Starting phenix.real_space_refine on Wed Aug 5 18:33:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pxg_71969/08_2026/9pxg_71969_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pxg_71969/08_2026/9pxg_71969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pxg_71969/08_2026/9pxg_71969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pxg_71969/08_2026/9pxg_71969.map" model { file = "/net/cci-nas-00/data/ceres_data/9pxg_71969/08_2026/9pxg_71969_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pxg_71969/08_2026/9pxg_71969_neut.cif" } resolution = 2.75 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= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 21 5.16 5 Na 1 4.78 5 C 6818 2.51 5 N 1890 2.21 5 O 2111 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 10841 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5417 Classifications: {'peptide': 691} Link IDs: {'PTRANS': 27, 'TRANS': 663} Chain breaks: 2 Chain: "B" Number of atoms: 2666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2666 Classifications: {'peptide': 355} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 343} Chain: "C" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 341 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 8, 'TRANS': 35} Chain: "D" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1727 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain: "E" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 689 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.26, per 1000 atoms: 0.21 Number of scatterers: 10841 At special positions: 0 Unit cell: (105.75, 132, 137.25, 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 21 16.00 Na 1 11.00 O 2111 8.00 N 1890 7.00 C 6818 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 737 " - pdb=" SG CYS A 745 " distance=2.03 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: 0.76 Conformation dependent library (CDL) restraints added in 379.1 milliseconds 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 15 sheets defined 22.7% alpha, 35.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 105 through 116 Processing helix chain 'A' and resid 125 through 143 Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 214 through 231 Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.768A pdb=" N VAL A 283 " --> pdb=" O PRO A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 313 Processing helix chain 'A' and resid 360 through 366 removed outlier: 3.701A pdb=" N LEU A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 390 removed outlier: 3.561A pdb=" N LEU A 388 " --> pdb=" O SER A 384 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 555 removed outlier: 3.572A pdb=" N TYR A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 641 removed outlier: 3.638A pdb=" N ASN A 641 " --> pdb=" O PHE A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 753 Processing helix chain 'D' and resid 38 through 44 Processing helix chain 'D' and resid 46 through 58 Processing helix chain 'D' and resid 68 through 81 removed outlier: 4.222A pdb=" N LEU D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 98 removed outlier: 3.569A pdb=" N GLU D 92 " --> pdb=" O ARG D 88 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG D 93 " --> pdb=" O ALA D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 118 removed outlier: 4.062A pdb=" N ALA D 107 " --> pdb=" O ASN D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 127 removed outlier: 3.559A pdb=" N LEU D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 134 removed outlier: 3.641A pdb=" N LYS D 133 " --> pdb=" O ASP D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 153 removed outlier: 3.640A pdb=" N SER D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N PHE D 143 " --> pdb=" O ALA D 139 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN D 144 " --> pdb=" O ARG D 140 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU D 145 " --> pdb=" O ASP D 141 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE D 146 " --> pdb=" O SER D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 188 removed outlier: 3.519A pdb=" N TYR D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU D 177 " --> pdb=" O LEU D 173 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 204 Processing helix chain 'D' and resid 209 through 225 removed outlier: 3.527A pdb=" N GLY D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 241 removed outlier: 3.680A pdb=" N THR D 232 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN D 240 " --> pdb=" O THR D 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 45 removed outlier: 4.214A pdb=" N GLN E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 58 removed outlier: 3.829A pdb=" N ILE E 58 " --> pdb=" O GLN E 54 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 99 removed outlier: 6.883A pdb=" N LEU A 164 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A 96 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE A 166 " --> pdb=" O ILE A 96 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ILE A 98 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ILE A 168 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN A 151 " --> pdb=" O ASN A 167 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 182 removed outlier: 4.125A pdb=" N HIS A 178 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN A 260 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE A 239 " --> pdb=" O ASN A 260 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR B 180 " --> pdb=" O VAL A 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 266 through 274 removed outlier: 7.445A pdb=" N VAL A 336 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL A 270 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N PHE A 338 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU A 272 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N VAL A 340 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLY A 274 " --> pdb=" O VAL A 340 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 353 removed outlier: 7.621A pdb=" N VAL A 413 " --> pdb=" O ASN A 349 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE A 351 " --> pdb=" O VAL A 413 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N TYR A 415 " --> pdb=" O ILE A 351 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE A 353 " --> pdb=" O TYR A 415 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL A 417 " --> pdb=" O PHE A 353 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN A 414 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL A 399 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N SER A 416 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL A 397 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLU A 418 " --> pdb=" O LYS A 395 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 423 through 426 removed outlier: 3.603A pdb=" N ASN A 487 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 506 " --> pdb=" O ASP A 538 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP A 538 " --> pdb=" O SER A 506 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N SER A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 605 " --> pdb=" O SER A 585 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N PHE A 599 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 754 " --> pdb=" O GLY A 730 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 423 through 426 removed outlier: 3.603A pdb=" N ASN A 487 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 506 " --> pdb=" O ASP A 538 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP A 538 " --> pdb=" O SER A 506 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N SER A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 605 " --> pdb=" O SER A 585 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N PHE A 599 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 754 " --> pdb=" O GLY A 730 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER A 755 " --> pdb=" O ILE A 778 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 40 through 48 removed outlier: 5.173A pdb=" N LEU B 41 " --> pdb=" O ARG B 380 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ARG B 380 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LYS B 43 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N THR B 378 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N TRP B 45 " --> pdb=" O ALA B 376 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 63 through 65 removed outlier: 4.264A pdb=" N TRP B 90 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLN B 82 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N VAL B 88 " --> pdb=" O GLN B 82 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 105 removed outlier: 5.822A pdb=" N VAL B 118 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR B 131 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA B 120 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 143 through 144 removed outlier: 3.695A pdb=" N VAL B 151 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP B 170 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASP B 162 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N GLN B 168 " --> pdb=" O ASP B 162 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 188 through 190 removed outlier: 3.503A pdb=" N GLN B 217 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA B 205 " --> pdb=" O TRP B 215 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TRP B 215 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 239 through 241 removed outlier: 3.535A pdb=" N GLY B 252 " --> pdb=" O ALA B 270 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA B 270 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP B 266 " --> pdb=" O ALA B 256 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 276 through 279 removed outlier: 3.687A pdb=" N GLU B 293 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL B 292 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASN B 305 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLY B 294 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 318 through 319 removed outlier: 3.792A pdb=" N VAL B 324 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL B 333 " --> pdb=" O ARG B 346 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG B 346 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU B 335 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 32 through 35 removed outlier: 7.065A pdb=" N ARG E 90 " --> pdb=" O GLY E 106 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLY E 106 " --> pdb=" O ARG E 90 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N SER E 92 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU E 104 " --> pdb=" O SER E 92 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE E 94 " --> pdb=" O ALA E 102 " (cutoff:3.500A) 530 hydrogen bonds defined for protein. 1476 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: 2.12 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2168 1.33 - 1.45: 2718 1.45 - 1.57: 6125 1.57 - 1.70: 0 1.70 - 1.82: 40 Bond restraints: 11051 Sorted by residual: bond pdb=" C ASN A 134 " pdb=" N GLU A 135 " ideal model delta sigma weight residual 1.334 1.252 0.083 1.33e-02 5.65e+03 3.87e+01 bond pdb=" CA ASP E 99 " pdb=" C ASP E 99 " ideal model delta sigma weight residual 1.530 1.491 0.039 1.17e-02 7.31e+03 1.13e+01 bond pdb=" CA GLN E 100 " pdb=" C GLN E 100 " ideal model delta sigma weight residual 1.520 1.480 0.040 1.20e-02 6.94e+03 1.09e+01 bond pdb=" CA TYR A 468 " pdb=" C TYR A 468 " ideal model delta sigma weight residual 1.520 1.486 0.035 1.20e-02 6.94e+03 8.41e+00 bond pdb=" C TYR A 468 " pdb=" O TYR A 468 " ideal model delta sigma weight residual 1.234 1.203 0.032 1.15e-02 7.56e+03 7.72e+00 ... (remaining 11046 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 14637 1.75 - 3.50: 299 3.50 - 5.25: 42 5.25 - 7.00: 5 7.00 - 8.75: 2 Bond angle restraints: 14985 Sorted by residual: angle pdb=" N TYR A 468 " pdb=" CA TYR A 468 " pdb=" C TYR A 468 " ideal model delta sigma weight residual 108.48 99.73 8.75 1.80e+00 3.09e-01 2.36e+01 angle pdb=" N TYR B 377 " pdb=" CA TYR B 377 " pdb=" C TYR B 377 " ideal model delta sigma weight residual 108.02 115.80 -7.78 1.78e+00 3.16e-01 1.91e+01 angle pdb=" N ILE A 166 " pdb=" CA ILE A 166 " pdb=" C ILE A 166 " ideal model delta sigma weight residual 107.77 113.33 -5.56 1.48e+00 4.57e-01 1.41e+01 angle pdb=" N ILE A 98 " pdb=" CA ILE A 98 " pdb=" C ILE A 98 " ideal model delta sigma weight residual 107.75 113.07 -5.32 1.46e+00 4.69e-01 1.33e+01 angle pdb=" O ASN A 134 " pdb=" C ASN A 134 " pdb=" N GLU A 135 " ideal model delta sigma weight residual 122.43 117.66 4.77 1.34e+00 5.57e-01 1.27e+01 ... (remaining 14980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 6030 17.61 - 35.21: 470 35.21 - 52.82: 83 52.82 - 70.42: 13 70.42 - 88.03: 11 Dihedral angle restraints: 6607 sinusoidal: 2640 harmonic: 3967 Sorted by residual: dihedral pdb=" CA ARG D 134 " pdb=" C ARG D 134 " pdb=" N ASP D 135 " pdb=" CA ASP D 135 " ideal model delta harmonic sigma weight residual -180.00 -160.38 -19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" C TYR A 468 " pdb=" N TYR A 468 " pdb=" CA TYR A 468 " pdb=" CB TYR A 468 " ideal model delta harmonic sigma weight residual -122.60 -113.35 -9.25 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" CA GLN D 37 " pdb=" C GLN D 37 " pdb=" N ALA D 38 " pdb=" CA ALA D 38 " ideal model delta harmonic sigma weight residual 180.00 161.56 18.44 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 6604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1059 0.033 - 0.067: 385 0.067 - 0.100: 143 0.100 - 0.134: 56 0.134 - 0.167: 8 Chirality restraints: 1651 Sorted by residual: chirality pdb=" CA VAL A 666 " pdb=" N VAL A 666 " pdb=" C VAL A 666 " pdb=" CB VAL A 666 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" CA GLU B 84 " pdb=" N GLU B 84 " pdb=" C GLU B 84 " pdb=" CB GLU B 84 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CA ASP B 156 " pdb=" N ASP B 156 " pdb=" C ASP B 156 " pdb=" CB ASP B 156 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.20e-01 ... (remaining 1648 not shown) Planarity restraints: 1977 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 247 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO A 248 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 248 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 248 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER E 98 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" C SER E 98 " 0.032 2.00e-02 2.50e+03 pdb=" O SER E 98 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP E 99 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 44 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.36e+00 pdb=" C GLN B 44 " 0.027 2.00e-02 2.50e+03 pdb=" O GLN B 44 " -0.010 2.00e-02 2.50e+03 pdb=" N TRP B 45 " -0.009 2.00e-02 2.50e+03 ... (remaining 1974 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2057 2.77 - 3.30: 10144 3.30 - 3.83: 17094 3.83 - 4.37: 19577 4.37 - 4.90: 34898 Nonbonded interactions: 83770 Sorted by model distance: nonbonded pdb=" OG SER D 46 " pdb=" OG SER D 49 " model vdw 2.237 3.040 nonbonded pdb=" OE1 GLU A 522 " pdb=" OH TYR E 28 " model vdw 2.247 3.040 nonbonded pdb=" OG1 THR B 153 " pdb=" OD1 ASP B 155 " model vdw 2.251 3.040 nonbonded pdb=" OE2 GLU A 546 " pdb=" OG1 THR A 739 " model vdw 2.273 3.040 nonbonded pdb=" O GLY B 183 " pdb="NA NA B 401 " model vdw 2.300 2.470 ... (remaining 83765 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.430 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 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 : 0.004 0.083 11052 Z= 0.225 Angle : 0.597 8.748 14987 Z= 0.342 Chirality : 0.043 0.167 1651 Planarity : 0.004 0.050 1977 Dihedral : 13.215 88.026 4084 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.23), residues: 1375 helix: 0.81 (0.32), residues: 285 sheet: -0.15 (0.26), residues: 441 loop : -1.06 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 187 TYR 0.020 0.001 TYR D 66 PHE 0.022 0.001 PHE D 63 TRP 0.008 0.001 TRP A 375 HIS 0.004 0.001 HIS C 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.22 (11051) covalent geometry : angle 0.59639 / 0.34 (14985) SS BOND : bond 0.00172 / 0.11 ( 1) SS BOND : angle 1.94718 / 1.03 ( 2) hydrogen bonds : bond 0.22766 / 15.27 ( 429) hydrogen bonds : angle 8.19350 / 5.78 ( 1476) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 GLN cc_start: 0.7128 (mp10) cc_final: 0.6760 (mp10) REVERT: A 251 LYS cc_start: 0.8378 (mmpt) cc_final: 0.7724 (mttm) REVERT: A 263 GLU cc_start: 0.7038 (tp30) cc_final: 0.6664 (tp30) REVERT: A 314 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7618 (mm-30) REVERT: A 534 ARG cc_start: 0.6315 (ttt-90) cc_final: 0.5997 (ttm-80) REVERT: A 616 TYR cc_start: 0.6023 (m-10) cc_final: 0.5766 (m-80) REVERT: A 654 LYS cc_start: 0.6640 (tttm) cc_final: 0.6370 (mtpp) REVERT: B 32 LEU cc_start: 0.5610 (tp) cc_final: 0.5323 (tp) REVERT: B 61 GLU cc_start: 0.7923 (pt0) cc_final: 0.7616 (pt0) REVERT: B 77 ARG cc_start: 0.7623 (ttt-90) cc_final: 0.7144 (tpt-90) REVERT: B 79 MET cc_start: 0.5578 (tpt) cc_final: 0.4804 (tpt) REVERT: B 106 TYR cc_start: 0.6572 (m-80) cc_final: 0.6259 (m-80) REVERT: B 137 GLU cc_start: 0.8226 (pm20) cc_final: 0.7958 (pm20) REVERT: B 263 ARG cc_start: 0.7112 (mmp80) cc_final: 0.6404 (ptp-170) REVERT: B 267 GLN cc_start: 0.7494 (pm20) cc_final: 0.7193 (pt0) REVERT: B 330 GLU cc_start: 0.6925 (mt-10) cc_final: 0.5761 (tm-30) REVERT: B 338 GLN cc_start: 0.5869 (tt0) cc_final: 0.5524 (mp-120) REVERT: B 343 PHE cc_start: 0.7429 (m-80) cc_final: 0.6913 (m-80) REVERT: C 81 ARG cc_start: 0.6707 (tpm170) cc_final: 0.6301 (tpp80) REVERT: D 206 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7320 (mm-30) REVERT: E 53 ARG cc_start: 0.7636 (ttp-110) cc_final: 0.7310 (mpt180) REVERT: E 86 ARG cc_start: 0.7552 (ttp80) cc_final: 0.7294 (ttp80) outliers start: 0 outliers final: 1 residues processed: 211 average time/residue: 0.5550 time to fit residues: 124.9598 Evaluate side-chains 132 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.0670 chunk 10 optimal weight: 0.0470 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 320 ASN B 287 GLN B 323 ASN D 205 GLN E 71 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.206468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.133353 restraints weight = 12802.249| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.53 r_work: 0.3665 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 11052 Z= 0.110 Angle : 0.559 9.049 14987 Z= 0.289 Chirality : 0.043 0.184 1651 Planarity : 0.004 0.049 1977 Dihedral : 3.882 18.465 1541 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.46 % Allowed : 9.11 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.23), residues: 1375 helix: 1.24 (0.32), residues: 289 sheet: -0.10 (0.25), residues: 455 loop : -1.07 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 47 TYR 0.021 0.001 TYR D 66 PHE 0.030 0.001 PHE A 791 TRP 0.009 0.001 TRP A 203 HIS 0.004 0.001 HIS C 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (11051) covalent geometry : angle 0.55875 / 0.29 (14985) SS BOND : bond 0.00128 / 0.09 ( 1) SS BOND : angle 1.11310 / 0.59 ( 2) hydrogen bonds : bond 0.04160 / 2.79 ( 429) hydrogen bonds : angle 4.95275 / 3.53 ( 1476) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 GLN cc_start: 0.7222 (mp10) cc_final: 0.6706 (mp10) REVERT: A 251 LYS cc_start: 0.8542 (mmpt) cc_final: 0.8054 (mttt) REVERT: A 263 GLU cc_start: 0.7537 (tp30) cc_final: 0.7282 (tp30) REVERT: A 293 GLN cc_start: 0.6758 (mt0) cc_final: 0.5986 (pt0) REVERT: A 314 GLU cc_start: 0.8290 (mm-30) cc_final: 0.8022 (mm-30) REVERT: A 368 MET cc_start: 0.8379 (mmp) cc_final: 0.8065 (mmp) REVERT: A 616 TYR cc_start: 0.6387 (m-10) cc_final: 0.6095 (m-80) REVERT: A 719 ARG cc_start: 0.7979 (mtm110) cc_final: 0.7729 (mtm110) REVERT: B 32 LEU cc_start: 0.5710 (tp) cc_final: 0.5327 (tp) REVERT: B 61 GLU cc_start: 0.7890 (pt0) cc_final: 0.7504 (pt0) REVERT: B 77 ARG cc_start: 0.7816 (ttt-90) cc_final: 0.7479 (ttp-170) REVERT: B 79 MET cc_start: 0.5999 (tpt) cc_final: 0.4634 (tpt) REVERT: B 137 GLU cc_start: 0.8011 (pm20) cc_final: 0.7585 (pm20) REVERT: B 154 GLN cc_start: 0.7643 (tm-30) cc_final: 0.7216 (tm130) REVERT: B 193 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.6382 (tpt) REVERT: B 263 ARG cc_start: 0.7113 (mmp80) cc_final: 0.6811 (ptp-170) REVERT: B 330 GLU cc_start: 0.6700 (mt-10) cc_final: 0.5666 (tm-30) REVERT: B 338 GLN cc_start: 0.5701 (tt0) cc_final: 0.5472 (mm-40) REVERT: B 343 PHE cc_start: 0.7374 (m-80) cc_final: 0.6918 (m-10) REVERT: C 81 ARG cc_start: 0.6747 (tpm170) cc_final: 0.4908 (tpp80) REVERT: E 53 ARG cc_start: 0.7793 (ttp-110) cc_final: 0.7299 (mmt180) outliers start: 17 outliers final: 9 residues processed: 163 average time/residue: 0.4445 time to fit residues: 78.5832 Evaluate side-chains 135 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain D residue 48 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 67 optimal weight: 0.9980 chunk 109 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 0.0070 chunk 38 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 168 GLN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.200320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.123409 restraints weight = 12705.114| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 3.18 r_work: 0.3390 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11052 Z= 0.127 Angle : 0.555 7.869 14987 Z= 0.286 Chirality : 0.044 0.191 1651 Planarity : 0.004 0.054 1977 Dihedral : 3.934 19.388 1541 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.98 % Allowed : 11.35 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.23), residues: 1375 helix: 1.23 (0.32), residues: 294 sheet: -0.12 (0.24), residues: 460 loop : -1.06 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 298 TYR 0.022 0.001 TYR D 66 PHE 0.029 0.001 PHE A 791 TRP 0.011 0.001 TRP A 203 HIS 0.003 0.001 HIS C 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (11051) covalent geometry : angle 0.55501 / 0.29 (14985) SS BOND : bond 0.00168 / 0.11 ( 1) SS BOND : angle 0.87806 / 0.46 ( 2) hydrogen bonds : bond 0.04245 / 2.83 ( 429) hydrogen bonds : angle 4.62880 / 3.31 ( 1476) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 GLN cc_start: 0.7449 (mp10) cc_final: 0.6927 (mp10) REVERT: A 251 LYS cc_start: 0.8525 (mmpt) cc_final: 0.7980 (mttm) REVERT: A 263 GLU cc_start: 0.7694 (tp30) cc_final: 0.7438 (tp30) REVERT: A 290 GLN cc_start: 0.7250 (mm-40) cc_final: 0.6868 (mm-40) REVERT: A 293 GLN cc_start: 0.6859 (mt0) cc_final: 0.6094 (pt0) REVERT: A 314 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8258 (mm-30) REVERT: A 616 TYR cc_start: 0.6465 (m-10) cc_final: 0.6202 (m-80) REVERT: B 32 LEU cc_start: 0.5802 (tp) cc_final: 0.5456 (tp) REVERT: B 61 GLU cc_start: 0.7899 (pt0) cc_final: 0.7582 (pt0) REVERT: B 77 ARG cc_start: 0.7836 (ttt-90) cc_final: 0.7277 (tpt90) REVERT: B 79 MET cc_start: 0.5816 (tpt) cc_final: 0.4610 (tpt) REVERT: B 137 GLU cc_start: 0.8167 (pm20) cc_final: 0.7745 (pm20) REVERT: B 154 GLN cc_start: 0.7562 (tm-30) cc_final: 0.7262 (tm-30) REVERT: B 193 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.6386 (tpt) REVERT: B 263 ARG cc_start: 0.7235 (mmp80) cc_final: 0.6947 (ptp-170) REVERT: B 298 ARG cc_start: 0.7117 (mmm160) cc_final: 0.6357 (mmp80) REVERT: B 330 GLU cc_start: 0.6749 (mt-10) cc_final: 0.5817 (tm-30) REVERT: B 338 GLN cc_start: 0.5791 (tt0) cc_final: 0.5406 (mm-40) REVERT: B 343 PHE cc_start: 0.7474 (m-80) cc_final: 0.7001 (m-80) REVERT: C 81 ARG cc_start: 0.6768 (tpm170) cc_final: 0.4813 (tpp80) REVERT: D 127 LEU cc_start: 0.6229 (OUTLIER) cc_final: 0.5993 (pp) REVERT: D 145 GLU cc_start: 0.7914 (mp0) cc_final: 0.7656 (mp0) REVERT: E 53 ARG cc_start: 0.7859 (ttp-110) cc_final: 0.7301 (mmt180) outliers start: 23 outliers final: 12 residues processed: 150 average time/residue: 0.4866 time to fit residues: 79.2467 Evaluate side-chains 139 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 685 ARG Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 78 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 26 optimal weight: 0.4980 chunk 88 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 GLN B 334 HIS D 78 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.196052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.118585 restraints weight = 12680.345| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 3.18 r_work: 0.3325 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11052 Z= 0.224 Angle : 0.648 8.552 14987 Z= 0.337 Chirality : 0.047 0.187 1651 Planarity : 0.005 0.055 1977 Dihedral : 4.471 24.722 1539 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.53 % Allowed : 12.64 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.22), residues: 1375 helix: 0.94 (0.31), residues: 288 sheet: -0.12 (0.24), residues: 453 loop : -1.20 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 369 TYR 0.023 0.002 TYR D 66 PHE 0.034 0.002 PHE A 791 TRP 0.011 0.001 TRP A 203 HIS 0.003 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.22 (11051) covalent geometry : angle 0.64800 / 0.34 (14985) SS BOND : bond 0.00247 / 0.16 ( 1) SS BOND : angle 0.93326 / 0.49 ( 2) hydrogen bonds : bond 0.05319 / 3.53 ( 429) hydrogen bonds : angle 4.83627 / 3.46 ( 1476) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 128 time to evaluate : 0.334 Fit side-chains REVERT: A 243 GLN cc_start: 0.7661 (mp10) cc_final: 0.7045 (mp10) REVERT: A 251 LYS cc_start: 0.8589 (mmpt) cc_final: 0.8116 (mttt) REVERT: A 263 GLU cc_start: 0.7764 (tp30) cc_final: 0.7503 (tp30) REVERT: A 293 GLN cc_start: 0.7071 (mt0) cc_final: 0.6300 (pt0) REVERT: A 314 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8288 (mm-30) REVERT: A 534 ARG cc_start: 0.7447 (ttt-90) cc_final: 0.7218 (ttm-80) REVERT: A 616 TYR cc_start: 0.6854 (m-10) cc_final: 0.6584 (m-80) REVERT: B 77 ARG cc_start: 0.7849 (ttt-90) cc_final: 0.7280 (ttp-170) REVERT: B 137 GLU cc_start: 0.8388 (pm20) cc_final: 0.7924 (pm20) REVERT: B 193 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.6760 (tpt) REVERT: B 263 ARG cc_start: 0.7210 (mmp80) cc_final: 0.6870 (ptp-170) REVERT: B 330 GLU cc_start: 0.6739 (mt-10) cc_final: 0.5840 (tm-30) REVERT: B 333 VAL cc_start: 0.7824 (t) cc_final: 0.7591 (m) REVERT: B 338 GLN cc_start: 0.5900 (tt0) cc_final: 0.5636 (mm-40) REVERT: B 365 MET cc_start: 0.5335 (tpp) cc_final: 0.4969 (tpp) REVERT: C 81 ARG cc_start: 0.6748 (tpm170) cc_final: 0.4858 (tpp80) REVERT: D 68 GLU cc_start: 0.7092 (pp20) cc_final: 0.6720 (mt-10) REVERT: D 92 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7407 (pm20) REVERT: D 127 LEU cc_start: 0.6180 (pp) cc_final: 0.5941 (pp) REVERT: D 145 GLU cc_start: 0.7948 (mp0) cc_final: 0.7584 (mp0) REVERT: D 152 ARG cc_start: 0.6920 (OUTLIER) cc_final: 0.6691 (mtt-85) REVERT: D 206 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8073 (mm-30) REVERT: E 53 ARG cc_start: 0.7863 (ttp-110) cc_final: 0.7281 (mmt180) REVERT: E 74 ASP cc_start: 0.9139 (OUTLIER) cc_final: 0.8793 (m-30) outliers start: 41 outliers final: 21 residues processed: 153 average time/residue: 0.4831 time to fit residues: 79.7018 Evaluate side-chains 141 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 685 ARG Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain D residue 78 ASN Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 152 ARG Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 91 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 101 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.198547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.122251 restraints weight = 12532.875| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.97 r_work: 0.3354 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11052 Z= 0.132 Angle : 0.570 7.521 14987 Z= 0.293 Chirality : 0.043 0.170 1651 Planarity : 0.004 0.060 1977 Dihedral : 4.176 21.020 1539 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.58 % Allowed : 14.19 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.22), residues: 1375 helix: 1.13 (0.32), residues: 288 sheet: -0.14 (0.24), residues: 459 loop : -1.14 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 298 TYR 0.022 0.001 TYR D 66 PHE 0.031 0.001 PHE A 791 TRP 0.012 0.001 TRP A 203 HIS 0.002 0.001 HIS A 621 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (11051) covalent geometry : angle 0.56968 / 0.29 (14985) SS BOND : bond 0.00145 / 0.10 ( 1) SS BOND : angle 0.84209 / 0.44 ( 2) hydrogen bonds : bond 0.04028 / 2.68 ( 429) hydrogen bonds : angle 4.50517 / 3.23 ( 1476) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 243 GLN cc_start: 0.7527 (mp10) cc_final: 0.7174 (mp10) REVERT: A 251 LYS cc_start: 0.8558 (mmpt) cc_final: 0.8170 (mttt) REVERT: A 293 GLN cc_start: 0.7030 (mt0) cc_final: 0.6198 (pt0) REVERT: A 314 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8269 (mm-30) REVERT: A 616 TYR cc_start: 0.6805 (m-10) cc_final: 0.6534 (m-80) REVERT: B 77 ARG cc_start: 0.7817 (ttt-90) cc_final: 0.7287 (ttp-170) REVERT: B 137 GLU cc_start: 0.8309 (pm20) cc_final: 0.7864 (pm20) REVERT: B 154 GLN cc_start: 0.7658 (tm-30) cc_final: 0.7355 (tm-30) REVERT: B 193 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.6725 (tpt) REVERT: B 263 ARG cc_start: 0.7296 (mmp80) cc_final: 0.7043 (ptp90) REVERT: B 330 GLU cc_start: 0.6667 (mt-10) cc_final: 0.5838 (tm-30) REVERT: B 333 VAL cc_start: 0.7888 (t) cc_final: 0.7641 (m) REVERT: B 338 GLN cc_start: 0.5912 (tt0) cc_final: 0.5561 (mm-40) REVERT: B 365 MET cc_start: 0.5333 (tpp) cc_final: 0.4989 (tpp) REVERT: C 81 ARG cc_start: 0.6805 (tpm170) cc_final: 0.4946 (tpp80) REVERT: D 78 ASN cc_start: 0.7400 (t0) cc_final: 0.7085 (t160) REVERT: D 92 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7375 (pm20) REVERT: D 127 LEU cc_start: 0.6050 (pp) cc_final: 0.5798 (pp) REVERT: D 145 GLU cc_start: 0.7918 (mp0) cc_final: 0.7538 (mp0) REVERT: E 53 ARG cc_start: 0.7864 (ttp-110) cc_final: 0.7273 (mmt180) REVERT: E 74 ASP cc_start: 0.9077 (OUTLIER) cc_final: 0.8728 (m-30) outliers start: 30 outliers final: 17 residues processed: 142 average time/residue: 0.4375 time to fit residues: 67.3240 Evaluate side-chains 135 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 685 ARG Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 109 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 28 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 107 optimal weight: 0.0980 chunk 15 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.199893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.121793 restraints weight = 12817.679| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.62 r_work: 0.3375 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11052 Z= 0.174 Angle : 0.596 8.629 14987 Z= 0.307 Chirality : 0.044 0.158 1651 Planarity : 0.004 0.063 1977 Dihedral : 4.299 22.994 1539 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.49 % Allowed : 15.31 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.22), residues: 1375 helix: 1.08 (0.32), residues: 288 sheet: -0.18 (0.23), residues: 464 loop : -1.16 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 285 TYR 0.023 0.002 TYR D 66 PHE 0.034 0.002 PHE A 791 TRP 0.011 0.001 TRP A 203 HIS 0.002 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.17 (11051) covalent geometry : angle 0.59572 / 0.31 (14985) SS BOND : bond 0.00208 / 0.14 ( 1) SS BOND : angle 0.86798 / 0.46 ( 2) hydrogen bonds : bond 0.04594 / 3.03 ( 429) hydrogen bonds : angle 4.57157 / 3.28 ( 1476) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 GLN cc_start: 0.7432 (mp10) cc_final: 0.6784 (mp10) REVERT: A 251 LYS cc_start: 0.8459 (mmpt) cc_final: 0.8078 (mttt) REVERT: A 314 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8097 (mm-30) REVERT: A 534 ARG cc_start: 0.7170 (ttt-90) cc_final: 0.6909 (ttm-80) REVERT: A 616 TYR cc_start: 0.6747 (m-10) cc_final: 0.6519 (m-80) REVERT: B 32 LEU cc_start: 0.5465 (OUTLIER) cc_final: 0.4979 (tp) REVERT: B 77 ARG cc_start: 0.7791 (ttt-90) cc_final: 0.7218 (ttp-170) REVERT: B 137 GLU cc_start: 0.8311 (pm20) cc_final: 0.7795 (pm20) REVERT: B 193 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.6788 (tpt) REVERT: B 263 ARG cc_start: 0.7243 (mmp80) cc_final: 0.6982 (ptp90) REVERT: B 330 GLU cc_start: 0.6662 (mt-10) cc_final: 0.5850 (tm-30) REVERT: B 333 VAL cc_start: 0.7832 (t) cc_final: 0.7603 (m) REVERT: B 338 GLN cc_start: 0.5886 (tt0) cc_final: 0.5512 (mm-40) REVERT: B 365 MET cc_start: 0.5239 (tpp) cc_final: 0.4890 (tpp) REVERT: C 81 ARG cc_start: 0.6641 (tpm170) cc_final: 0.4665 (tpp80) REVERT: D 92 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7422 (pm20) REVERT: D 127 LEU cc_start: 0.5945 (pp) cc_final: 0.5706 (pp) REVERT: D 145 GLU cc_start: 0.7808 (mp0) cc_final: 0.7358 (mp0) REVERT: D 206 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7963 (mm-30) REVERT: E 53 ARG cc_start: 0.7669 (ttp-110) cc_final: 0.7093 (mmt180) REVERT: E 74 ASP cc_start: 0.9109 (OUTLIER) cc_final: 0.8719 (m-30) outliers start: 29 outliers final: 16 residues processed: 133 average time/residue: 0.4535 time to fit residues: 65.3324 Evaluate side-chains 128 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 685 ARG Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 91 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 80 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 chunk 14 optimal weight: 0.1980 chunk 87 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.203399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.127545 restraints weight = 12734.978| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 3.09 r_work: 0.3414 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11052 Z= 0.103 Angle : 0.545 11.059 14987 Z= 0.275 Chirality : 0.043 0.154 1651 Planarity : 0.004 0.065 1977 Dihedral : 3.945 19.889 1539 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.41 % Allowed : 15.65 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.23), residues: 1375 helix: 1.42 (0.32), residues: 285 sheet: -0.10 (0.23), residues: 457 loop : -1.06 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 285 TYR 0.022 0.001 TYR D 66 PHE 0.034 0.001 PHE A 791 TRP 0.013 0.001 TRP A 203 HIS 0.003 0.001 HIS A 621 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (11051) covalent geometry : angle 0.54542 / 0.27 (14985) SS BOND : bond 0.00093 / 0.06 ( 1) SS BOND : angle 0.82625 / 0.44 ( 2) hydrogen bonds : bond 0.03296 / 2.19 ( 429) hydrogen bonds : angle 4.25860 / 3.05 ( 1476) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 GLN cc_start: 0.7287 (mp10) cc_final: 0.6624 (mp10) REVERT: A 251 LYS cc_start: 0.8410 (mmpt) cc_final: 0.8046 (mttt) REVERT: A 285 ARG cc_start: 0.7764 (ttm-80) cc_final: 0.7369 (mpp80) REVERT: A 293 GLN cc_start: 0.6790 (mt0) cc_final: 0.6006 (pt0) REVERT: A 314 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7948 (mm-30) REVERT: A 616 TYR cc_start: 0.6573 (m-10) cc_final: 0.6295 (m-80) REVERT: B 137 GLU cc_start: 0.8178 (pm20) cc_final: 0.7648 (pm20) REVERT: B 138 VAL cc_start: 0.7208 (OUTLIER) cc_final: 0.6861 (p) REVERT: B 154 GLN cc_start: 0.7587 (tm-30) cc_final: 0.7261 (tm130) REVERT: B 193 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.6903 (tpt) REVERT: B 330 GLU cc_start: 0.6557 (mt-10) cc_final: 0.5742 (tm-30) REVERT: B 333 VAL cc_start: 0.7839 (t) cc_final: 0.7636 (m) REVERT: B 338 GLN cc_start: 0.5810 (tt0) cc_final: 0.5476 (mm-40) REVERT: B 365 MET cc_start: 0.5223 (tpp) cc_final: 0.4893 (tpp) REVERT: C 81 ARG cc_start: 0.6567 (tpm170) cc_final: 0.4580 (tpp80) REVERT: D 92 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7336 (pm20) REVERT: D 127 LEU cc_start: 0.5957 (pp) cc_final: 0.5738 (pp) REVERT: D 131 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6624 (mmp) REVERT: D 145 GLU cc_start: 0.7818 (mp0) cc_final: 0.7327 (mp0) REVERT: E 53 ARG cc_start: 0.7654 (ttp-110) cc_final: 0.7073 (mmt180) outliers start: 28 outliers final: 12 residues processed: 141 average time/residue: 0.5147 time to fit residues: 78.6278 Evaluate side-chains 128 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain D residue 78 ASN Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 109 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 5 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 135 ASN D 78 ASN D 205 GLN E 71 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.199960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.121176 restraints weight = 12868.734| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.68 r_work: 0.3391 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11052 Z= 0.178 Angle : 0.603 11.757 14987 Z= 0.307 Chirality : 0.045 0.160 1651 Planarity : 0.004 0.067 1977 Dihedral : 4.232 22.363 1539 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.32 % Allowed : 16.34 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.22), residues: 1375 helix: 1.16 (0.32), residues: 287 sheet: -0.16 (0.23), residues: 464 loop : -1.09 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 285 TYR 0.022 0.002 TYR D 66 PHE 0.037 0.002 PHE A 791 TRP 0.017 0.001 TRP A 203 HIS 0.002 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (11051) covalent geometry : angle 0.60295 / 0.31 (14985) SS BOND : bond 0.00235 / 0.16 ( 1) SS BOND : angle 0.80473 / 0.42 ( 2) hydrogen bonds : bond 0.04486 / 2.97 ( 429) hydrogen bonds : angle 4.49302 / 3.22 ( 1476) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 243 GLN cc_start: 0.7376 (mp10) cc_final: 0.6967 (mp10) REVERT: A 251 LYS cc_start: 0.8378 (mmpt) cc_final: 0.8016 (mttt) REVERT: A 314 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7953 (mm-30) REVERT: A 534 ARG cc_start: 0.7109 (ttt-90) cc_final: 0.6835 (ttm-80) REVERT: A 616 TYR cc_start: 0.6659 (m-10) cc_final: 0.6391 (m-80) REVERT: B 32 LEU cc_start: 0.5394 (OUTLIER) cc_final: 0.4876 (tp) REVERT: B 77 ARG cc_start: 0.7480 (ttt-90) cc_final: 0.6937 (tpt-90) REVERT: B 79 MET cc_start: 0.6280 (mmm) cc_final: 0.5888 (mmm) REVERT: B 137 GLU cc_start: 0.8235 (pm20) cc_final: 0.7685 (pm20) REVERT: B 138 VAL cc_start: 0.7180 (OUTLIER) cc_final: 0.6861 (p) REVERT: B 154 GLN cc_start: 0.7618 (tm-30) cc_final: 0.7272 (tm130) REVERT: B 193 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.6903 (tpt) REVERT: B 330 GLU cc_start: 0.6452 (mt-10) cc_final: 0.5582 (tm-30) REVERT: B 333 VAL cc_start: 0.7764 (t) cc_final: 0.7554 (m) REVERT: B 338 GLN cc_start: 0.5872 (tt0) cc_final: 0.5464 (mm-40) REVERT: B 365 MET cc_start: 0.5184 (tpp) cc_final: 0.4844 (tpp) REVERT: C 81 ARG cc_start: 0.6648 (tpm170) cc_final: 0.4676 (tpp80) REVERT: D 92 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7414 (pm20) REVERT: D 127 LEU cc_start: 0.5991 (pp) cc_final: 0.5768 (pp) REVERT: D 145 GLU cc_start: 0.7761 (mp0) cc_final: 0.7295 (mp0) REVERT: E 53 ARG cc_start: 0.7656 (ttp-110) cc_final: 0.7061 (mmt180) REVERT: E 74 ASP cc_start: 0.9094 (OUTLIER) cc_final: 0.8742 (m-30) outliers start: 27 outliers final: 15 residues processed: 127 average time/residue: 0.4650 time to fit residues: 64.0825 Evaluate side-chains 127 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 685 ARG Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 91 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 55 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 123 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 84 optimal weight: 0.0770 chunk 126 optimal weight: 0.5980 chunk 127 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 752 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.203783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.123985 restraints weight = 12645.007| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.67 r_work: 0.3515 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11052 Z= 0.100 Angle : 0.542 10.941 14987 Z= 0.273 Chirality : 0.043 0.148 1651 Planarity : 0.004 0.068 1977 Dihedral : 3.903 19.392 1539 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.72 % Allowed : 17.20 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.23), residues: 1375 helix: 1.40 (0.32), residues: 284 sheet: -0.08 (0.23), residues: 459 loop : -1.00 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 285 TYR 0.021 0.001 TYR D 66 PHE 0.036 0.001 PHE A 791 TRP 0.016 0.001 TRP A 203 HIS 0.003 0.001 HIS A 621 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (11051) covalent geometry : angle 0.54223 / 0.27 (14985) SS BOND : bond 0.00092 / 0.06 ( 1) SS BOND : angle 0.83298 / 0.45 ( 2) hydrogen bonds : bond 0.03196 / 2.12 ( 429) hydrogen bonds : angle 4.19785 / 3.01 ( 1476) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 243 GLN cc_start: 0.7359 (mp10) cc_final: 0.6695 (mp10) REVERT: A 251 LYS cc_start: 0.8428 (mmpt) cc_final: 0.8067 (mttt) REVERT: A 285 ARG cc_start: 0.7802 (ttm-80) cc_final: 0.7423 (mpp80) REVERT: A 293 GLN cc_start: 0.6921 (mt0) cc_final: 0.6153 (pt0) REVERT: A 314 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7924 (mm-30) REVERT: A 616 TYR cc_start: 0.6711 (m-10) cc_final: 0.6448 (m-80) REVERT: B 77 ARG cc_start: 0.7544 (ttt-90) cc_final: 0.7013 (tmt90) REVERT: B 79 MET cc_start: 0.6232 (mmm) cc_final: 0.5954 (mmm) REVERT: B 137 GLU cc_start: 0.8109 (pm20) cc_final: 0.7633 (pm20) REVERT: B 138 VAL cc_start: 0.7193 (OUTLIER) cc_final: 0.6900 (p) REVERT: B 154 GLN cc_start: 0.7585 (tm-30) cc_final: 0.7334 (tm130) REVERT: B 193 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.6939 (tpt) REVERT: B 330 GLU cc_start: 0.6412 (mt-10) cc_final: 0.5492 (tm-30) REVERT: B 333 VAL cc_start: 0.7865 (t) cc_final: 0.7660 (m) REVERT: B 336 LEU cc_start: 0.6281 (mm) cc_final: 0.6055 (mt) REVERT: B 338 GLN cc_start: 0.5798 (tt0) cc_final: 0.5580 (mm-40) REVERT: B 365 MET cc_start: 0.5237 (tpp) cc_final: 0.4928 (tpp) REVERT: C 81 ARG cc_start: 0.6730 (tpm170) cc_final: 0.4746 (tpp80) REVERT: D 92 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7365 (pm20) REVERT: D 131 MET cc_start: 0.6897 (OUTLIER) cc_final: 0.6585 (mmp) REVERT: D 145 GLU cc_start: 0.7792 (mp0) cc_final: 0.7290 (mp0) REVERT: E 53 ARG cc_start: 0.7727 (ttp-110) cc_final: 0.7184 (mmt180) REVERT: E 74 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8627 (m-30) outliers start: 20 outliers final: 11 residues processed: 127 average time/residue: 0.4809 time to fit residues: 66.1962 Evaluate side-chains 122 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 685 ARG Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 78 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 64 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 53 optimal weight: 0.0870 chunk 36 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 76 optimal weight: 0.0970 chunk 72 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 overall best weight: 1.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 78 ASN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.201656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.120532 restraints weight = 12706.440| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.69 r_work: 0.3466 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11052 Z= 0.143 Angle : 0.579 10.915 14987 Z= 0.293 Chirality : 0.044 0.143 1651 Planarity : 0.004 0.068 1977 Dihedral : 4.077 20.929 1539 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.24 % Allowed : 16.94 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.23), residues: 1375 helix: 1.35 (0.32), residues: 286 sheet: -0.09 (0.23), residues: 462 loop : -1.02 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 285 TYR 0.022 0.001 TYR D 66 PHE 0.036 0.001 PHE A 791 TRP 0.020 0.001 TRP A 203 HIS 0.002 0.001 HIS A 621 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (11051) covalent geometry : angle 0.57944 / 0.29 (14985) SS BOND : bond 0.00199 / 0.13 ( 1) SS BOND : angle 0.83099 / 0.44 ( 2) hydrogen bonds : bond 0.04023 / 2.65 ( 429) hydrogen bonds : angle 4.35180 / 3.12 ( 1476) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 243 GLN cc_start: 0.7423 (mp10) cc_final: 0.7105 (mp10) REVERT: A 251 LYS cc_start: 0.8402 (mmpt) cc_final: 0.8033 (mttt) REVERT: A 263 GLU cc_start: 0.7617 (tp30) cc_final: 0.7388 (tp30) REVERT: A 285 ARG cc_start: 0.7828 (ttm-80) cc_final: 0.7412 (mpp80) REVERT: A 293 GLN cc_start: 0.7043 (mt0) cc_final: 0.6237 (pt0) REVERT: A 314 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7980 (mm-30) REVERT: A 616 TYR cc_start: 0.6774 (m-10) cc_final: 0.6504 (m-80) REVERT: B 32 LEU cc_start: 0.5340 (OUTLIER) cc_final: 0.4813 (tp) REVERT: B 77 ARG cc_start: 0.7529 (ttt-90) cc_final: 0.7008 (tmt90) REVERT: B 79 MET cc_start: 0.6178 (mmm) cc_final: 0.5872 (mmm) REVERT: B 137 GLU cc_start: 0.8145 (pm20) cc_final: 0.7637 (pm20) REVERT: B 138 VAL cc_start: 0.7262 (OUTLIER) cc_final: 0.6959 (p) REVERT: B 193 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.6972 (tpt) REVERT: B 330 GLU cc_start: 0.6425 (mt-10) cc_final: 0.5513 (tm-30) REVERT: B 333 VAL cc_start: 0.7818 (t) cc_final: 0.7607 (m) REVERT: B 338 GLN cc_start: 0.5936 (tt0) cc_final: 0.5541 (mm-40) REVERT: B 365 MET cc_start: 0.5357 (tpp) cc_final: 0.5052 (tpp) REVERT: C 81 ARG cc_start: 0.6774 (tpm170) cc_final: 0.4749 (tpp80) REVERT: D 92 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7421 (pm20) REVERT: D 145 GLU cc_start: 0.7797 (mp0) cc_final: 0.7318 (mp0) REVERT: E 53 ARG cc_start: 0.7781 (ttp-110) cc_final: 0.7196 (mmt180) REVERT: E 74 ASP cc_start: 0.9044 (OUTLIER) cc_final: 0.8685 (m-30) outliers start: 26 outliers final: 17 residues processed: 122 average time/residue: 0.4920 time to fit residues: 65.1223 Evaluate side-chains 125 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 685 ARG Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain D residue 78 ASN Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 67 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 53 GLN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.201777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.120830 restraints weight = 12764.567| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.69 r_work: 0.3468 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11052 Z= 0.140 Angle : 0.587 10.820 14987 Z= 0.295 Chirality : 0.044 0.147 1651 Planarity : 0.004 0.068 1977 Dihedral : 4.074 20.629 1539 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.15 % Allowed : 17.28 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.22), residues: 1375 helix: 1.37 (0.33), residues: 282 sheet: -0.04 (0.24), residues: 458 loop : -1.10 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 298 TYR 0.021 0.001 TYR D 66 PHE 0.036 0.001 PHE A 791 TRP 0.026 0.001 TRP A 203 HIS 0.002 0.001 HIS A 621 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (11051) covalent geometry : angle 0.58647 / 0.30 (14985) SS BOND : bond 0.00175 / 0.12 ( 1) SS BOND : angle 0.82696 / 0.44 ( 2) hydrogen bonds : bond 0.03958 / 2.62 ( 429) hydrogen bonds : angle 4.35010 / 3.11 ( 1476) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4745.81 seconds wall clock time: 80 minutes 59.01 seconds (4859.01 seconds total)