Starting phenix.real_space_refine on Thu Aug 6 08:17:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/23bb_68823/08_2026/23bb_68823.cif Found real_map, /net/cci-nas-00/data/ceres_data/23bb_68823/08_2026/23bb_68823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/23bb_68823/08_2026/23bb_68823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/23bb_68823/08_2026/23bb_68823.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/23bb_68823/08_2026/23bb_68823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/23bb_68823/08_2026/23bb_68823.map" } resolution = 3.6 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= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians S 43 5.16 5 C 4414 2.51 5 N 1198 2.21 5 O 1302 1.98 5 H 6928 0.53 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13885 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 2654 Classifications: {'peptide': 165} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain: "E" Number of atoms: 2666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2666 Classifications: {'peptide': 166} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 158} Chain: "C" Number of atoms: 1444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1444 Classifications: {'peptide': 88} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 83} Chain: "D" Number of atoms: 1444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1444 Classifications: {'peptide': 88} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 83} Chain: "A" Number of atoms: 5677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 5677 Classifications: {'peptide': 365} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 342} Chain breaks: 3 Time building chain proxies: 2.25, per 1000 atoms: 0.16 Number of scatterers: 13885 At special positions: 0 Unit cell: (123.25, 73.95, 96.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 43 16.00 O 1302 8.00 N 1198 7.00 C 4414 6.00 H 6928 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 338.4 milliseconds 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1650 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 8 sheets defined 39.0% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'B' and resid 110 through 121 Processing helix chain 'B' and resid 155 through 169 removed outlier: 3.703A pdb=" N GLY B 161 " --> pdb=" O PHE B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 193 Processing helix chain 'B' and resid 195 through 200 removed outlier: 4.385A pdb=" N SER B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 239 Processing helix chain 'E' and resid 110 through 121 Processing helix chain 'E' and resid 154 through 169 removed outlier: 3.893A pdb=" N ASP E 158 " --> pdb=" O GLY E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 193 Processing helix chain 'E' and resid 195 through 200 removed outlier: 4.341A pdb=" N SER E 199 " --> pdb=" O PRO E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 239 Processing helix chain 'C' and resid 320 through 334 Processing helix chain 'C' and resid 338 through 350 removed outlier: 3.605A pdb=" N PHE C 350 " --> pdb=" O VAL C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 333 Processing helix chain 'D' and resid 338 through 350 removed outlier: 3.615A pdb=" N PHE D 350 " --> pdb=" O VAL D 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 13 removed outlier: 3.918A pdb=" N ARG A 10 " --> pdb=" O GLU A 6 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A 11 " --> pdb=" O ARG A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 137 removed outlier: 3.833A pdb=" N TRP A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLN A 131 " --> pdb=" O PRO A 127 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 154 removed outlier: 3.620A pdb=" N GLN A 148 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER A 152 " --> pdb=" O GLN A 148 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG A 153 " --> pdb=" O GLN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 302 Processing helix chain 'A' and resid 309 through 321 removed outlier: 3.843A pdb=" N GLY A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 removed outlier: 3.553A pdb=" N GLY A 336 " --> pdb=" O ALA A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 355 removed outlier: 3.623A pdb=" N ALA A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 352 " --> pdb=" O PRO A 348 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 381 Proline residue: A 370 - end of helix removed outlier: 3.544A pdb=" N MET A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 396 removed outlier: 3.722A pdb=" N HIS A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 410 Processing helix chain 'A' and resid 424 through 429 Processing helix chain 'A' and resid 436 through 446 removed outlier: 4.070A pdb=" N LEU A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N CYS A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 480 Processing sheet with id=AA1, first strand: chain 'B' and resid 171 through 177 removed outlier: 3.824A pdb=" N SER B 172 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU B 137 " --> pdb=" O PHE B 204 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N VAL B 206 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU B 139 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N MET B 208 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE B 141 " --> pdb=" O MET B 208 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N THR B 203 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE B 254 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU B 205 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLN B 256 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N LEU B 207 " --> pdb=" O GLN B 256 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LYS B 251 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N PHE C 303 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ILE B 253 " --> pdb=" O PHE C 303 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE C 300 " --> pdb=" O LEU C 365 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU C 365 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU D 365 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLU D 363 " --> pdb=" O ARG C 364 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA D 302 " --> pdb=" O GLU D 363 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LEU D 365 " --> pdb=" O PHE D 300 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N PHE D 300 " --> pdb=" O LEU D 365 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE D 301 " --> pdb=" O LYS E 251 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL E 255 " --> pdb=" O PHE D 303 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N THR E 203 " --> pdb=" O VAL E 252 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ILE E 254 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU E 205 " --> pdb=" O ILE E 254 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N GLN E 256 " --> pdb=" O LEU E 205 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU E 207 " --> pdb=" O GLN E 256 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU E 137 " --> pdb=" O PHE E 204 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N VAL E 206 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU E 139 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N MET E 208 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE E 141 " --> pdb=" O MET E 208 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA E 138 " --> pdb=" O ASP E 174 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N GLU E 176 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE E 140 " --> pdb=" O GLU E 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 215 through 217 Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 268 removed outlier: 3.629A pdb=" N VAL B 268 " --> pdb=" O TYR D 292 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 211 through 212 removed outlier: 3.526A pdb=" N GLY E 215 " --> pdb=" O ILE E 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 266 through 269 Processing sheet with id=AA6, first strand: chain 'D' and resid 313 through 315 Processing sheet with id=AA7, first strand: chain 'A' and resid 23 through 24 removed outlier: 6.827A pdb=" N THR A 213 " --> pdb=" O GLN A 165 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN A 165 " --> pdb=" O THR A 213 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA A 215 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL A 163 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ARG A 217 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL A 157 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 55 through 56 removed outlier: 3.998A pdb=" N ASN A 156 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL A 157 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ARG A 217 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL A 163 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA A 215 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN A 165 " --> pdb=" O THR A 213 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR A 213 " --> pdb=" O GLN A 165 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN A 220 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 230 " --> pdb=" O GLN A 220 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A 228 " --> pdb=" O VAL A 222 " (cutoff:3.500A) 246 hydrogen bonds defined for protein. 720 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.10 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6903 1.03 - 1.23: 28 1.23 - 1.42: 2937 1.42 - 1.61: 4102 1.61 - 1.81: 61 Bond restraints: 14031 Sorted by residual: bond pdb=" N ASP E 270 " pdb=" CA ASP E 270 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.90e-02 2.77e+03 2.22e+00 bond pdb=" CB GLU E 223 " pdb=" CG GLU E 223 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.82e+00 bond pdb=" N ARG C 354 " pdb=" CA ARG C 354 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.70e+00 bond pdb=" C ARG E 269 " pdb=" N ASP E 270 " ideal model delta sigma weight residual 1.329 1.345 -0.016 1.40e-02 5.10e+03 1.27e+00 bond pdb=" C TRP B 267 " pdb=" N VAL B 268 " ideal model delta sigma weight residual 1.332 1.319 0.013 1.36e-02 5.41e+03 9.19e-01 ... (remaining 14026 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 23911 1.10 - 2.19: 1370 2.19 - 3.29: 73 3.29 - 4.39: 28 4.39 - 5.49: 5 Bond angle restraints: 25387 Sorted by residual: angle pdb=" CB GLU E 223 " pdb=" CG GLU E 223 " pdb=" CD GLU E 223 " ideal model delta sigma weight residual 112.60 118.01 -5.41 1.70e+00 3.46e-01 1.01e+01 angle pdb=" CA GLU E 223 " pdb=" CB GLU E 223 " pdb=" CG GLU E 223 " ideal model delta sigma weight residual 114.10 119.42 -5.32 2.00e+00 2.50e-01 7.08e+00 angle pdb=" C ARG C 354 " pdb=" CA ARG C 354 " pdb=" CB ARG C 354 " ideal model delta sigma weight residual 110.42 115.68 -5.26 1.99e+00 2.53e-01 6.99e+00 angle pdb=" N ILE E 140 " pdb=" CA ILE E 140 " pdb=" C ILE E 140 " ideal model delta sigma weight residual 106.32 109.67 -3.35 1.61e+00 3.86e-01 4.34e+00 angle pdb=" CA VAL A 13 " pdb=" C VAL A 13 " pdb=" N GLN A 14 " ideal model delta sigma weight residual 116.60 119.52 -2.92 1.45e+00 4.76e-01 4.05e+00 ... (remaining 25382 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 5729 17.51 - 35.02: 597 35.02 - 52.53: 183 52.53 - 70.04: 57 70.04 - 87.55: 16 Dihedral angle restraints: 6582 sinusoidal: 3618 harmonic: 2964 Sorted by residual: dihedral pdb=" CA ILE D 362 " pdb=" C ILE D 362 " pdb=" N GLU D 363 " pdb=" CA GLU D 363 " ideal model delta harmonic sigma weight residual -180.00 -160.89 -19.11 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA ASN B 133 " pdb=" C ASN B 133 " pdb=" N ARG B 134 " pdb=" CA ARG B 134 " ideal model delta harmonic sigma weight residual -180.00 -163.18 -16.82 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA TYR E 171 " pdb=" C TYR E 171 " pdb=" N SER E 172 " pdb=" CA SER E 172 " ideal model delta harmonic sigma weight residual 180.00 163.36 16.64 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 6579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 635 0.027 - 0.053: 301 0.053 - 0.080: 69 0.080 - 0.106: 51 0.106 - 0.132: 23 Chirality restraints: 1079 Sorted by residual: chirality pdb=" CA ILE D 362 " pdb=" N ILE D 362 " pdb=" C ILE D 362 " pdb=" CB ILE D 362 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE B 140 " pdb=" N ILE B 140 " pdb=" C ILE B 140 " pdb=" CB ILE B 140 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE E 253 " pdb=" N ILE E 253 " pdb=" C ILE E 253 " pdb=" CB ILE E 253 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.84e-01 ... (remaining 1076 not shown) Planarity restraints: 2064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 269 " -0.024 2.00e-02 2.50e+03 4.87e-02 2.37e+01 pdb=" C ARG E 269 " 0.084 2.00e-02 2.50e+03 pdb=" O ARG E 269 " -0.032 2.00e-02 2.50e+03 pdb=" N ASP E 270 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 263 " -0.123 9.50e-02 1.11e+02 4.13e-02 2.25e+00 pdb=" NE ARG B 263 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B 263 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 263 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 263 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG B 263 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG B 263 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG B 263 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 263 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 269 " -0.007 2.00e-02 2.50e+03 1.39e-02 1.93e+00 pdb=" N ASP E 270 " 0.024 2.00e-02 2.50e+03 pdb=" CA ASP E 270 " -0.006 2.00e-02 2.50e+03 pdb=" H ASP E 270 " -0.010 2.00e-02 2.50e+03 ... (remaining 2061 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 824 2.19 - 2.80: 28839 2.80 - 3.40: 38415 3.40 - 4.00: 49723 4.00 - 4.60: 77337 Nonbonded interactions: 195138 Sorted by model distance: nonbonded pdb="HD21 ASN B 132 " pdb=" OD1 ASN B 133 " model vdw 1.593 2.450 nonbonded pdb=" O ASN A 58 " pdb="HD21 ASN A 58 " model vdw 1.754 2.450 nonbonded pdb=" HE ARG E 134 " pdb=" HE ARG E 136 " model vdw 1.867 2.100 nonbonded pdb=" HD2 PHE E 191 " pdb=" HZ PHE E 238 " model vdw 1.870 2.100 nonbonded pdb=" OE1 GLU E 223 " pdb=" H GLU E 223 " model vdw 1.876 2.450 ... (remaining 195133 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 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'E' and resid 105 through 269) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 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: 0.090 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.660 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 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 0.041 7103 Z= 0.129 Angle : 0.536 5.486 9618 Z= 0.289 Chirality : 0.039 0.132 1079 Planarity : 0.004 0.055 1244 Dihedral : 16.960 85.610 2659 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.81 % Allowed : 17.98 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 856 helix: 0.34 (0.31), residues: 298 sheet: -2.36 (0.59), residues: 74 loop : -0.97 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 263 TYR 0.007 0.001 TYR A 470 PHE 0.016 0.001 PHE C 374 TRP 0.018 0.001 TRP A 48 HIS 0.003 0.001 HIS D 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 7103) covalent geometry : angle 0.53591 / 0.29 ( 9618) hydrogen bonds : bond 0.20400 / 13.69 ( 242) hydrogen bonds : angle 8.10695 / 5.82 ( 720) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8846 (mtpt) cc_final: 0.8516 (ttpp) REVERT: A 128 ASN cc_start: 0.9068 (t0) cc_final: 0.8763 (p0) REVERT: A 299 LYS cc_start: 0.9451 (ttpt) cc_final: 0.9242 (ttpp) outliers start: 14 outliers final: 9 residues processed: 95 average time/residue: 0.2259 time to fit residues: 27.3010 Evaluate side-chains 69 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 121 TYR Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 316 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.0970 chunk 74 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.065857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.051111 restraints weight = 80802.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.053461 restraints weight = 28683.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.054957 restraints weight = 14728.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.055899 restraints weight = 9356.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.056458 restraints weight = 6908.900| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7103 Z= 0.127 Angle : 0.529 6.060 9618 Z= 0.275 Chirality : 0.039 0.142 1079 Planarity : 0.004 0.046 1244 Dihedral : 5.716 53.274 956 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.81 % Allowed : 18.89 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: -0.54 (0.29), residues: 856 helix: 0.81 (0.30), residues: 313 sheet: -2.03 (0.57), residues: 82 loop : -0.83 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 263 TYR 0.007 0.001 TYR B 171 PHE 0.009 0.001 PHE C 374 TRP 0.012 0.001 TRP A 48 HIS 0.006 0.001 HIS A 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 7103) covalent geometry : angle 0.52904 / 0.28 ( 9618) hydrogen bonds : bond 0.03932 / 2.63 ( 242) hydrogen bonds : angle 5.64377 / 4.09 ( 720) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 318 MET cc_start: 0.8118 (mmt) cc_final: 0.7863 (mmm) REVERT: A 55 LYS cc_start: 0.8640 (mtpt) cc_final: 0.8120 (ttpp) REVERT: A 128 ASN cc_start: 0.9376 (t0) cc_final: 0.9016 (p0) REVERT: A 299 LYS cc_start: 0.9563 (ttpt) cc_final: 0.8911 (tptp) outliers start: 14 outliers final: 11 residues processed: 76 average time/residue: 0.2169 time to fit residues: 21.1776 Evaluate side-chains 70 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 118 CYS Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 121 TYR Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 316 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 0.0010 chunk 37 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 50 optimal weight: 0.1980 chunk 54 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN A 128 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.065085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.050148 restraints weight = 82496.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.052540 restraints weight = 28289.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.054076 restraints weight = 14278.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.055017 restraints weight = 9006.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.055567 restraints weight = 6632.932| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7103 Z= 0.138 Angle : 0.506 6.510 9618 Z= 0.263 Chirality : 0.038 0.138 1079 Planarity : 0.003 0.048 1244 Dihedral : 5.354 53.987 950 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.33 % Allowed : 18.11 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: -0.34 (0.29), residues: 856 helix: 1.09 (0.30), residues: 314 sheet: -1.78 (0.54), residues: 87 loop : -0.81 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 263 TYR 0.007 0.001 TYR A 37 PHE 0.007 0.001 PHE A 287 TRP 0.013 0.001 TRP A 48 HIS 0.007 0.001 HIS A 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 7103) covalent geometry : angle 0.50650 / 0.26 ( 9618) hydrogen bonds : bond 0.03456 / 2.34 ( 242) hydrogen bonds : angle 5.26739 / 3.82 ( 720) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 318 MET cc_start: 0.8099 (mmt) cc_final: 0.7850 (mmm) REVERT: A 1 MET cc_start: 0.3694 (tpt) cc_final: 0.3362 (tpt) REVERT: A 55 LYS cc_start: 0.8614 (mtpt) cc_final: 0.8114 (ttpp) REVERT: A 128 ASN cc_start: 0.9363 (t0) cc_final: 0.9049 (p0) REVERT: A 299 LYS cc_start: 0.9556 (ttpt) cc_final: 0.8928 (tptp) outliers start: 18 outliers final: 16 residues processed: 77 average time/residue: 0.2089 time to fit residues: 20.8017 Evaluate side-chains 77 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 118 CYS Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 224 LYS Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 121 TYR Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 355 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 81 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.063281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.048375 restraints weight = 82614.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.050710 restraints weight = 28775.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.052190 restraints weight = 14731.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.053095 restraints weight = 9357.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.053625 restraints weight = 6946.257| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7103 Z= 0.238 Angle : 0.556 6.587 9618 Z= 0.296 Chirality : 0.040 0.134 1079 Planarity : 0.004 0.047 1244 Dihedral : 5.603 55.211 950 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.10 % Allowed : 18.24 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: -0.47 (0.29), residues: 856 helix: 1.03 (0.31), residues: 315 sheet: -1.67 (0.54), residues: 87 loop : -0.98 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 10 TYR 0.013 0.001 TYR A 37 PHE 0.012 0.001 PHE A 287 TRP 0.012 0.001 TRP A 48 HIS 0.010 0.001 HIS A 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.24 ( 7103) covalent geometry : angle 0.55592 / 0.30 ( 9618) hydrogen bonds : bond 0.03556 / 2.40 ( 242) hydrogen bonds : angle 5.33628 / 3.86 ( 720) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 119 LYS cc_start: 0.9449 (mmmm) cc_final: 0.9126 (mmtm) REVERT: C 318 MET cc_start: 0.8131 (mmt) cc_final: 0.7916 (mmm) REVERT: A 55 LYS cc_start: 0.8667 (mtpt) cc_final: 0.8187 (ttpp) REVERT: A 128 ASN cc_start: 0.9359 (t0) cc_final: 0.8999 (p0) REVERT: A 299 LYS cc_start: 0.9563 (ttpt) cc_final: 0.8974 (tptp) outliers start: 24 outliers final: 18 residues processed: 88 average time/residue: 0.1988 time to fit residues: 22.5801 Evaluate side-chains 78 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 118 CYS Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain A residue 121 TYR Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 355 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.063823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.048966 restraints weight = 81914.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.051293 restraints weight = 28736.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.052727 restraints weight = 14710.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.053603 restraints weight = 9432.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.054114 restraints weight = 7042.330| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7103 Z= 0.157 Angle : 0.511 6.527 9618 Z= 0.267 Chirality : 0.039 0.135 1079 Planarity : 0.004 0.047 1244 Dihedral : 5.494 56.381 950 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.72 % Allowed : 18.50 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: -0.34 (0.29), residues: 856 helix: 1.21 (0.31), residues: 315 sheet: -1.66 (0.54), residues: 87 loop : -0.95 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 364 TYR 0.009 0.001 TYR A 37 PHE 0.008 0.001 PHE A 287 TRP 0.013 0.001 TRP A 48 HIS 0.008 0.001 HIS A 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 ( 7103) covalent geometry : angle 0.51109 / 0.27 ( 9618) hydrogen bonds : bond 0.03205 / 2.17 ( 242) hydrogen bonds : angle 5.06526 / 3.66 ( 720) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 318 MET cc_start: 0.8155 (mmt) cc_final: 0.7929 (mmm) REVERT: A 55 LYS cc_start: 0.8626 (mtpt) cc_final: 0.8156 (ttpp) REVERT: A 128 ASN cc_start: 0.9383 (t0) cc_final: 0.9017 (p0) REVERT: A 299 LYS cc_start: 0.9560 (ttpt) cc_final: 0.8976 (tptp) outliers start: 21 outliers final: 21 residues processed: 82 average time/residue: 0.2088 time to fit residues: 22.0825 Evaluate side-chains 82 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 118 CYS Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain A residue 121 TYR Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 367 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 57 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.062766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.048167 restraints weight = 81633.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.050488 restraints weight = 28100.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.051946 restraints weight = 14224.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.052878 restraints weight = 9002.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.053462 restraints weight = 6601.425| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7103 Z= 0.182 Angle : 0.518 6.525 9618 Z= 0.272 Chirality : 0.039 0.135 1079 Planarity : 0.004 0.047 1244 Dihedral : 5.523 57.934 950 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.23 % Allowed : 18.11 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: -0.29 (0.29), residues: 856 helix: 1.30 (0.31), residues: 312 sheet: -1.58 (0.54), residues: 87 loop : -0.97 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 136 TYR 0.010 0.001 TYR A 37 PHE 0.008 0.001 PHE A 287 TRP 0.008 0.001 TRP C 313 HIS 0.009 0.001 HIS A 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 ( 7103) covalent geometry : angle 0.51806 / 0.27 ( 9618) hydrogen bonds : bond 0.03176 / 2.15 ( 242) hydrogen bonds : angle 5.03270 / 3.62 ( 720) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 61 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 318 MET cc_start: 0.8154 (mmt) cc_final: 0.7869 (mmm) REVERT: A 55 LYS cc_start: 0.8655 (mtpt) cc_final: 0.8190 (ttpp) REVERT: A 128 ASN cc_start: 0.9347 (t0) cc_final: 0.8971 (p0) REVERT: A 299 LYS cc_start: 0.9568 (ttpt) cc_final: 0.9000 (tptp) outliers start: 25 outliers final: 24 residues processed: 83 average time/residue: 0.2113 time to fit residues: 22.8088 Evaluate side-chains 83 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 118 CYS Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain A residue 121 TYR Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 367 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.064209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.049465 restraints weight = 81887.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.051785 restraints weight = 29655.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.053217 restraints weight = 15375.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.054152 restraints weight = 9942.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.054658 restraints weight = 7405.003| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7103 Z= 0.115 Angle : 0.487 6.536 9618 Z= 0.252 Chirality : 0.038 0.134 1079 Planarity : 0.003 0.044 1244 Dihedral : 5.405 58.626 950 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.59 % Allowed : 18.89 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.29), residues: 856 helix: 1.50 (0.31), residues: 312 sheet: -1.54 (0.54), residues: 87 loop : -0.86 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 364 TYR 0.007 0.001 TYR A 37 PHE 0.007 0.001 PHE B 238 TRP 0.012 0.001 TRP A 48 HIS 0.002 0.001 HIS D 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 7103) covalent geometry : angle 0.48735 / 0.25 ( 9618) hydrogen bonds : bond 0.02870 / 1.94 ( 242) hydrogen bonds : angle 4.81416 / 3.46 ( 720) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 318 MET cc_start: 0.8064 (mmt) cc_final: 0.7804 (mmm) REVERT: A 55 LYS cc_start: 0.8607 (mtpt) cc_final: 0.8130 (ttpp) REVERT: A 128 ASN cc_start: 0.9361 (t0) cc_final: 0.8969 (p0) REVERT: A 299 LYS cc_start: 0.9555 (ttpt) cc_final: 0.9027 (tptp) outliers start: 20 outliers final: 20 residues processed: 80 average time/residue: 0.2175 time to fit residues: 22.4324 Evaluate side-chains 82 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 118 CYS Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain A residue 121 TYR Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 367 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 29 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.063776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.049007 restraints weight = 81898.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.051313 restraints weight = 29824.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.052754 restraints weight = 15511.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.053647 restraints weight = 10033.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.054235 restraints weight = 7548.140| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7103 Z= 0.134 Angle : 0.493 6.469 9618 Z= 0.255 Chirality : 0.038 0.137 1079 Planarity : 0.003 0.045 1244 Dihedral : 5.389 59.554 950 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.10 % Allowed : 18.63 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: -0.04 (0.29), residues: 856 helix: 1.56 (0.31), residues: 312 sheet: -1.50 (0.55), residues: 89 loop : -0.84 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 364 TYR 0.008 0.001 TYR A 37 PHE 0.007 0.001 PHE A 287 TRP 0.014 0.001 TRP A 48 HIS 0.002 0.001 HIS D 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 7103) covalent geometry : angle 0.49276 / 0.25 ( 9618) hydrogen bonds : bond 0.02837 / 1.91 ( 242) hydrogen bonds : angle 4.69671 / 3.34 ( 720) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 318 MET cc_start: 0.8062 (mmt) cc_final: 0.7821 (mmm) REVERT: A 55 LYS cc_start: 0.8606 (mtpt) cc_final: 0.8129 (ttpp) REVERT: A 128 ASN cc_start: 0.9363 (t0) cc_final: 0.8977 (p0) REVERT: A 299 LYS cc_start: 0.9559 (ttpt) cc_final: 0.9028 (tptp) outliers start: 24 outliers final: 24 residues processed: 83 average time/residue: 0.2255 time to fit residues: 24.2645 Evaluate side-chains 85 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 118 CYS Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 121 TYR Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 367 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 8 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.062857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.048221 restraints weight = 83182.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.050487 restraints weight = 30382.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.051889 restraints weight = 15871.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.052782 restraints weight = 10300.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.053285 restraints weight = 7700.824| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7103 Z= 0.183 Angle : 0.516 6.468 9618 Z= 0.270 Chirality : 0.039 0.130 1079 Planarity : 0.004 0.046 1244 Dihedral : 5.507 59.849 950 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.23 % Allowed : 18.37 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.29), residues: 856 helix: 1.51 (0.31), residues: 315 sheet: -1.41 (0.56), residues: 87 loop : -0.89 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 10 TYR 0.010 0.001 TYR A 37 PHE 0.009 0.001 PHE A 287 TRP 0.013 0.001 TRP A 48 HIS 0.003 0.001 HIS E 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 ( 7103) covalent geometry : angle 0.51634 / 0.27 ( 9618) hydrogen bonds : bond 0.03074 / 2.06 ( 242) hydrogen bonds : angle 4.81841 / 3.42 ( 720) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 61 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8662 (mtpt) cc_final: 0.8204 (ttpp) REVERT: A 128 ASN cc_start: 0.9387 (t0) cc_final: 0.8995 (p0) REVERT: A 299 LYS cc_start: 0.9568 (ttpt) cc_final: 0.9042 (tptp) outliers start: 25 outliers final: 24 residues processed: 83 average time/residue: 0.2352 time to fit residues: 25.3626 Evaluate side-chains 84 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 118 CYS Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 121 TYR Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 367 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.062722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.048099 restraints weight = 82523.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.050357 restraints weight = 29901.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.051751 restraints weight = 15631.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.052630 restraints weight = 10121.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.053213 restraints weight = 7579.327| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7103 Z= 0.178 Angle : 0.521 6.523 9618 Z= 0.273 Chirality : 0.039 0.137 1079 Planarity : 0.004 0.045 1244 Dihedral : 5.483 59.116 950 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.36 % Allowed : 18.50 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.29), residues: 856 helix: 1.52 (0.31), residues: 315 sheet: -1.46 (0.55), residues: 87 loop : -0.91 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 10 TYR 0.009 0.001 TYR A 37 PHE 0.009 0.001 PHE A 287 TRP 0.038 0.002 TRP A 48 HIS 0.003 0.001 HIS E 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 ( 7103) covalent geometry : angle 0.52104 / 0.27 ( 9618) hydrogen bonds : bond 0.03073 / 2.08 ( 242) hydrogen bonds : angle 4.77182 / 3.39 ( 720) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 202 SER cc_start: 0.9621 (OUTLIER) cc_final: 0.9223 (m) REVERT: C 363 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8084 (mt-10) REVERT: A 55 LYS cc_start: 0.8681 (mtpt) cc_final: 0.8203 (ttpp) REVERT: A 128 ASN cc_start: 0.9373 (t0) cc_final: 0.8969 (p0) REVERT: A 299 LYS cc_start: 0.9569 (ttpt) cc_final: 0.9045 (tptp) outliers start: 26 outliers final: 23 residues processed: 83 average time/residue: 0.2271 time to fit residues: 24.6582 Evaluate side-chains 84 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 118 CYS Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 121 TYR Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 367 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 9 optimal weight: 0.6980 chunk 23 optimal weight: 0.0870 chunk 52 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 2 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.064225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.049622 restraints weight = 80851.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.051899 restraints weight = 29532.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.053323 restraints weight = 15362.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.054214 restraints weight = 9928.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.054777 restraints weight = 7421.283| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 7103 Z= 0.093 Angle : 0.496 6.445 9618 Z= 0.253 Chirality : 0.038 0.138 1079 Planarity : 0.003 0.042 1244 Dihedral : 5.243 58.086 950 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.33 % Allowed : 19.53 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 0.28 (0.30), residues: 856 helix: 1.86 (0.31), residues: 312 sheet: -1.43 (0.55), residues: 87 loop : -0.65 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 194 TYR 0.005 0.001 TYR E 171 PHE 0.006 0.001 PHE B 238 TRP 0.034 0.001 TRP A 48 HIS 0.003 0.001 HIS D 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.09 ( 7103) covalent geometry : angle 0.49618 / 0.25 ( 9618) hydrogen bonds : bond 0.02612 / 1.76 ( 242) hydrogen bonds : angle 4.46290 / 3.15 ( 720) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2362.53 seconds wall clock time: 41 minutes 3.48 seconds (2463.48 seconds total)