Starting phenix.real_space_refine on Wed Jun 3 15:34:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t1d_55431/06_2026/9t1d_55431.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t1d_55431/06_2026/9t1d_55431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9t1d_55431/06_2026/9t1d_55431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t1d_55431/06_2026/9t1d_55431.map" model { file = "/net/cci-nas-00/data/ceres_data/9t1d_55431/06_2026/9t1d_55431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t1d_55431/06_2026/9t1d_55431.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.026 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 5 5.49 5 Mg 1 5.21 5 S 46 5.16 5 C 4239 2.51 5 N 1151 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 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6746 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "B" Number of atoms: 3335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3335 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 20, 'TRANS': 403} Chain breaks: 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} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.98, per 1000 atoms: 0.29 Number of scatterers: 6746 At special positions: 0 Unit cell: (66.154, 70.422, 112.035, 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 46 16.00 P 5 15.00 Mg 1 11.99 O 1304 8.00 N 1151 7.00 C 4239 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: 0.54 Conformation dependent library (CDL) restraints added in 398.8 milliseconds 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1578 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 6 sheets defined 53.3% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 71 through 80 removed outlier: 4.621A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 128 removed outlier: 3.816A pdb=" N ILE A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.242A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 239 removed outlier: 3.627A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.604A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.916A pdb=" N GLN A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 401 removed outlier: 4.170A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 412 removed outlier: 3.922A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 437 removed outlier: 4.133A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 41 through 46 removed outlier: 4.342A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 69 through 78 removed outlier: 4.384A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.887A pdb=" N PHE B 85 " --> pdb=" O GLY B 82 " (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 107 through 126 removed outlier: 3.624A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.681A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 238 removed outlier: 3.806A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 241 No H-bonds generated for 'chain 'B' and resid 239 through 241' Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 324 through 337 Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.601A pdb=" N PHE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 374 through 391 removed outlier: 3.577A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.370A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 428 Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.206A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA4, first strand: chain 'A' and resid 272 through 273 removed outlier: 6.572A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.041A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY B 132 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N SER B 138 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N MET B 164 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 10.479A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 13.749A pdb=" N ASP B 203 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N SER B 364 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE B 317 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N THR B 366 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA B 315 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE B 368 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL B 313 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ASN B 370 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N LYS B 350 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL B 313 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ALA B 352 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA B 315 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N CYS B 354 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N PHE B 317 " --> pdb=" O CYS B 354 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.707A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) 305 hydrogen bonds defined for protein. 894 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: 0.86 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2239 1.34 - 1.46: 1557 1.46 - 1.58: 3024 1.58 - 1.70: 8 1.70 - 1.81: 72 Bond restraints: 6900 Sorted by residual: bond pdb=" N ARG B 2 " pdb=" CA ARG B 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N ARG A 2 " pdb=" CA ARG A 2 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.69e+00 bond pdb=" N THR A 340 " pdb=" CA THR A 340 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.14e+00 bond pdb=" CB ARG B 213 " pdb=" CG ARG B 213 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.09e+00 bond pdb=" C5 GDP B 501 " pdb=" C4 GDP B 501 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.04e+00 ... (remaining 6895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 9244 2.50 - 5.01: 117 5.01 - 7.51: 9 7.51 - 10.02: 2 10.02 - 12.52: 1 Bond angle restraints: 9373 Sorted by residual: angle pdb=" N THR A 340 " pdb=" CA THR A 340 " pdb=" C THR A 340 " ideal model delta sigma weight residual 110.80 123.32 -12.52 2.13e+00 2.20e-01 3.46e+01 angle pdb=" C ARG A 339 " pdb=" N THR A 340 " pdb=" CA THR A 340 " ideal model delta sigma weight residual 121.54 130.64 -9.10 1.91e+00 2.74e-01 2.27e+01 angle pdb=" N ARG A 339 " pdb=" CA ARG A 339 " pdb=" C ARG A 339 " ideal model delta sigma weight residual 108.23 113.69 -5.46 1.72e+00 3.38e-01 1.01e+01 angle pdb=" CA ILE B 163 " pdb=" CB ILE B 163 " pdb=" CG1 ILE B 163 " ideal model delta sigma weight residual 110.40 115.76 -5.36 1.70e+00 3.46e-01 9.95e+00 angle pdb=" N PHE A 343 " pdb=" CA PHE A 343 " pdb=" C PHE A 343 " ideal model delta sigma weight residual 110.80 104.66 6.14 2.13e+00 2.20e-01 8.31e+00 ... (remaining 9368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.97: 3808 27.97 - 55.94: 259 55.94 - 83.92: 28 83.92 - 111.89: 3 111.89 - 139.86: 1 Dihedral angle restraints: 4099 sinusoidal: 1639 harmonic: 2460 Sorted by residual: dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -35.27 139.86 1 2.00e+01 2.50e-03 4.23e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 175.94 -106.67 1 2.00e+01 2.50e-03 3.09e+01 dihedral pdb=" CA LYS A 336 " pdb=" C LYS A 336 " pdb=" N THR A 337 " pdb=" CA THR A 337 " ideal model delta harmonic sigma weight residual 180.00 153.09 26.91 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 4096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 827 0.050 - 0.100: 157 0.100 - 0.150: 38 0.150 - 0.200: 1 0.200 - 0.250: 2 Chirality restraints: 1025 Sorted by residual: chirality pdb=" CB ILE A 212 " pdb=" CA ILE A 212 " pdb=" CG1 ILE A 212 " pdb=" CG2 ILE A 212 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA THR A 340 " pdb=" N THR A 340 " pdb=" C THR A 340 " pdb=" CB THR A 340 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ILE B 345 " pdb=" N ILE B 345 " pdb=" C ILE B 345 " pdb=" CB ILE B 345 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.87e-01 ... (remaining 1022 not shown) Planarity restraints: 1220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 326 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.23e+00 pdb=" C LYS A 326 " 0.053 2.00e-02 2.50e+03 pdb=" O LYS A 326 " -0.020 2.00e-02 2.50e+03 pdb=" N ASP A 327 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 333 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.88e+00 pdb=" C ALA A 333 " 0.042 2.00e-02 2.50e+03 pdb=" O ALA A 333 " -0.016 2.00e-02 2.50e+03 pdb=" N THR A 334 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 161 " 0.019 2.00e-02 2.50e+03 1.70e-02 5.80e+00 pdb=" CG TYR A 161 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR A 161 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 161 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 161 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 161 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 161 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 161 " 0.002 2.00e-02 2.50e+03 ... (remaining 1217 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 18 2.52 - 3.11: 5018 3.11 - 3.71: 10693 3.71 - 4.30: 15502 4.30 - 4.90: 26305 Nonbonded interactions: 57536 Sorted by model distance: nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 1.921 2.170 nonbonded pdb=" O THR B 219 " pdb=" OG1 THR B 219 " model vdw 2.365 3.040 nonbonded pdb=" O ASN B 347 " pdb=" OD1 ASN B 347 " model vdw 2.389 3.040 nonbonded pdb=" O ASP A 116 " pdb=" OD1 ASP A 120 " model vdw 2.396 3.040 nonbonded pdb=" O PRO A 222 " pdb=" O MET B 323 " model vdw 2.409 3.040 ... (remaining 57531 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.260 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 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 : 0.003 0.033 6900 Z= 0.139 Angle : 0.685 12.521 9373 Z= 0.354 Chirality : 0.044 0.250 1025 Planarity : 0.004 0.035 1220 Dihedral : 17.782 139.861 2521 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.59 % Allowed : 4.62 % Favored : 94.79 % Rotamer: Outliers : 3.45 % Allowed : 24.97 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.41 (0.29), residues: 844 helix: 1.47 (0.27), residues: 373 sheet: 0.62 (0.49), residues: 124 loop : -1.20 (0.30), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 306 TYR 0.042 0.002 TYR A 161 PHE 0.013 0.001 PHE A 149 TRP 0.013 0.001 TRP A 346 HIS 0.004 0.001 HIS A 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 6900) covalent geometry : angle 0.68464 / 0.35 ( 9373) hydrogen bonds : bond 0.12344 / 8.85 ( 305) hydrogen bonds : angle 5.94837 / 4.29 ( 894) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 46 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 8 residues processed: 70 average time/residue: 0.7171 time to fit residues: 52.5166 Evaluate side-chains 44 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 395 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN A 216 ASN B 83 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.047046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.038921 restraints weight = 32000.534| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 4.17 r_work: 0.2857 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6900 Z= 0.146 Angle : 0.617 11.906 9373 Z= 0.309 Chirality : 0.043 0.146 1025 Planarity : 0.004 0.031 1220 Dihedral : 8.604 135.554 966 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.15 % Favored : 95.62 % Rotamer: Outliers : 4.41 % Allowed : 21.52 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.85 (0.29), residues: 844 helix: 1.80 (0.27), residues: 376 sheet: 0.45 (0.48), residues: 125 loop : -0.79 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 320 TYR 0.024 0.001 TYR A 24 PHE 0.014 0.001 PHE A 149 TRP 0.009 0.001 TRP A 21 HIS 0.006 0.001 HIS A 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 ( 6900) covalent geometry : angle 0.61671 / 0.31 ( 9373) hydrogen bonds : bond 0.04326 / 2.91 ( 305) hydrogen bonds : angle 4.65690 / 3.38 ( 894) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 40 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ASP cc_start: 0.9338 (OUTLIER) cc_final: 0.8940 (t0) REVERT: A 215 ARG cc_start: 0.9307 (OUTLIER) cc_final: 0.9013 (mtp-110) REVERT: A 313 MET cc_start: 0.9269 (OUTLIER) cc_final: 0.8732 (mtm) REVERT: A 377 MET cc_start: 0.8851 (ttp) cc_final: 0.8562 (ttp) REVERT: B 201 CYS cc_start: 0.8806 (m) cc_final: 0.8284 (p) REVERT: B 293 MET cc_start: 0.9025 (mtp) cc_final: 0.8729 (mtp) REVERT: B 321 MET cc_start: 0.8894 (ptp) cc_final: 0.8598 (ptp) REVERT: B 324 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8703 (tptp) outliers start: 32 outliers final: 8 residues processed: 68 average time/residue: 0.6458 time to fit residues: 46.1557 Evaluate side-chains 48 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 395 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 77 optimal weight: 0.0370 chunk 55 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 63 optimal weight: 0.0770 overall best weight: 3.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.045896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.038064 restraints weight = 32495.632| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 4.08 r_work: 0.2841 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6900 Z= 0.189 Angle : 0.620 11.074 9373 Z= 0.310 Chirality : 0.043 0.136 1025 Planarity : 0.004 0.029 1220 Dihedral : 7.953 135.306 954 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.03 % Favored : 95.73 % Rotamer: Outliers : 4.00 % Allowed : 21.93 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.92 (0.29), residues: 844 helix: 1.97 (0.27), residues: 374 sheet: 0.28 (0.47), residues: 129 loop : -0.79 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 320 TYR 0.026 0.002 TYR A 24 PHE 0.016 0.001 PHE A 169 TRP 0.012 0.001 TRP A 21 HIS 0.008 0.001 HIS A 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 ( 6900) covalent geometry : angle 0.62023 / 0.31 ( 9373) hydrogen bonds : bond 0.04318 / 2.89 ( 305) hydrogen bonds : angle 4.52085 / 3.28 ( 894) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 38 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ASP cc_start: 0.9358 (OUTLIER) cc_final: 0.8835 (t0) REVERT: A 215 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.8822 (mtp-110) REVERT: A 282 TYR cc_start: 0.8164 (OUTLIER) cc_final: 0.7918 (p90) REVERT: A 313 MET cc_start: 0.9284 (OUTLIER) cc_final: 0.8705 (mtm) REVERT: A 377 MET cc_start: 0.8840 (ttp) cc_final: 0.8534 (ttp) REVERT: B 201 CYS cc_start: 0.8774 (m) cc_final: 0.8305 (p) REVERT: B 293 MET cc_start: 0.9093 (mtp) cc_final: 0.8842 (mtp) REVERT: B 321 MET cc_start: 0.9013 (ptp) cc_final: 0.8768 (ptp) REVERT: B 324 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8790 (tptp) outliers start: 29 outliers final: 11 residues processed: 63 average time/residue: 0.6858 time to fit residues: 45.2298 Evaluate side-chains 50 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 34 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 395 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 65 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 0.3980 chunk 37 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.044928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.037207 restraints weight = 33438.035| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 4.11 r_work: 0.2820 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6900 Z= 0.207 Angle : 0.627 11.265 9373 Z= 0.312 Chirality : 0.043 0.152 1025 Planarity : 0.004 0.029 1220 Dihedral : 8.019 135.885 953 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.03 % Favored : 95.73 % Rotamer: Outliers : 4.41 % Allowed : 21.38 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.98 (0.29), residues: 844 helix: 2.04 (0.27), residues: 372 sheet: 0.36 (0.49), residues: 121 loop : -0.77 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 320 TYR 0.032 0.002 TYR A 24 PHE 0.017 0.001 PHE A 169 TRP 0.010 0.001 TRP A 21 HIS 0.005 0.001 HIS A 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.21 ( 6900) covalent geometry : angle 0.62748 / 0.31 ( 9373) hydrogen bonds : bond 0.04210 / 2.82 ( 305) hydrogen bonds : angle 4.46139 / 3.24 ( 894) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 37 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ASP cc_start: 0.9336 (OUTLIER) cc_final: 0.8753 (t70) REVERT: A 215 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.8728 (mtp-110) REVERT: A 230 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9371 (mt) REVERT: A 282 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.7982 (p90) REVERT: A 313 MET cc_start: 0.9312 (OUTLIER) cc_final: 0.8761 (mtm) REVERT: A 377 MET cc_start: 0.8869 (ttp) cc_final: 0.8555 (ttp) REVERT: B 201 CYS cc_start: 0.8853 (m) cc_final: 0.8420 (p) REVERT: B 321 MET cc_start: 0.8959 (ptp) cc_final: 0.8720 (ptp) REVERT: B 324 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8802 (tptp) outliers start: 32 outliers final: 10 residues processed: 66 average time/residue: 0.6884 time to fit residues: 47.6180 Evaluate side-chains 50 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 34 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 395 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 68 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.045198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.037274 restraints weight = 33293.299| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 4.16 r_work: 0.2831 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6900 Z= 0.155 Angle : 0.614 11.341 9373 Z= 0.300 Chirality : 0.043 0.130 1025 Planarity : 0.003 0.029 1220 Dihedral : 7.901 135.240 953 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.91 % Favored : 95.85 % Rotamer: Outliers : 3.45 % Allowed : 21.93 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.93 (0.29), residues: 844 helix: 2.00 (0.27), residues: 385 sheet: 0.27 (0.49), residues: 121 loop : -0.90 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 282 TYR 0.026 0.001 TYR A 24 PHE 0.015 0.001 PHE A 169 TRP 0.010 0.001 TRP A 21 HIS 0.005 0.001 HIS A 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 ( 6900) covalent geometry : angle 0.61381 / 0.30 ( 9373) hydrogen bonds : bond 0.03833 / 2.56 ( 305) hydrogen bonds : angle 4.30689 / 3.14 ( 894) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 35 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.8547 (tpt) cc_final: 0.8336 (tpt) REVERT: A 109 THR cc_start: 0.9085 (OUTLIER) cc_final: 0.8648 (p) REVERT: A 230 LEU cc_start: 0.9620 (OUTLIER) cc_final: 0.9367 (mt) REVERT: A 282 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.8027 (p90) REVERT: A 313 MET cc_start: 0.9308 (OUTLIER) cc_final: 0.8748 (mtm) REVERT: A 329 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8551 (p0) REVERT: A 377 MET cc_start: 0.8849 (ttp) cc_final: 0.8544 (ttp) REVERT: B 201 CYS cc_start: 0.8808 (m) cc_final: 0.8361 (p) REVERT: B 257 MET cc_start: 0.9143 (mpp) cc_final: 0.8845 (mpp) REVERT: B 293 MET cc_start: 0.9041 (mtp) cc_final: 0.8798 (mtp) REVERT: B 321 MET cc_start: 0.8913 (ptp) cc_final: 0.8710 (ptp) REVERT: B 324 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8763 (tptp) outliers start: 25 outliers final: 10 residues processed: 57 average time/residue: 0.6278 time to fit residues: 37.7285 Evaluate side-chains 49 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 33 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 395 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.045073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.037321 restraints weight = 33513.752| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 4.12 r_work: 0.2831 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6900 Z= 0.164 Angle : 0.610 11.263 9373 Z= 0.297 Chirality : 0.043 0.142 1025 Planarity : 0.003 0.029 1220 Dihedral : 7.848 134.765 952 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.15 % Favored : 95.62 % Rotamer: Outliers : 3.31 % Allowed : 22.90 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.97 (0.29), residues: 844 helix: 2.08 (0.27), residues: 381 sheet: 0.26 (0.49), residues: 121 loop : -0.88 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 282 TYR 0.021 0.001 TYR A 24 PHE 0.017 0.001 PHE A 169 TRP 0.009 0.001 TRP B 21 HIS 0.004 0.001 HIS A 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 6900) covalent geometry : angle 0.60994 / 0.30 ( 9373) hydrogen bonds : bond 0.03870 / 2.59 ( 305) hydrogen bonds : angle 4.28962 / 3.12 ( 894) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 34 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.8963 (m-80) cc_final: 0.8736 (m-80) REVERT: A 36 MET cc_start: 0.8542 (tpt) cc_final: 0.8326 (tpt) REVERT: A 109 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8655 (p) REVERT: A 230 LEU cc_start: 0.9620 (OUTLIER) cc_final: 0.9364 (mt) REVERT: A 313 MET cc_start: 0.9333 (OUTLIER) cc_final: 0.8823 (mtm) REVERT: A 329 ASN cc_start: 0.8855 (OUTLIER) cc_final: 0.8552 (p0) REVERT: A 377 MET cc_start: 0.8835 (ttp) cc_final: 0.8525 (ttp) REVERT: B 201 CYS cc_start: 0.8879 (m) cc_final: 0.8351 (p) REVERT: B 257 MET cc_start: 0.9153 (mpp) cc_final: 0.8826 (mpp) REVERT: B 293 MET cc_start: 0.9040 (mtp) cc_final: 0.8802 (mtp) REVERT: B 324 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8744 (tptp) outliers start: 24 outliers final: 12 residues processed: 56 average time/residue: 0.5959 time to fit residues: 35.2837 Evaluate side-chains 50 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 33 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 395 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 12 optimal weight: 9.9990 chunk 77 optimal weight: 0.4980 chunk 51 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 6 optimal weight: 0.4980 chunk 13 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.045338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.037635 restraints weight = 32721.747| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 4.09 r_work: 0.2835 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6900 Z= 0.136 Angle : 0.600 11.391 9373 Z= 0.289 Chirality : 0.042 0.138 1025 Planarity : 0.003 0.032 1220 Dihedral : 7.754 133.866 952 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.03 % Favored : 95.73 % Rotamer: Outliers : 3.45 % Allowed : 23.59 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.03 (0.30), residues: 844 helix: 2.10 (0.27), residues: 384 sheet: 0.09 (0.48), residues: 131 loop : -0.77 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 339 TYR 0.020 0.001 TYR A 24 PHE 0.015 0.001 PHE A 169 TRP 0.009 0.001 TRP A 21 HIS 0.004 0.001 HIS A 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 6900) covalent geometry : angle 0.60047 / 0.29 ( 9373) hydrogen bonds : bond 0.03645 / 2.42 ( 305) hydrogen bonds : angle 4.23218 / 3.08 ( 894) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 34 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.8937 (m-80) cc_final: 0.8681 (m-80) REVERT: A 36 MET cc_start: 0.8449 (tpt) cc_final: 0.8230 (tpt) REVERT: A 109 THR cc_start: 0.9086 (OUTLIER) cc_final: 0.8671 (p) REVERT: A 230 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9367 (mt) REVERT: A 313 MET cc_start: 0.9319 (OUTLIER) cc_final: 0.8825 (mtm) REVERT: A 329 ASN cc_start: 0.8837 (OUTLIER) cc_final: 0.8542 (p0) REVERT: A 377 MET cc_start: 0.8738 (ttp) cc_final: 0.8338 (ttp) REVERT: B 147 MET cc_start: 0.9088 (mmm) cc_final: 0.8854 (mmm) REVERT: B 201 CYS cc_start: 0.8860 (m) cc_final: 0.8378 (p) REVERT: B 257 MET cc_start: 0.9131 (mpp) cc_final: 0.8834 (mpp) REVERT: B 293 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8797 (mtp) REVERT: B 324 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8719 (tptp) outliers start: 25 outliers final: 12 residues processed: 55 average time/residue: 0.5980 time to fit residues: 34.7317 Evaluate side-chains 50 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 32 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 395 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN ** B 256 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 = 0.3258 r_free = 0.3258 target = 0.045823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.038016 restraints weight = 33285.945| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 4.18 r_work: 0.2855 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6900 Z= 0.114 Angle : 0.601 11.432 9373 Z= 0.285 Chirality : 0.042 0.131 1025 Planarity : 0.003 0.030 1220 Dihedral : 7.591 131.680 952 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.91 % Favored : 95.85 % Rotamer: Outliers : 2.76 % Allowed : 24.55 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 (0.30), residues: 844 helix: 2.16 (0.27), residues: 384 sheet: 0.10 (0.48), residues: 131 loop : -0.71 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 339 TYR 0.019 0.001 TYR A 24 PHE 0.013 0.001 PHE A 169 TRP 0.009 0.001 TRP A 21 HIS 0.003 0.001 HIS A 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 6900) covalent geometry : angle 0.60064 / 0.28 ( 9373) hydrogen bonds : bond 0.03422 / 2.27 ( 305) hydrogen bonds : angle 4.13355 / 3.01 ( 894) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 36 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.8928 (m-80) cc_final: 0.8691 (m-80) REVERT: A 36 MET cc_start: 0.8468 (tpt) cc_final: 0.7930 (tpt) REVERT: A 109 THR cc_start: 0.9136 (OUTLIER) cc_final: 0.8740 (p) REVERT: A 230 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9357 (mt) REVERT: A 313 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.8726 (mtm) REVERT: A 329 ASN cc_start: 0.8815 (OUTLIER) cc_final: 0.8520 (p0) REVERT: A 377 MET cc_start: 0.8719 (ttp) cc_final: 0.8323 (ttp) REVERT: B 201 CYS cc_start: 0.8880 (m) cc_final: 0.8408 (p) REVERT: B 257 MET cc_start: 0.9086 (mpp) cc_final: 0.8813 (mpp) REVERT: B 293 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8796 (mtp) REVERT: B 324 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8592 (tptp) outliers start: 20 outliers final: 9 residues processed: 52 average time/residue: 0.5935 time to fit residues: 32.7420 Evaluate side-chains 48 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 33 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 395 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 9 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 0.0370 chunk 31 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.046325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.038592 restraints weight = 32846.644| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 4.16 r_work: 0.2871 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6900 Z= 0.101 Angle : 0.609 11.444 9373 Z= 0.286 Chirality : 0.042 0.139 1025 Planarity : 0.003 0.029 1220 Dihedral : 7.432 129.079 952 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.15 % Favored : 95.62 % Rotamer: Outliers : 2.90 % Allowed : 24.83 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.30), residues: 844 helix: 2.10 (0.27), residues: 386 sheet: 0.14 (0.48), residues: 131 loop : -0.58 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 339 TYR 0.020 0.001 TYR A 24 PHE 0.014 0.001 PHE A 255 TRP 0.009 0.001 TRP A 21 HIS 0.003 0.001 HIS A 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 ( 6900) covalent geometry : angle 0.60933 / 0.29 ( 9373) hydrogen bonds : bond 0.03255 / 2.17 ( 305) hydrogen bonds : angle 4.09686 / 2.99 ( 894) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 36 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.8929 (m-80) cc_final: 0.8664 (m-80) REVERT: A 36 MET cc_start: 0.8467 (tpt) cc_final: 0.7861 (tpt) REVERT: A 329 ASN cc_start: 0.8829 (OUTLIER) cc_final: 0.8523 (p0) REVERT: A 377 MET cc_start: 0.8709 (ttp) cc_final: 0.8339 (ttp) REVERT: B 201 CYS cc_start: 0.8879 (m) cc_final: 0.8459 (p) REVERT: B 293 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8789 (mtp) REVERT: B 324 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8526 (tptp) outliers start: 21 outliers final: 11 residues processed: 53 average time/residue: 0.5617 time to fit residues: 31.5164 Evaluate side-chains 49 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 395 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 34 optimal weight: 0.0770 chunk 19 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 63 optimal weight: 0.0020 chunk 40 optimal weight: 0.9980 overall best weight: 0.8148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.046547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.038848 restraints weight = 32786.665| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 4.17 r_work: 0.2888 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6900 Z= 0.101 Angle : 0.620 11.922 9373 Z= 0.289 Chirality : 0.042 0.131 1025 Planarity : 0.003 0.029 1220 Dihedral : 7.351 127.971 952 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.03 % Favored : 95.73 % Rotamer: Outliers : 2.21 % Allowed : 25.24 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.22 (0.30), residues: 844 helix: 2.13 (0.27), residues: 387 sheet: 0.11 (0.48), residues: 131 loop : -0.48 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 339 TYR 0.019 0.001 TYR A 24 PHE 0.013 0.001 PHE A 255 TRP 0.009 0.001 TRP A 21 HIS 0.003 0.001 HIS A 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 6900) covalent geometry : angle 0.61971 / 0.29 ( 9373) hydrogen bonds : bond 0.03126 / 2.08 ( 305) hydrogen bonds : angle 4.09266 / 2.97 ( 894) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 34 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.8973 (m-80) cc_final: 0.8712 (m-80) REVERT: A 36 MET cc_start: 0.8470 (tpt) cc_final: 0.7865 (tpt) REVERT: A 329 ASN cc_start: 0.8818 (OUTLIER) cc_final: 0.8553 (p0) REVERT: A 377 MET cc_start: 0.8722 (ttp) cc_final: 0.8383 (ttp) REVERT: B 147 MET cc_start: 0.8854 (mmm) cc_final: 0.8531 (mmm) REVERT: B 201 CYS cc_start: 0.8892 (m) cc_final: 0.8460 (p) REVERT: B 293 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8799 (mtp) outliers start: 16 outliers final: 11 residues processed: 46 average time/residue: 0.5534 time to fit residues: 27.1032 Evaluate side-chains 47 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain B residue 395 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 GLN ** B 256 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 = 0.3260 r_free = 0.3260 target = 0.045712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.038057 restraints weight = 33121.217| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 4.15 r_work: 0.2861 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6900 Z= 0.127 Angle : 0.621 11.794 9373 Z= 0.293 Chirality : 0.042 0.130 1025 Planarity : 0.003 0.029 1220 Dihedral : 7.430 129.098 952 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.15 % Favored : 95.62 % Rotamer: Outliers : 2.21 % Allowed : 24.97 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.23 (0.30), residues: 844 helix: 2.13 (0.27), residues: 387 sheet: 0.11 (0.48), residues: 131 loop : -0.45 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 320 TYR 0.019 0.001 TYR A 24 PHE 0.013 0.001 PHE A 169 TRP 0.008 0.001 TRP A 21 HIS 0.003 0.001 HIS A 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 6900) covalent geometry : angle 0.62105 / 0.29 ( 9373) hydrogen bonds : bond 0.03389 / 2.28 ( 305) hydrogen bonds : angle 4.12096 / 2.99 ( 894) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1917.86 seconds wall clock time: 34 minutes 2.67 seconds (2042.67 seconds total)