07: 2 Dihedral angle restraints: 4111 sinusoidal: 1642 harmonic: 2469 Sorted by residual: dihedral pdb=" C5' GTP A 502 " pdb=" O5' GTP A 502 " pdb=" PA GTP A 502 " pdb=" O3A GTP A 502 " ideal model delta sinusoidal sigma weight residual 69.27 -133.66 -157.07 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" C8 GTP A 502 " pdb=" C1' GTP A 502 " pdb=" N9 GTP A 502 " pdb=" O4' GTP A 502 " ideal model delta sinusoidal sigma weight residual 104.59 -41.98 146.57 1 2.00e+01 2.50e-03 4.40e+01 dihedral pdb=" O3B GTP A 502 " pdb=" O3A GTP A 502 " pdb=" PB GTP A 502 " pdb=" PA GTP A 502 " ideal model delta sinusoidal sigma weight residual 291.08 171.08 120.00 1 2.00e+01 2.50e-03 3.60e+01 ... (remaining 4108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 572 0.030 - 0.061: 302 0.061 - 0.091: 101 0.091 - 0.122: 43 0.122 - 0.152: 10 Chirality restraints: 1028 Sorted by residual: chirality pdb=" CA VAL A 363 " pdb=" N VAL A 363 " pdb=" C VAL A 363 " pdb=" CB VAL A 363 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.78e-01 chirality pdb=" CB ILE A 115 " pdb=" CA ILE A 115 " pdb=" CG1 ILE A 115 " pdb=" CG2 ILE A 115 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CA ILE B 368 " pdb=" N ILE B 368 " pdb=" C ILE B 368 " pdb=" CB ILE B 368 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 1025 not shown) Planarity restraints: 1221 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 79 " -0.172 9.50e-02 1.11e+02 7.73e-02 3.68e+00 pdb=" NE ARG A 79 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 79 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 79 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 79 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 267 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.38e+00 pdb=" N PRO B 268 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 268 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 268 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 356 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.87e+00 pdb=" N PRO B 357 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 357 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 357 " 0.024 5.00e-02 4.00e+02 ... (remaining 1218 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 99 2.59 - 3.17: 6292 3.17 - 3.74: 10676 3.74 - 4.32: 15716 4.32 - 4.90: 25100 Nonbonded interactions: 57883 Sorted by model distance: nonbonded pdb="MG MG B 501 " pdb=" O1G G2P B 502 " model vdw 2.009 2.170 nonbonded pdb="MG MG A 501 " pdb=" O3G GTP A 502 " model vdw 2.012 2.170 nonbonded pdb="MG MG B 501 " pdb=" O1B G2P B 502 " model vdw 2.049 2.170 nonbonded pdb="MG MG B 501 " pdb=" O3B G2P B 502 " model vdw 2.069 2.170 nonbonded pdb=" OE1 GLU A 71 " pdb="MG MG A 501 " model vdw 2.099 2.170 ... (remaining 57878 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: 9.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.090 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 : 0.006 0.109 6928 Z= 0.274 Angle : 0.828 12.742 9409 Z= 0.401 Chirality : 0.043 0.152 1028 Planarity : 0.004 0.077 1221 Dihedral : 11.475 157.073 2527 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.14 % Allowed : 3.84 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.13 (0.25), residues: 848 helix: -2.97 (0.19), residues: 352 sheet: -3.95 (0.43), residues: 93 loop : -2.06 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 241 TYR 0.013 0.002 TYR B 208 PHE 0.019 0.002 PHE B 212 TRP 0.014 0.002 TRP A 21 HIS 0.008 0.001 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.27 ( 6928) covalent geometry : angle 0.82842 / 0.40 ( 9409) hydrogen bonds : bond 0.28612 / 19.13 ( 278) hydrogen bonds : angle 10.12227 / 6.93 ( 828) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 223 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 100 ASN cc_start: 0.7481 (t0) cc_final: 0.7193 (t0) REVERT: B 289 LEU cc_start: 0.8010 (mp) cc_final: 0.7744 (mp) REVERT: B 403 MET cc_start: 0.7705 (tpt) cc_final: 0.6434 (mmm) REVERT: A 50 ASN cc_start: 0.7276 (t0) cc_final: 0.7027 (t0) REVERT: A 203 MET cc_start: 0.7696 (mmm) cc_final: 0.7314 (mmm) outliers start: 1 outliers final: 1 residues processed: 224 average time/residue: 0.0975 time to fit residues: 27.6012 Evaluate side-chains 135 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 52 ASN B 291 GLN B 329 GLN A 11 GLN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 197 HIS A 206 ASN A 258 ASN A 300 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.129455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.111842 restraints weight = 9841.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.115692 restraints weight = 5342.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.118388 restraints weight = 3478.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.120266 restraints weight = 2514.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.121643 restraints weight = 1948.554| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 6928 Z= 0.258 Angle : 0.746 7.121 9409 Z= 0.384 Chirality : 0.050 0.159 1028 Planarity : 0.005 0.057 1221 Dihedral : 9.995 161.902 948 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.74 % Allowed : 11.39 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.26), residues: 848 helix: -1.44 (0.23), residues: 363 sheet: -3.35 (0.44), residues: 93 loop : -1.62 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 84 TYR 0.018 0.002 TYR B 36 PHE 0.027 0.003 PHE A 255 TRP 0.020 0.002 TRP A 21 HIS 0.008 0.001 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.26 ( 6928) covalent geometry : angle 0.74613 / 0.38 ( 9409) hydrogen bonds : bond 0.05434 / 3.32 ( 278) hydrogen bonds : angle 5.82785 / 3.96 ( 828) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.7068 (mmp-170) cc_final: 0.6425 (tpm170) REVERT: B 406 MET cc_start: 0.6878 (ptm) cc_final: 0.6553 (tpp) REVERT: A 103 TYR cc_start: 0.7004 (t80) cc_final: 0.6530 (t80) REVERT: A 108 TYR cc_start: 0.6255 (OUTLIER) cc_final: 0.5937 (t80) REVERT: A 147 SER cc_start: 0.8668 (m) cc_final: 0.8238 (p) outliers start: 20 outliers final: 11 residues processed: 165 average time/residue: 0.0788 time to fit residues: 17.4508 Evaluate side-chains 130 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 367 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 80 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 72 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 245 GLN B 298 ASN A 50 ASN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.133328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.116047 restraints weight = 9554.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.120015 restraints weight = 5173.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.122739 restraints weight = 3332.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.124507 restraints weight = 2384.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.125957 restraints weight = 1856.641| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6928 Z= 0.130 Angle : 0.610 7.946 9409 Z= 0.311 Chirality : 0.044 0.143 1028 Planarity : 0.004 0.036 1221 Dihedral : 9.658 172.719 946 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.88 % Allowed : 14.40 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.27), residues: 848 helix: -0.72 (0.25), residues: 373 sheet: -2.69 (0.48), residues: 103 loop : -1.46 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 2 TYR 0.012 0.001 TYR A 399 PHE 0.035 0.002 PHE B 20 TRP 0.013 0.001 TRP A 21 HIS 0.006 0.001 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 6928) covalent geometry : angle 0.61014 / 0.31 ( 9409) hydrogen bonds : bond 0.04447 / 2.75 ( 278) hydrogen bonds : angle 5.23458 / 3.57 ( 828) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 77 ARG cc_start: 0.8199 (mtt90) cc_final: 0.7995 (mtt-85) REVERT: B 86 ARG cc_start: 0.6929 (mmp-170) cc_final: 0.5222 (tpt170) REVERT: B 118 ASP cc_start: 0.7289 (m-30) cc_final: 0.7064 (m-30) REVERT: B 276 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6849 (mmm160) REVERT: A 108 TYR cc_start: 0.6037 (OUTLIER) cc_final: 0.5786 (t80) REVERT: A 147 SER cc_start: 0.8472 (m) cc_final: 0.8034 (p) REVERT: A 225 THR cc_start: 0.8819 (p) cc_final: 0.8618 (t) REVERT: A 234 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8193 (mt) REVERT: A 269 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8314 (pt) outliers start: 21 outliers final: 9 residues processed: 161 average time/residue: 0.0877 time to fit residues: 18.5694 Evaluate side-chains 129 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 269 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.1980 chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 65 optimal weight: 0.0970 chunk 42 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 298 ASN A 18 ASN A 50 ASN ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.134159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.117458 restraints weight = 9658.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.121288 restraints weight = 5114.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.123965 restraints weight = 3261.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.125791 restraints weight = 2315.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.127051 restraints weight = 1773.127| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6928 Z= 0.131 Angle : 0.602 8.899 9409 Z= 0.304 Chirality : 0.044 0.157 1028 Planarity : 0.004 0.036 1221 Dihedral : 9.534 179.670 946 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.57 % Allowed : 16.60 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.28), residues: 848 helix: -0.42 (0.25), residues: 374 sheet: -2.45 (0.47), residues: 110 loop : -1.24 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 359 TYR 0.013 0.001 TYR A 357 PHE 0.030 0.002 PHE B 20 TRP 0.014 0.001 TRP A 21 HIS 0.003 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 6928) covalent geometry : angle 0.60218 / 0.30 ( 9409) hydrogen bonds : bond 0.04085 / 2.52 ( 278) hydrogen bonds : angle 4.96619 / 3.39 ( 828) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8254 (mtt) REVERT: B 77 ARG cc_start: 0.8201 (mtt90) cc_final: 0.7990 (mtt-85) REVERT: B 245 GLN cc_start: 0.8428 (mt0) cc_final: 0.8123 (mt0) REVERT: B 276 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6901 (mmm160) REVERT: B 406 MET cc_start: 0.7609 (tpp) cc_final: 0.7100 (ptm) REVERT: A 56 THR cc_start: 0.8269 (m) cc_final: 0.7829 (p) REVERT: A 103 TYR cc_start: 0.7133 (t80) cc_final: 0.6497 (t80) REVERT: A 108 TYR cc_start: 0.6078 (OUTLIER) cc_final: 0.5479 (t80) REVERT: A 147 SER cc_start: 0.8423 (m) cc_final: 0.7994 (p) REVERT: A 234 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8229 (mt) REVERT: A 269 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8226 (pt) outliers start: 26 outliers final: 12 residues processed: 153 average time/residue: 0.0783 time to fit residues: 16.1388 Evaluate side-chains 136 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 378 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 26 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 298 ASN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.133945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.116279 restraints weight = 9572.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.120215 restraints weight = 5127.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.122950 restraints weight = 3310.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.124775 restraints weight = 2383.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.126186 restraints weight = 1861.043| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6928 Z= 0.118 Angle : 0.572 8.484 9409 Z= 0.289 Chirality : 0.043 0.142 1028 Planarity : 0.004 0.035 1221 Dihedral : 9.145 171.491 946 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.98 % Allowed : 16.60 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.28), residues: 848 helix: -0.16 (0.26), residues: 375 sheet: -2.20 (0.48), residues: 109 loop : -1.07 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 359 TYR 0.008 0.001 TYR A 399 PHE 0.020 0.001 PHE B 385 TRP 0.012 0.001 TRP A 21 HIS 0.007 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 6928) covalent geometry : angle 0.57233 / 0.29 ( 9409) hydrogen bonds : bond 0.03857 / 2.39 ( 278) hydrogen bonds : angle 4.81703 / 3.29 ( 828) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 ARG cc_start: 0.8059 (ptp-110) cc_final: 0.7790 (ptp-110) REVERT: B 276 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6900 (mmm160) REVERT: B 406 MET cc_start: 0.7626 (tpp) cc_final: 0.7050 (ptm) REVERT: B 407 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7370 (tm-30) REVERT: A 56 THR cc_start: 0.8249 (m) cc_final: 0.8002 (p) REVERT: A 108 TYR cc_start: 0.5975 (OUTLIER) cc_final: 0.5450 (t80) REVERT: A 147 SER cc_start: 0.8386 (m) cc_final: 0.7940 (p) REVERT: A 212 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.8058 (mt) REVERT: A 269 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8097 (pt) outliers start: 29 outliers final: 19 residues processed: 155 average time/residue: 0.0731 time to fit residues: 15.2487 Evaluate side-chains 143 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 361 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 19 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 298 ASN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 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 = 0.3804 r_free = 0.3804 target = 0.126305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.108784 restraints weight = 9742.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.112516 restraints weight = 5261.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.115126 restraints weight = 3437.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.116932 restraints weight = 2505.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.118279 restraints weight = 1959.409| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.5502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6928 Z= 0.189 Angle : 0.647 7.392 9409 Z= 0.325 Chirality : 0.046 0.168 1028 Planarity : 0.004 0.038 1221 Dihedral : 9.146 165.770 946 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 5.08 % Allowed : 17.83 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.28), residues: 848 helix: -0.19 (0.26), residues: 380 sheet: -2.31 (0.47), residues: 110 loop : -1.08 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 359 TYR 0.011 0.001 TYR B 310 PHE 0.021 0.002 PHE B 385 TRP 0.013 0.002 TRP A 388 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 ( 6928) covalent geometry : angle 0.64652 / 0.33 ( 9409) hydrogen bonds : bond 0.04128 / 2.58 ( 278) hydrogen bonds : angle 5.01075 / 3.43 ( 828) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 HIS cc_start: 0.5918 (t-90) cc_final: 0.5689 (t-90) REVERT: B 213 ARG cc_start: 0.8095 (ptp-110) cc_final: 0.7827 (ptp-110) REVERT: B 276 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.7047 (mmm160) REVERT: B 406 MET cc_start: 0.7891 (tpp) cc_final: 0.7041 (tpp) REVERT: A 56 THR cc_start: 0.8237 (m) cc_final: 0.7757 (p) REVERT: A 103 TYR cc_start: 0.7273 (t80) cc_final: 0.6768 (t80) REVERT: A 108 TYR cc_start: 0.6148 (OUTLIER) cc_final: 0.5407 (t80) REVERT: A 147 SER cc_start: 0.8431 (m) cc_final: 0.8224 (p) REVERT: A 212 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8173 (mt) REVERT: A 269 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8083 (pt) outliers start: 37 outliers final: 26 residues processed: 154 average time/residue: 0.0810 time to fit residues: 16.8413 Evaluate side-chains 146 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 83 HIS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 361 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 6 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 45 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 60.1489 > 50:) chunk 19 optimal weight: 0.3980 chunk 71 optimal weight: 0.0270 chunk 37 optimal weight: 0.8980 overall best weight: 1.2642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 57 HIS B 298 ASN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.129358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.112099 restraints weight = 9662.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.115722 restraints weight = 5254.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.118247 restraints weight = 3455.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.120009 restraints weight = 2532.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.121197 restraints weight = 1993.745| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.5672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6928 Z= 0.138 Angle : 0.607 7.557 9409 Z= 0.306 Chirality : 0.044 0.162 1028 Planarity : 0.004 0.034 1221 Dihedral : 8.945 162.178 946 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.98 % Allowed : 19.75 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.28), residues: 848 helix: 0.03 (0.26), residues: 375 sheet: -2.03 (0.49), residues: 110 loop : -0.98 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 320 TYR 0.008 0.001 TYR B 310 PHE 0.022 0.002 PHE B 385 TRP 0.013 0.002 TRP A 21 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 6928) covalent geometry : angle 0.60737 / 0.31 ( 9409) hydrogen bonds : bond 0.03923 / 2.42 ( 278) hydrogen bonds : angle 4.88716 / 3.32 ( 828) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 190 HIS cc_start: 0.8455 (t70) cc_final: 0.8138 (t-90) REVERT: B 213 ARG cc_start: 0.8096 (ptp-110) cc_final: 0.7797 (ptp-110) REVERT: B 403 MET cc_start: 0.8173 (mmm) cc_final: 0.7209 (mmm) REVERT: B 406 MET cc_start: 0.7847 (tpp) cc_final: 0.7533 (tpp) REVERT: A 56 THR cc_start: 0.8171 (m) cc_final: 0.7836 (p) REVERT: A 103 TYR cc_start: 0.7175 (t80) cc_final: 0.6768 (t80) REVERT: A 108 TYR cc_start: 0.5990 (OUTLIER) cc_final: 0.5376 (t80) REVERT: A 147 SER cc_start: 0.8398 (m) cc_final: 0.8145 (p) REVERT: A 212 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8127 (mt) REVERT: A 269 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8096 (pt) REVERT: A 279 GLU cc_start: 0.7378 (pp20) cc_final: 0.7169 (pp20) outliers start: 29 outliers final: 23 residues processed: 159 average time/residue: 0.0785 time to fit residues: 16.7949 Evaluate side-chains 142 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 361 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 57 HIS B 329 GLN A 11 GLN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.129251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.111132 restraints weight = 9850.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.114917 restraints weight = 5343.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.117541 restraints weight = 3527.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.119306 restraints weight = 2595.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.120634 restraints weight = 2056.944| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.5849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6928 Z= 0.136 Angle : 0.605 7.900 9409 Z= 0.306 Chirality : 0.045 0.170 1028 Planarity : 0.004 0.033 1221 Dihedral : 8.886 159.625 946 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.12 % Allowed : 20.03 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.28), residues: 848 helix: 0.04 (0.27), residues: 373 sheet: -1.83 (0.50), residues: 107 loop : -0.95 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 320 TYR 0.010 0.001 TYR A 103 PHE 0.023 0.002 PHE B 385 TRP 0.014 0.001 TRP A 21 HIS 0.004 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 6928) covalent geometry : angle 0.60464 / 0.31 ( 9409) hydrogen bonds : bond 0.03846 / 2.34 ( 278) hydrogen bonds : angle 4.90229 / 3.32 ( 828) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.8606 (mpp) cc_final: 0.7910 (mpp) REVERT: B 213 ARG cc_start: 0.8030 (ptp-110) cc_final: 0.7695 (ptp-110) REVERT: B 323 MET cc_start: 0.8445 (mmm) cc_final: 0.8241 (tpp) REVERT: B 406 MET cc_start: 0.7837 (tpp) cc_final: 0.7215 (tpp) REVERT: A 56 THR cc_start: 0.8214 (m) cc_final: 0.7899 (p) REVERT: A 103 TYR cc_start: 0.7336 (t80) cc_final: 0.7021 (t80) REVERT: A 108 TYR cc_start: 0.5965 (OUTLIER) cc_final: 0.5351 (t80) REVERT: A 147 SER cc_start: 0.8382 (m) cc_final: 0.8113 (p) REVERT: A 203 MET cc_start: 0.7873 (mmm) cc_final: 0.7299 (mmm) REVERT: A 212 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8139 (mt) REVERT: A 269 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8063 (pt) outliers start: 30 outliers final: 23 residues processed: 149 average time/residue: 0.0700 time to fit residues: 14.1864 Evaluate side-chains 141 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 83 HIS Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 361 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.9980 chunk 3 optimal weight: 0.0010 chunk 39 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 67 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 57 HIS A 11 GLN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.129898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.113021 restraints weight = 9818.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.116743 restraints weight = 5230.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.119260 restraints weight = 3382.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.120954 restraints weight = 2450.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.122297 restraints weight = 1920.330| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.5959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6928 Z= 0.141 Angle : 0.628 10.459 9409 Z= 0.316 Chirality : 0.044 0.175 1028 Planarity : 0.004 0.034 1221 Dihedral : 8.808 155.434 946 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.53 % Allowed : 19.62 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.29), residues: 848 helix: 0.19 (0.27), residues: 369 sheet: -1.76 (0.51), residues: 107 loop : -0.90 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 276 TYR 0.010 0.001 TYR A 103 PHE 0.027 0.002 PHE B 20 TRP 0.013 0.001 TRP A 21 HIS 0.014 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 6928) covalent geometry : angle 0.62750 / 0.32 ( 9409) hydrogen bonds : bond 0.03814 / 2.35 ( 278) hydrogen bonds : angle 4.91765 / 3.33 ( 828) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 3 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.4703 (pm20) REVERT: B 73 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.7774 (mpp) REVERT: B 164 MET cc_start: 0.6909 (OUTLIER) cc_final: 0.6500 (ttt) REVERT: B 213 ARG cc_start: 0.8008 (ptp-110) cc_final: 0.7686 (ptp-110) REVERT: B 276 ARG cc_start: 0.7252 (mmm160) cc_final: 0.6955 (mmm160) REVERT: B 406 MET cc_start: 0.7778 (tpp) cc_final: 0.7211 (tpp) REVERT: A 56 THR cc_start: 0.8193 (m) cc_final: 0.7902 (p) REVERT: A 103 TYR cc_start: 0.7337 (t80) cc_final: 0.7073 (t80) REVERT: A 108 TYR cc_start: 0.5933 (OUTLIER) cc_final: 0.5360 (t80) REVERT: A 147 SER cc_start: 0.8442 (m) cc_final: 0.8127 (p) REVERT: A 203 MET cc_start: 0.7950 (mmm) cc_final: 0.7221 (mmm) REVERT: A 212 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8111 (mt) REVERT: A 269 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8008 (pt) outliers start: 33 outliers final: 22 residues processed: 147 average time/residue: 0.0753 time to fit residues: 15.1409 Evaluate side-chains 143 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 361 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 53 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 0.0980 chunk 59 optimal weight: 3.9990 chunk 3 optimal weight: 0.0020 chunk 46 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 57 HIS B 245 GLN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.131475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.113229 restraints weight = 9655.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.117306 restraints weight = 5015.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.120103 restraints weight = 3192.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.121924 restraints weight = 2286.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.123354 restraints weight = 1787.964| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.6065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6928 Z= 0.123 Angle : 0.638 8.805 9409 Z= 0.321 Chirality : 0.044 0.182 1028 Planarity : 0.004 0.031 1221 Dihedral : 8.740 153.017 946 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.43 % Allowed : 21.95 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.29), residues: 848 helix: 0.28 (0.27), residues: 368 sheet: -1.73 (0.52), residues: 105 loop : -0.91 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 276 TYR 0.013 0.001 TYR A 185 PHE 0.026 0.002 PHE B 20 TRP 0.014 0.002 TRP A 346 HIS 0.008 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 6928) covalent geometry : angle 0.63767 / 0.32 ( 9409) hydrogen bonds : bond 0.03761 / 2.32 ( 278) hydrogen bonds : angle 4.93235 / 3.34 ( 828) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: B 73 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.7827 (mpp) REVERT: B 151 LEU cc_start: 0.8358 (tp) cc_final: 0.8134 (tp) REVERT: B 164 MET cc_start: 0.6902 (OUTLIER) cc_final: 0.6372 (ttt) REVERT: B 203 ASP cc_start: 0.7197 (t0) cc_final: 0.6832 (p0) REVERT: B 276 ARG cc_start: 0.7324 (mmm160) cc_final: 0.6977 (mmm160) REVERT: B 306 ARG cc_start: 0.7644 (mpt90) cc_final: 0.7322 (mtt90) REVERT: B 323 MET cc_start: 0.8290 (tpp) cc_final: 0.7919 (mpp) REVERT: B 406 MET cc_start: 0.7795 (tpp) cc_final: 0.7176 (tpp) REVERT: A 103 TYR cc_start: 0.7275 (t80) cc_final: 0.7052 (t80) REVERT: A 108 TYR cc_start: 0.5974 (OUTLIER) cc_final: 0.5424 (t80) REVERT: A 147 SER cc_start: 0.8485 (m) cc_final: 0.8117 (p) REVERT: A 203 MET cc_start: 0.8009 (mmm) cc_final: 0.7273 (mmm) REVERT: A 212 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.8080 (mt) outliers start: 25 outliers final: 18 residues processed: 150 average time/residue: 0.0836 time to fit residues: 16.6764 Evaluate side-chains 139 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 361 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 75 optimal weight: 0.0670 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 291 GLN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** 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 = 0.3831 r_free = 0.3831 target = 0.128237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.110329 restraints weight = 9707.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.114085 restraints weight = 5281.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.116717 restraints weight = 3472.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.118459 restraints weight = 2548.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.119800 restraints weight = 2017.394| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.6173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6928 Z= 0.152 Angle : 0.643 9.680 9409 Z= 0.324 Chirality : 0.045 0.167 1028 Planarity : 0.004 0.032 1221 Dihedral : 8.779 153.135 946 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.70 % Allowed : 21.54 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.29), residues: 848 helix: 0.12 (0.27), residues: 372 sheet: -1.58 (0.52), residues: 107 loop : -0.83 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 213 TYR 0.021 0.001 TYR B 310 PHE 0.047 0.002 PHE B 20 TRP 0.022 0.002 TRP A 388 HIS 0.009 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 6928) covalent geometry : angle 0.64343 / 0.32 ( 9409) hydrogen bonds : bond 0.03875 / 2.40 ( 278) hydrogen bonds : angle 4.93415 / 3.34 ( 828) =============================================================================== Job complete usr+sys time: 1346.18 seconds wall clock time: 24 minutes 1.28 seconds (1441.28 seconds total)