Starting phenix.real_space_refine on Fri Jul 3 00:42:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pxg_71969/07_2026/9pxg_71969_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pxg_71969/07_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_71969/07_2026/9pxg_71969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pxg_71969/07_2026/9pxg_71969.map" model { file = "/net/cci-nas-00/data/ceres_data/9pxg_71969/07_2026/9pxg_71969_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pxg_71969/07_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-dev-6108/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, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Time building chain proxies: 2.18, per 1000 atoms: 0.20 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: 1.19 Conformation dependent library (CDL) restraints added in 390.5 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: 0.34 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: 1.98 Time building geometry restraints manager: 1.37 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 3.210 ... (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: 2.610 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: 0.240 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.420 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.200 ------------------------------------------------------------------------------- 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 : 0.351 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: 0.5860 time to fit residues: 132.5327 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 : 0.371 ------------------------------------------------------------------------------- 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 = 0.4416 r_free = 0.4416 target = 0.206150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.132938 restraints weight = 12788.416| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.53 r_work: 0.3567 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11052 Z= 0.110 Angle : 0.559 8.774 14987 Z= 0.289 Chirality : 0.043 0.186 1651 Planarity : 0.004 0.049 1977 Dihedral : 3.887 18.504 1541 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.55 % Allowed : 9.20 % Favored : 89.25 % 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: 289 sheet: -0.06 (0.25), residues: 453 loop : -1.08 (0.24), residues: 633 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 0.028 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 0.00235 / 0.11 (11051) covalent geometry : angle 0.55925 / 0.29 (14985) SS BOND : bond 0.00112 / 0.07 ( 1) SS BOND : angle 1.08219 / 0.57 ( 2) hydrogen bonds : bond 0.04302 / 2.89 ( 429) hydrogen bonds : angle 4.98964 / 3.56 ( 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 171 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 GLN cc_start: 0.7237 (mp10) cc_final: 0.6677 (mp10) REVERT: A 251 LYS cc_start: 0.8564 (mmpt) cc_final: 0.7968 (mttm) REVERT: A 263 GLU cc_start: 0.7524 (tp30) cc_final: 0.7265 (tp30) REVERT: A 293 GLN cc_start: 0.6728 (mt0) cc_final: 0.5985 (pt0) REVERT: A 314 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8029 (mm-30) REVERT: A 368 MET cc_start: 0.8384 (mmp) cc_final: 0.8035 (mmp) REVERT: A 616 TYR cc_start: 0.6362 (m-10) cc_final: 0.6074 (m-80) REVERT: A 719 ARG cc_start: 0.7957 (mtm110) cc_final: 0.7718 (mtm110) REVERT: B 32 LEU cc_start: 0.5693 (tp) cc_final: 0.5304 (tp) REVERT: B 61 GLU cc_start: 0.7858 (pt0) cc_final: 0.7482 (pt0) REVERT: B 77 ARG cc_start: 0.7820 (ttt-90) cc_final: 0.7453 (ttp-170) REVERT: B 79 MET cc_start: 0.5993 (tpt) cc_final: 0.4646 (tpt) REVERT: B 95 GLU cc_start: 0.7856 (mp0) cc_final: 0.7549 (pt0) REVERT: B 106 TYR cc_start: 0.6471 (m-80) cc_final: 0.6139 (m-80) REVERT: B 137 GLU cc_start: 0.8015 (pm20) cc_final: 0.7565 (pm20) REVERT: B 154 GLN cc_start: 0.7585 (tm-30) cc_final: 0.7139 (tm130) REVERT: B 193 MET cc_start: 0.7220 (OUTLIER) cc_final: 0.6348 (tpt) REVERT: B 263 ARG cc_start: 0.7144 (mmp80) cc_final: 0.6804 (ptp-170) REVERT: B 330 GLU cc_start: 0.6651 (mt-10) cc_final: 0.5599 (tm-30) REVERT: B 338 GLN cc_start: 0.5690 (tt0) cc_final: 0.5479 (mm-40) REVERT: B 343 PHE cc_start: 0.7342 (m-80) cc_final: 0.6882 (m-10) REVERT: C 81 ARG cc_start: 0.6709 (tpm170) cc_final: 0.4852 (tpp80) REVERT: D 206 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7674 (mm-30) REVERT: E 53 ARG cc_start: 0.7783 (ttp-110) cc_final: 0.7257 (mmt180) outliers start: 18 outliers final: 10 residues processed: 163 average time/residue: 0.5122 time to fit residues: 90.6224 Evaluate side-chains 134 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain E residue 39 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 67 optimal weight: 0.7980 chunk 109 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 26 optimal weight: 0.0980 chunk 38 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 GLN B 168 GLN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.202424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.127769 restraints weight = 12900.528| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.58 r_work: 0.3489 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11052 Z= 0.182 Angle : 0.607 8.007 14987 Z= 0.315 Chirality : 0.045 0.191 1651 Planarity : 0.005 0.052 1977 Dihedral : 4.245 23.380 1541 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.58 % Allowed : 11.26 % Favored : 86.16 % 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 (0.23), residues: 1375 helix: 1.13 (0.32), residues: 288 sheet: -0.20 (0.24), residues: 459 loop : -1.08 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 298 TYR 0.023 0.002 TYR D 66 PHE 0.030 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 0.00436 / 0.18 (11051) covalent geometry : angle 0.60663 / 0.32 (14985) SS BOND : bond 0.00220 / 0.15 ( 1) SS BOND : angle 0.97234 / 0.51 ( 2) hydrogen bonds : bond 0.05044 / 3.36 ( 429) hydrogen bonds : angle 4.82757 / 3.46 ( 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 166 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 GLN cc_start: 0.7452 (mp10) cc_final: 0.6946 (mp10) REVERT: A 251 LYS cc_start: 0.8534 (mmpt) cc_final: 0.8066 (mttt) REVERT: A 263 GLU cc_start: 0.7616 (tp30) cc_final: 0.7360 (tp30) REVERT: A 293 GLN cc_start: 0.6996 (mt0) cc_final: 0.6171 (pt0) REVERT: A 314 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8231 (mm-30) REVERT: A 534 ARG cc_start: 0.7170 (ttt-90) cc_final: 0.6930 (ttm-80) REVERT: A 616 TYR cc_start: 0.6721 (m-10) cc_final: 0.6449 (m-80) REVERT: B 32 LEU cc_start: 0.5905 (tp) cc_final: 0.5652 (tp) REVERT: B 77 ARG cc_start: 0.7823 (ttt-90) cc_final: 0.7366 (ttp-170) REVERT: B 106 TYR cc_start: 0.6434 (m-80) cc_final: 0.6031 (m-80) REVERT: B 137 GLU cc_start: 0.8272 (pm20) cc_final: 0.7824 (pm20) REVERT: B 193 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.6359 (tpt) REVERT: B 263 ARG cc_start: 0.7138 (mmp80) cc_final: 0.6882 (ptp90) REVERT: B 330 GLU cc_start: 0.6835 (mt-10) cc_final: 0.5905 (tm-30) REVERT: B 338 GLN cc_start: 0.5843 (tt0) cc_final: 0.5481 (mm-40) REVERT: B 343 PHE cc_start: 0.7720 (m-80) cc_final: 0.7351 (m-80) REVERT: B 365 MET cc_start: 0.5614 (tpp) cc_final: 0.5389 (tpp) REVERT: C 81 ARG cc_start: 0.6783 (tpm170) cc_final: 0.4866 (tpp80) REVERT: D 127 LEU cc_start: 0.6234 (OUTLIER) cc_final: 0.6000 (pp) REVERT: D 145 GLU cc_start: 0.7902 (mp0) cc_final: 0.7611 (mp0) REVERT: D 206 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7765 (mm-30) REVERT: E 53 ARG cc_start: 0.7782 (ttp-110) cc_final: 0.7231 (mmt180) outliers start: 30 outliers final: 18 residues processed: 153 average time/residue: 0.5158 time to fit residues: 85.5358 Evaluate side-chains 143 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 531 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 685 ARG Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 765 THR 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 155 ASP 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 274 VAL Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain D residue 48 ASN Chi-restraints excluded: chain D residue 127 LEU 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: 9.9990 chunk 52 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 70 optimal weight: 20.0000 chunk 42 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 GLN A 258 ASN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 HIS D 78 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 = 0.196420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.118768 restraints weight = 12719.621| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 3.19 r_work: 0.3329 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11052 Z= 0.207 Angle : 0.628 7.826 14987 Z= 0.327 Chirality : 0.046 0.162 1651 Planarity : 0.005 0.056 1977 Dihedral : 4.431 24.010 1541 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.53 % Allowed : 12.30 % Favored : 84.18 % 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 (0.22), residues: 1375 helix: 0.92 (0.31), residues: 287 sheet: -0.13 (0.24), residues: 459 loop : -1.18 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 285 TYR 0.023 0.002 TYR D 66 PHE 0.033 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 0.00506 / 0.21 (11051) covalent geometry : angle 0.62781 / 0.33 (14985) SS BOND : bond 0.00220 / 0.15 ( 1) SS BOND : angle 0.91621 / 0.48 ( 2) hydrogen bonds : bond 0.05028 / 3.33 ( 429) hydrogen bonds : angle 4.76390 / 3.42 ( 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 167 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 GLN cc_start: 0.7556 (mp10) cc_final: 0.6875 (mp10) REVERT: A 251 LYS cc_start: 0.8587 (mmpt) cc_final: 0.8143 (mttm) REVERT: A 293 GLN cc_start: 0.7012 (mt0) cc_final: 0.6223 (pt0) REVERT: A 314 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8288 (mm-30) REVERT: A 534 ARG cc_start: 0.7413 (ttt-90) cc_final: 0.7180 (ttm-80) REVERT: A 616 TYR cc_start: 0.6826 (m-10) cc_final: 0.6553 (m-80) REVERT: A 675 MET cc_start: 0.7026 (mmt) cc_final: 0.6787 (mmt) REVERT: B 32 LEU cc_start: 0.6143 (tp) cc_final: 0.5826 (tp) REVERT: B 77 ARG cc_start: 0.7853 (ttt-90) cc_final: 0.7242 (ttp-170) REVERT: B 106 TYR cc_start: 0.6487 (m-80) cc_final: 0.6120 (m-80) REVERT: B 137 GLU cc_start: 0.8389 (pm20) cc_final: 0.7979 (pm20) REVERT: B 154 GLN cc_start: 0.7563 (tm-30) cc_final: 0.7279 (tm-30) REVERT: B 193 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.6776 (tpt) REVERT: B 263 ARG cc_start: 0.7261 (mmp80) cc_final: 0.6880 (ptp-170) REVERT: B 330 GLU cc_start: 0.6752 (mt-10) cc_final: 0.5829 (tm-30) REVERT: B 333 VAL cc_start: 0.7786 (t) cc_final: 0.7566 (m) REVERT: B 338 GLN cc_start: 0.5882 (tt0) cc_final: 0.5553 (mm-40) REVERT: B 365 MET cc_start: 0.5640 (tpp) cc_final: 0.5356 (tpp) REVERT: C 81 ARG cc_start: 0.6701 (tpm170) cc_final: 0.4827 (tpp80) REVERT: D 68 GLU cc_start: 0.7092 (pp20) cc_final: 0.6687 (mt-10) REVERT: D 92 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7413 (pm20) REVERT: D 127 LEU cc_start: 0.6024 (pp) cc_final: 0.5780 (pp) REVERT: D 145 GLU cc_start: 0.7878 (mp0) cc_final: 0.7510 (mp0) REVERT: D 152 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.6651 (mtt-85) REVERT: D 206 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7900 (mm-30) REVERT: E 53 ARG cc_start: 0.7879 (ttp-110) cc_final: 0.7270 (mmt180) REVERT: E 74 ASP cc_start: 0.9138 (OUTLIER) cc_final: 0.8779 (m-30) outliers start: 41 outliers final: 22 residues processed: 151 average time/residue: 0.5519 time to fit residues: 89.9648 Evaluate side-chains 145 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 565 ILE 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 73 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 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: 0.9990 chunk 116 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 133 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.198693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.121666 restraints weight = 12539.445| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 3.17 r_work: 0.3369 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11052 Z= 0.127 Angle : 0.548 7.494 14987 Z= 0.284 Chirality : 0.043 0.148 1651 Planarity : 0.004 0.060 1977 Dihedral : 4.124 21.995 1539 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.84 % Allowed : 13.59 % Favored : 83.58 % 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: -0.45 (0.22), residues: 1375 helix: 1.20 (0.32), residues: 285 sheet: -0.10 (0.24), residues: 461 loop : -1.12 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 285 TYR 0.023 0.001 TYR D 66 PHE 0.032 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 0.00297 / 0.13 (11051) covalent geometry : angle 0.54752 / 0.28 (14985) SS BOND : bond 0.00151 / 0.10 ( 1) SS BOND : angle 0.84023 / 0.44 ( 2) hydrogen bonds : bond 0.03997 / 2.65 ( 429) hydrogen bonds : angle 4.50262 / 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 152 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 243 GLN cc_start: 0.7460 (mp10) cc_final: 0.6715 (mp10) REVERT: A 251 LYS cc_start: 0.8518 (mmpt) cc_final: 0.8114 (mttt) REVERT: A 293 GLN cc_start: 0.7034 (mt0) cc_final: 0.6192 (pt0) REVERT: A 314 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8263 (mm-30) REVERT: A 616 TYR cc_start: 0.6823 (m-10) cc_final: 0.6551 (m-80) REVERT: B 77 ARG cc_start: 0.7823 (ttt-90) cc_final: 0.7454 (ttp-170) REVERT: B 79 MET cc_start: 0.5891 (tpt) cc_final: 0.4618 (tpt) REVERT: B 106 TYR cc_start: 0.6489 (m-80) cc_final: 0.6142 (m-80) REVERT: B 137 GLU cc_start: 0.8286 (pm20) cc_final: 0.7849 (pm20) REVERT: B 154 GLN cc_start: 0.7672 (tm-30) cc_final: 0.7296 (tm-30) REVERT: B 193 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.6761 (tpt) REVERT: B 257 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7906 (mt) REVERT: B 263 ARG cc_start: 0.7251 (mmp80) cc_final: 0.6919 (ptp-170) REVERT: B 330 GLU cc_start: 0.6673 (mt-10) cc_final: 0.5835 (tm-30) REVERT: B 333 VAL cc_start: 0.7910 (t) cc_final: 0.7660 (m) REVERT: B 338 GLN cc_start: 0.5862 (tt0) cc_final: 0.5501 (mm-40) REVERT: B 365 MET cc_start: 0.5710 (tpp) cc_final: 0.5498 (tpp) REVERT: C 81 ARG cc_start: 0.6722 (tpm170) cc_final: 0.4830 (tpp80) REVERT: D 78 ASN cc_start: 0.7322 (t0) cc_final: 0.7022 (t160) REVERT: D 92 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7414 (pm20) REVERT: D 127 LEU cc_start: 0.5972 (pp) cc_final: 0.5697 (pp) REVERT: D 131 MET cc_start: 0.7111 (OUTLIER) cc_final: 0.6715 (mmp) REVERT: D 145 GLU cc_start: 0.7915 (mp0) cc_final: 0.7527 (mp0) REVERT: D 152 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.6628 (mtt-85) REVERT: D 206 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7862 (mm-30) REVERT: E 53 ARG cc_start: 0.7861 (ttp-110) cc_final: 0.7292 (mmt180) REVERT: E 74 ASP cc_start: 0.9077 (OUTLIER) cc_final: 0.8749 (m-30) outliers start: 33 outliers final: 15 residues processed: 142 average time/residue: 0.4793 time to fit residues: 73.8068 Evaluate side-chains 134 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 193 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 274 VAL 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 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: 4.9990 chunk 10 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 51 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 217 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 = 0.4377 r_free = 0.4377 target = 0.199551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.123627 restraints weight = 12610.908| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.08 r_work: 0.3397 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11052 Z= 0.110 Angle : 0.546 10.835 14987 Z= 0.276 Chirality : 0.043 0.146 1651 Planarity : 0.004 0.063 1977 Dihedral : 3.984 20.745 1539 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.58 % Allowed : 14.10 % Favored : 83.32 % 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: -0.37 (0.23), residues: 1375 helix: 1.34 (0.32), residues: 285 sheet: -0.12 (0.23), residues: 464 loop : -1.05 (0.24), residues: 626 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 0.033 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 0.00255 / 0.11 (11051) covalent geometry : angle 0.54626 / 0.28 (14985) SS BOND : bond 0.00125 / 0.08 ( 1) SS BOND : angle 0.79033 / 0.42 ( 2) hydrogen bonds : bond 0.03535 / 2.35 ( 429) hydrogen bonds : angle 4.29776 / 3.08 ( 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 151 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 GLN cc_start: 0.7462 (mp10) cc_final: 0.6909 (mp10) REVERT: A 251 LYS cc_start: 0.8501 (mmpt) cc_final: 0.8122 (mttt) REVERT: A 293 GLN cc_start: 0.6993 (mt0) cc_final: 0.6208 (pt0) REVERT: A 314 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8149 (mm-30) REVERT: A 616 TYR cc_start: 0.6793 (m-10) cc_final: 0.6522 (m-80) REVERT: B 106 TYR cc_start: 0.6507 (m-80) cc_final: 0.6167 (m-80) REVERT: B 137 GLU cc_start: 0.8213 (pm20) cc_final: 0.7761 (pm20) REVERT: B 154 GLN cc_start: 0.7642 (tm-30) cc_final: 0.7292 (tm-30) REVERT: B 193 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.6782 (tpt) REVERT: B 263 ARG cc_start: 0.7155 (mmp80) cc_final: 0.6814 (ptp-170) REVERT: B 330 GLU cc_start: 0.6635 (mt-10) cc_final: 0.5787 (tm-30) REVERT: B 333 VAL cc_start: 0.7931 (t) cc_final: 0.7701 (m) REVERT: B 338 GLN cc_start: 0.5900 (tt0) cc_final: 0.5555 (mm-40) REVERT: B 343 PHE cc_start: 0.7285 (m-80) cc_final: 0.6909 (m-80) REVERT: B 365 MET cc_start: 0.5775 (tpp) cc_final: 0.5491 (tpp) REVERT: C 81 ARG cc_start: 0.6679 (tpm170) cc_final: 0.4827 (tpp80) REVERT: D 92 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7372 (pm20) REVERT: D 127 LEU cc_start: 0.6109 (OUTLIER) cc_final: 0.5862 (pp) REVERT: D 131 MET cc_start: 0.7148 (OUTLIER) cc_final: 0.6773 (mmp) REVERT: D 145 GLU cc_start: 0.7966 (mp0) cc_final: 0.7560 (mp0) REVERT: D 152 ARG cc_start: 0.6873 (OUTLIER) cc_final: 0.6636 (mtt-85) REVERT: D 206 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7917 (mm-30) REVERT: E 53 ARG cc_start: 0.7866 (ttp-110) cc_final: 0.7318 (mmt180) REVERT: E 74 ASP cc_start: 0.9037 (OUTLIER) cc_final: 0.8704 (m-30) outliers start: 30 outliers final: 16 residues processed: 138 average time/residue: 0.5485 time to fit residues: 82.1248 Evaluate side-chains 136 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 685 ARG Chi-restraints excluded: chain A residue 765 THR 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 119 ASP Chi-restraints excluded: chain D residue 127 LEU 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 109 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 80 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 127 optimal weight: 0.0980 chunk 89 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN A 465 GLN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.200253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.122155 restraints weight = 12733.556| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.62 r_work: 0.3385 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2612 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= 0.162 Angle : 0.583 10.221 14987 Z= 0.299 Chirality : 0.044 0.144 1651 Planarity : 0.004 0.064 1977 Dihedral : 4.191 22.093 1539 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.58 % Allowed : 14.96 % Favored : 82.46 % 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: -0.45 (0.22), residues: 1375 helix: 1.27 (0.32), residues: 285 sheet: -0.17 (0.23), residues: 469 loop : -1.09 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 285 TYR 0.022 0.002 TYR D 66 PHE 0.035 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 0.00391 / 0.16 (11051) covalent geometry : angle 0.58340 / 0.30 (14985) SS BOND : bond 0.00208 / 0.14 ( 1) SS BOND : angle 0.79852 / 0.42 ( 2) hydrogen bonds : bond 0.04436 / 2.94 ( 429) hydrogen bonds : angle 4.47580 / 3.20 ( 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 148 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.439 Fit side-chains REVERT: A 243 GLN cc_start: 0.7401 (mp10) cc_final: 0.7135 (mp10) REVERT: A 251 LYS cc_start: 0.8431 (mmpt) cc_final: 0.8038 (mttt) REVERT: A 263 GLU cc_start: 0.7585 (tp30) cc_final: 0.7246 (tp30) REVERT: A 285 ARG cc_start: 0.7756 (ttm-80) cc_final: 0.7330 (mpp80) REVERT: A 293 GLN cc_start: 0.6893 (mt0) cc_final: 0.6088 (pt0) REVERT: A 314 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7975 (mm-30) REVERT: A 534 ARG cc_start: 0.7178 (ttt-90) cc_final: 0.6910 (ttm-80) REVERT: A 616 TYR cc_start: 0.6762 (m-10) cc_final: 0.6503 (m-80) REVERT: B 32 LEU cc_start: 0.5437 (OUTLIER) cc_final: 0.5150 (tp) REVERT: B 77 ARG cc_start: 0.7550 (ttt-90) cc_final: 0.6923 (tpt-90) REVERT: B 79 MET cc_start: 0.6339 (mmm) cc_final: 0.5956 (mmm) REVERT: B 106 TYR cc_start: 0.6472 (m-80) cc_final: 0.6126 (m-80) REVERT: B 137 GLU cc_start: 0.8271 (pm20) cc_final: 0.7738 (pm20) REVERT: B 154 GLN cc_start: 0.7562 (tm-30) cc_final: 0.7281 (tm-30) REVERT: B 193 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.6885 (tpt) REVERT: B 263 ARG cc_start: 0.7131 (mmp80) cc_final: 0.6898 (ptp-170) REVERT: B 330 GLU cc_start: 0.6573 (mt-10) cc_final: 0.5767 (tm-30) REVERT: B 333 VAL cc_start: 0.7893 (t) cc_final: 0.7687 (m) REVERT: B 338 GLN cc_start: 0.5950 (tt0) cc_final: 0.5547 (mm-40) REVERT: B 365 MET cc_start: 0.5784 (tpp) cc_final: 0.5411 (tpp) REVERT: C 81 ARG cc_start: 0.6628 (tpm170) cc_final: 0.4743 (tpp80) REVERT: D 68 GLU cc_start: 0.7073 (pp20) cc_final: 0.6663 (mt-10) REVERT: D 92 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7407 (pm20) REVERT: D 127 LEU cc_start: 0.6022 (pp) cc_final: 0.5801 (pp) REVERT: D 131 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.6551 (mmp) REVERT: D 145 GLU cc_start: 0.7805 (mp0) cc_final: 0.7389 (mp0) REVERT: D 152 ARG cc_start: 0.6708 (OUTLIER) cc_final: 0.6496 (mtt-85) REVERT: D 206 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7785 (mm-30) REVERT: E 53 ARG cc_start: 0.7704 (ttp-110) cc_final: 0.7101 (mmt180) REVERT: E 74 ASP cc_start: 0.9082 (OUTLIER) cc_final: 0.8703 (m-30) outliers start: 30 outliers final: 19 residues processed: 138 average time/residue: 0.5892 time to fit residues: 87.9938 Evaluate side-chains 134 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 B residue 32 LEU 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 5 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 53 GLN B 58 ASN ** B 217 GLN ** 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 = 0.4336 r_free = 0.4336 target = 0.196329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.115845 restraints weight = 12828.963| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.63 r_work: 0.3319 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 11052 Z= 0.318 Angle : 0.736 11.099 14987 Z= 0.381 Chirality : 0.050 0.173 1651 Planarity : 0.005 0.066 1977 Dihedral : 4.910 25.823 1539 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.75 % Allowed : 16.51 % Favored : 80.74 % 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: -0.90 (0.22), residues: 1375 helix: 0.66 (0.31), residues: 280 sheet: -0.25 (0.24), residues: 468 loop : -1.42 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 140 TYR 0.021 0.002 TYR D 66 PHE 0.038 0.003 PHE A 791 TRP 0.013 0.002 TRP A 203 HIS 0.004 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00785 / 0.32 (11051) covalent geometry : angle 0.73595 / 0.38 (14985) SS BOND : bond 0.00392 / 0.26 ( 1) SS BOND : angle 0.98672 / 0.52 ( 2) hydrogen bonds : bond 0.06042 / 4.01 ( 429) hydrogen bonds : angle 4.88636 / 3.51 ( 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 140 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.438 Fit side-chains REVERT: A 243 GLN cc_start: 0.7480 (mp10) cc_final: 0.7201 (mp10) REVERT: A 251 LYS cc_start: 0.8377 (mmpt) cc_final: 0.8045 (mttt) REVERT: A 263 GLU cc_start: 0.7650 (tp30) cc_final: 0.7313 (tp30) REVERT: A 314 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8106 (mm-30) REVERT: A 534 ARG cc_start: 0.7421 (ttt-90) cc_final: 0.7186 (ttm-80) REVERT: A 616 TYR cc_start: 0.6940 (m-10) cc_final: 0.6724 (m-80) REVERT: B 77 ARG cc_start: 0.7539 (ttt-90) cc_final: 0.6908 (tpt-90) REVERT: B 79 MET cc_start: 0.6350 (mmm) cc_final: 0.5928 (mmm) REVERT: B 95 GLU cc_start: 0.7908 (mp0) cc_final: 0.7673 (mp0) REVERT: B 106 TYR cc_start: 0.6292 (m-80) cc_final: 0.6021 (m-80) REVERT: B 137 GLU cc_start: 0.8394 (pm20) cc_final: 0.7905 (pm20) REVERT: B 193 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7170 (mmt) REVERT: B 263 ARG cc_start: 0.7241 (mmp80) cc_final: 0.6769 (ptp-170) REVERT: B 330 GLU cc_start: 0.6846 (mt-10) cc_final: 0.5892 (tm-30) REVERT: B 333 VAL cc_start: 0.7893 (t) cc_final: 0.7688 (m) REVERT: B 338 GLN cc_start: 0.6108 (tt0) cc_final: 0.5595 (mp-120) REVERT: B 365 MET cc_start: 0.5792 (tpp) cc_final: 0.5324 (tpp) REVERT: C 81 ARG cc_start: 0.6951 (tpm170) cc_final: 0.6623 (tpm-80) REVERT: D 92 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7361 (pm20) REVERT: D 127 LEU cc_start: 0.6210 (pp) cc_final: 0.5986 (pp) REVERT: D 145 GLU cc_start: 0.7871 (mp0) cc_final: 0.7496 (mp0) REVERT: D 152 ARG cc_start: 0.6749 (OUTLIER) cc_final: 0.6547 (mtt-85) REVERT: E 53 ARG cc_start: 0.7791 (ttp-110) cc_final: 0.7222 (mmt180) REVERT: E 74 ASP cc_start: 0.9156 (OUTLIER) cc_final: 0.8747 (m-30) outliers start: 32 outliers final: 19 residues processed: 128 average time/residue: 0.5984 time to fit residues: 82.9697 Evaluate side-chains 126 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 443 ILE 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 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 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 92 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 55 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 126 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 21 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 168 GLN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN E 71 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.201328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.123540 restraints weight = 12769.807| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.67 r_work: 0.3423 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11052 Z= 0.111 Angle : 0.576 11.371 14987 Z= 0.293 Chirality : 0.043 0.166 1651 Planarity : 0.004 0.067 1977 Dihedral : 4.219 21.739 1539 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.06 % Allowed : 17.54 % Favored : 80.40 % 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 (0.22), residues: 1375 helix: 1.16 (0.32), residues: 280 sheet: -0.17 (0.23), residues: 466 loop : -1.24 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 285 TYR 0.019 0.001 TYR D 66 PHE 0.036 0.001 PHE A 791 TRP 0.016 0.001 TRP A 203 HIS 0.007 0.001 HIS D 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (11051) covalent geometry : angle 0.57597 / 0.29 (14985) SS BOND : bond 0.00109 / 0.07 ( 1) SS BOND : angle 0.94235 / 0.50 ( 2) hydrogen bonds : bond 0.03614 / 2.40 ( 429) hydrogen bonds : angle 4.35816 / 3.13 ( 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 136 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.423 Fit side-chains REVERT: A 243 GLN cc_start: 0.7306 (mp10) cc_final: 0.6592 (mp10) REVERT: A 251 LYS cc_start: 0.8315 (mmpt) cc_final: 0.7973 (mttt) REVERT: A 263 GLU cc_start: 0.7503 (tp30) cc_final: 0.7181 (tp30) REVERT: A 285 ARG cc_start: 0.7767 (ttm-80) cc_final: 0.7377 (mpp80) REVERT: A 314 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7904 (mm-30) REVERT: A 616 TYR cc_start: 0.6614 (m-10) cc_final: 0.6353 (m-80) REVERT: B 79 MET cc_start: 0.6348 (mmm) cc_final: 0.6041 (mmm) REVERT: B 106 TYR cc_start: 0.6513 (m-80) cc_final: 0.6207 (m-80) REVERT: B 130 TRP cc_start: 0.7341 (p-90) cc_final: 0.7137 (p-90) REVERT: B 137 GLU cc_start: 0.8229 (pm20) cc_final: 0.7675 (pm20) REVERT: B 193 MET cc_start: 0.7443 (OUTLIER) cc_final: 0.6990 (tpt) REVERT: B 263 ARG cc_start: 0.7260 (mmp80) cc_final: 0.6853 (ptp-170) REVERT: B 330 GLU cc_start: 0.6529 (mt-10) cc_final: 0.5636 (tm-30) REVERT: B 338 GLN cc_start: 0.5996 (tt0) cc_final: 0.5654 (mm-40) REVERT: B 365 MET cc_start: 0.5791 (tpp) cc_final: 0.5367 (tpp) REVERT: C 81 ARG cc_start: 0.6690 (tpm170) cc_final: 0.6355 (tpm-80) REVERT: D 92 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7378 (pm20) REVERT: D 127 LEU cc_start: 0.5972 (pp) cc_final: 0.5722 (pp) REVERT: D 131 MET cc_start: 0.6812 (tpt) cc_final: 0.6505 (mmp) REVERT: D 145 GLU cc_start: 0.7712 (mp0) cc_final: 0.7242 (mp0) REVERT: D 206 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7717 (mm-30) REVERT: E 53 ARG cc_start: 0.7630 (ttp-110) cc_final: 0.7083 (mpt180) REVERT: E 74 ASP cc_start: 0.9049 (OUTLIER) cc_final: 0.8694 (m-30) outliers start: 24 outliers final: 14 residues processed: 128 average time/residue: 0.6014 time to fit residues: 83.3898 Evaluate side-chains 121 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 443 ILE 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 238 LEU 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 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 64 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 217 GLN D 78 ASN E 71 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.199856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.121401 restraints weight = 12827.737| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.66 r_work: 0.3399 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2872 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= 0.162 Angle : 0.608 13.119 14987 Z= 0.310 Chirality : 0.044 0.210 1651 Planarity : 0.004 0.068 1977 Dihedral : 4.311 22.666 1539 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.15 % Allowed : 17.71 % Favored : 80.14 % 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 (0.22), residues: 1375 helix: 1.15 (0.32), residues: 280 sheet: -0.20 (0.23), residues: 471 loop : -1.22 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 285 TYR 0.023 0.002 TYR B 284 PHE 0.037 0.002 PHE A 791 TRP 0.023 0.001 TRP A 203 HIS 0.006 0.001 HIS D 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 (11051) covalent geometry : angle 0.60777 / 0.31 (14985) SS BOND : bond 0.00213 / 0.14 ( 1) SS BOND : angle 0.97024 / 0.51 ( 2) hydrogen bonds : bond 0.04343 / 2.87 ( 429) hydrogen bonds : angle 4.44305 / 3.18 ( 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 130 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.434 Fit side-chains REVERT: A 243 GLN cc_start: 0.7378 (mp10) cc_final: 0.6577 (mp10) REVERT: A 251 LYS cc_start: 0.8308 (mmpt) cc_final: 0.7977 (mttt) REVERT: A 263 GLU cc_start: 0.7504 (tp30) cc_final: 0.7169 (tp30) REVERT: A 285 ARG cc_start: 0.7773 (ttm-80) cc_final: 0.7357 (mpp80) REVERT: A 314 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7941 (mm-30) REVERT: A 534 ARG cc_start: 0.7095 (ttt-90) cc_final: 0.6825 (ttm-80) REVERT: A 616 TYR cc_start: 0.6637 (m-10) cc_final: 0.6365 (m-80) REVERT: B 77 ARG cc_start: 0.7590 (ttt-90) cc_final: 0.6959 (tpt-90) REVERT: B 79 MET cc_start: 0.6384 (mmm) cc_final: 0.6040 (mmm) REVERT: B 106 TYR cc_start: 0.6495 (m-80) cc_final: 0.6209 (m-80) REVERT: B 130 TRP cc_start: 0.7342 (p-90) cc_final: 0.7095 (p-90) REVERT: B 137 GLU cc_start: 0.8259 (pm20) cc_final: 0.7801 (pm20) REVERT: B 154 GLN cc_start: 0.7617 (tm-30) cc_final: 0.7368 (tm130) REVERT: B 193 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.7007 (tpt) REVERT: B 263 ARG cc_start: 0.7169 (mmp80) cc_final: 0.6833 (ptp-170) REVERT: B 330 GLU cc_start: 0.6515 (mt-10) cc_final: 0.5606 (tm-30) REVERT: B 338 GLN cc_start: 0.5952 (tt0) cc_final: 0.5634 (mm-40) REVERT: B 365 MET cc_start: 0.5809 (tpp) cc_final: 0.5361 (tpp) REVERT: C 81 ARG cc_start: 0.6712 (tpm170) cc_final: 0.6457 (tpm-80) REVERT: D 92 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7354 (pm20) REVERT: D 127 LEU cc_start: 0.5990 (pp) cc_final: 0.5744 (pp) REVERT: D 131 MET cc_start: 0.6804 (tpt) cc_final: 0.6489 (mmp) REVERT: D 206 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7851 (mm-30) REVERT: E 53 ARG cc_start: 0.7666 (ttp-110) cc_final: 0.7089 (mmt180) REVERT: E 74 ASP cc_start: 0.9094 (OUTLIER) cc_final: 0.8719 (m-30) outliers start: 25 outliers final: 15 residues processed: 122 average time/residue: 0.5868 time to fit residues: 77.3543 Evaluate side-chains 119 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 443 ILE 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 189 ILE Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 238 LEU 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 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: 1.9990 chunk 44 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 107 optimal weight: 9.9990 chunk 102 optimal weight: 0.0870 chunk 5 optimal weight: 0.0570 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.203382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.125674 restraints weight = 12867.636| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.67 r_work: 0.3451 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11052 Z= 0.101 Angle : 0.552 12.213 14987 Z= 0.277 Chirality : 0.043 0.157 1651 Planarity : 0.004 0.068 1977 Dihedral : 3.933 20.208 1539 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.29 % Allowed : 18.49 % Favored : 80.22 % 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 (0.22), residues: 1375 helix: 1.41 (0.32), residues: 281 sheet: -0.10 (0.23), residues: 464 loop : -1.12 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 285 TYR 0.022 0.001 TYR B 284 PHE 0.036 0.001 PHE A 791 TRP 0.022 0.001 TRP A 203 HIS 0.003 0.001 HIS A 621 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (11051) covalent geometry : angle 0.55154 / 0.28 (14985) SS BOND : bond 0.00094 / 0.06 ( 1) SS BOND : angle 0.99476 / 0.53 ( 2) hydrogen bonds : bond 0.03189 / 2.12 ( 429) hydrogen bonds : angle 4.17585 / 2.98 ( 1476) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5756.05 seconds wall clock time: 98 minutes 22.65 seconds (5902.65 seconds total)