Starting phenix.real_space_refine on Tue Mar 3 15:38:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qud_14148/03_2026/7qud_14148.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qud_14148/03_2026/7qud_14148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qud_14148/03_2026/7qud_14148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qud_14148/03_2026/7qud_14148.map" model { file = "/net/cci-nas-00/data/ceres_data/7qud_14148/03_2026/7qud_14148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qud_14148/03_2026/7qud_14148.cif" } resolution = 3.47 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 1 5.21 5 S 47 5.16 5 C 4214 2.51 5 N 1137 2.21 5 O 1291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6696 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3350 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Chain breaks: 1 Chain: "B" Number of atoms: 3281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3281 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 397} Chain breaks: 2 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.27, per 1000 atoms: 0.19 Number of scatterers: 6696 At special positions: 0 Unit cell: (97.032, 74.64, 101.386, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 47 16.00 P 6 15.00 Mg 1 11.99 O 1291 8.00 N 1137 7.00 C 4214 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 257.3 milliseconds 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1564 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 53.6% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.951A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 109 through 128 removed outlier: 4.513A pdb=" N GLU A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.475A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.505A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.741A pdb=" N PHE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 281 Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.910A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 4.132A pdb=" N GLN A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.508A pdb=" N THR A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 400 removed outlier: 4.264A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.945A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 436 removed outlier: 4.200A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 41 through 45 Processing helix chain 'B' and resid 46 through 49 removed outlier: 3.719A pdb=" N VAL B 49 " --> pdb=" O ARG B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 49' Processing helix chain 'B' and resid 71 through 79 removed outlier: 3.744A pdb=" N SER B 75 " --> pdb=" O GLY B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 125 removed outlier: 3.787A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 159 Processing helix chain 'B' and resid 180 through 195 removed outlier: 3.983A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 222 through 242 removed outlier: 4.678A pdb=" N CYS B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.954A pdb=" N PHE B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 299 removed outlier: 3.790A pdb=" N MET B 299 " --> pdb=" O ALA B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.500A pdb=" N GLY B 308 " --> pdb=" O PRO B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 373 through 390 removed outlier: 4.053A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG B 390 " --> pdb=" O THR B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 404 through 428 removed outlier: 3.895A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 93 removed outlier: 7.899A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N GLU A 3 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N LEU A 136 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE A 5 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N PHE A 138 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE A 7 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 135 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA4, first strand: chain 'A' and resid 269 through 273 removed outlier: 6.779A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N CYS A 376 " --> pdb=" O MET A 317 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N MET A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 9.573A pdb=" N LYS A 352 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N CYS A 315 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N GLY A 354 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N MET A 317 " --> pdb=" O GLY A 354 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.134A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N VAL B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N HIS B 6 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY B 132 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 134 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N TYR B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 135 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 10.884A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 13.208A pdb=" N ASP B 203 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N SER B 364 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N PHE B 317 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR B 366 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA B 315 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE B 368 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL B 313 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASN B 370 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N LYS B 350 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL B 313 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ALA B 352 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA B 315 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N CYS B 354 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE B 317 " --> pdb=" O CYS B 354 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 51 through 52 303 hydrogen bonds defined for protein. 870 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: 1.01 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2212 1.34 - 1.46: 1547 1.46 - 1.58: 3004 1.58 - 1.70: 10 1.70 - 1.82: 74 Bond restraints: 6847 Sorted by residual: bond pdb=" CG1 ILE A 122 " pdb=" CD1 ILE A 122 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.16e+00 bond pdb=" CG1 ILE A 234 " pdb=" CD1 ILE A 234 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.34e+00 bond pdb=" CA THR B 219 " pdb=" C THR B 219 " ideal model delta sigma weight residual 1.531 1.524 0.007 7.40e-03 1.83e+04 9.16e-01 bond pdb=" CB GLN A 35 " pdb=" CG GLN A 35 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.53e-01 bond pdb=" CG GLN B 245 " pdb=" CD GLN B 245 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 7.31e-01 ... (remaining 6842 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 8946 1.38 - 2.75: 291 2.75 - 4.13: 47 4.13 - 5.51: 11 5.51 - 6.89: 7 Bond angle restraints: 9302 Sorted by residual: angle pdb=" C THR B 218 " pdb=" N THR B 219 " pdb=" CA THR B 219 " ideal model delta sigma weight residual 122.83 126.19 -3.36 1.08e+00 8.57e-01 9.67e+00 angle pdb=" C PRO B 261 " pdb=" N ARG B 262 " pdb=" CA ARG B 262 " ideal model delta sigma weight residual 124.82 129.55 -4.73 1.78e+00 3.16e-01 7.07e+00 angle pdb=" CA MET A 317 " pdb=" CB MET A 317 " pdb=" CG MET A 317 " ideal model delta sigma weight residual 114.10 119.02 -4.92 2.00e+00 2.50e-01 6.06e+00 angle pdb=" CB MET B 300 " pdb=" CG MET B 300 " pdb=" SD MET B 300 " ideal model delta sigma weight residual 112.70 119.59 -6.89 3.00e+00 1.11e-01 5.27e+00 angle pdb=" C2' GTP A 501 " pdb=" C3' GTP A 501 " pdb=" C4' GTP A 501 " ideal model delta sigma weight residual 111.00 104.56 6.44 3.00e+00 1.11e-01 4.60e+00 ... (remaining 9297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.24: 3956 33.24 - 66.49: 85 66.49 - 99.73: 21 99.73 - 132.97: 2 132.97 - 166.22: 3 Dihedral angle restraints: 4067 sinusoidal: 1630 harmonic: 2437 Sorted by residual: dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -61.62 166.22 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C5' GTP B 501 " pdb=" O5' GTP B 501 " pdb=" PA GTP B 501 " pdb=" O3A GTP B 501 " ideal model delta sinusoidal sigma weight residual 69.27 -128.12 -162.61 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -82.06 151.33 1 2.00e+01 2.50e-03 4.51e+01 ... (remaining 4064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 792 0.050 - 0.100: 190 0.100 - 0.150: 38 0.150 - 0.200: 0 0.200 - 0.250: 1 Chirality restraints: 1021 Sorted by residual: chirality pdb=" CG LEU A 425 " pdb=" CB LEU A 425 " pdb=" CD1 LEU A 425 " pdb=" CD2 LEU A 425 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA GLU B 181 " pdb=" N GLU B 181 " pdb=" C GLU B 181 " pdb=" CB GLU B 181 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA LEU A 425 " pdb=" N LEU A 425 " pdb=" C LEU A 425 " pdb=" CB LEU A 425 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 1018 not shown) Planarity restraints: 1206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 260 " -0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO B 261 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 267 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO B 268 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 268 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 268 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 271 " -0.032 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO B 272 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 272 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 272 " -0.025 5.00e-02 4.00e+02 ... (remaining 1203 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 88 2.61 - 3.18: 6002 3.18 - 3.75: 10602 3.75 - 4.33: 14901 4.33 - 4.90: 24707 Nonbonded interactions: 56300 Sorted by model distance: nonbonded pdb=" O2B GTP A 501 " pdb="MG MG A 502 " model vdw 2.033 2.170 nonbonded pdb=" O GLY B 141 " pdb=" OG SER B 145 " model vdw 2.143 3.040 nonbonded pdb=" OD1 ASN A 186 " pdb=" OH TYR A 408 " model vdw 2.184 3.040 nonbonded pdb=" O GLY A 416 " pdb=" OG SER A 419 " model vdw 2.184 3.040 nonbonded pdb=" OH TYR A 210 " pdb=" NH1 ARG A 221 " model vdw 2.185 3.120 ... (remaining 56295 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.240 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 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 0.057 6847 Z= 0.181 Angle : 0.616 6.887 9302 Z= 0.324 Chirality : 0.044 0.250 1021 Planarity : 0.005 0.067 1206 Dihedral : 16.741 166.216 2503 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.13 (0.29), residues: 834 helix: 0.70 (0.27), residues: 362 sheet: -0.69 (0.45), residues: 127 loop : -0.56 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 79 TYR 0.017 0.002 TYR B 36 PHE 0.011 0.002 PHE A 138 TRP 0.009 0.001 TRP B 21 HIS 0.006 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 6847) covalent geometry : angle 0.61567 ( 9302) hydrogen bonds : bond 0.15859 ( 303) hydrogen bonds : angle 6.76406 ( 870) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3968 (tmm) cc_final: 0.3312 (tmm) REVERT: A 27 GLU cc_start: 0.6971 (tp30) cc_final: 0.6656 (tp30) REVERT: A 155 GLU cc_start: 0.6877 (mt-10) cc_final: 0.6578 (mt-10) REVERT: A 311 LYS cc_start: 0.7075 (mtpp) cc_final: 0.6317 (mmtp) REVERT: B 23 ILE cc_start: 0.8787 (mm) cc_final: 0.8586 (mm) REVERT: B 30 ILE cc_start: 0.6442 (mt) cc_final: 0.6235 (mt) REVERT: B 69 GLU cc_start: 0.6817 (pt0) cc_final: 0.6412 (pm20) REVERT: B 108 GLU cc_start: 0.6631 (mm-30) cc_final: 0.6351 (tt0) REVERT: B 202 ILE cc_start: 0.8107 (mm) cc_final: 0.7907 (mt) REVERT: B 207 LEU cc_start: 0.8440 (mm) cc_final: 0.8202 (mm) REVERT: B 256 ASN cc_start: 0.7643 (t160) cc_final: 0.7441 (t0) REVERT: B 257 MET cc_start: 0.8263 (mmm) cc_final: 0.7295 (mmt) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.0862 time to fit residues: 20.4486 Evaluate side-chains 130 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 0.0970 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN B 48 ASN B 134 GLN B 375 GLN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.163625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.139199 restraints weight = 10627.309| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.69 r_work: 0.3746 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6847 Z= 0.168 Angle : 0.607 6.355 9302 Z= 0.313 Chirality : 0.045 0.213 1021 Planarity : 0.005 0.067 1206 Dihedral : 12.455 166.006 942 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.25 % Allowed : 10.86 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.13 (0.29), residues: 834 helix: 1.04 (0.27), residues: 365 sheet: -0.64 (0.45), residues: 132 loop : -0.56 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 309 TYR 0.014 0.001 TYR A 262 PHE 0.019 0.001 PHE A 49 TRP 0.017 0.001 TRP A 346 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 6847) covalent geometry : angle 0.60682 ( 9302) hydrogen bonds : bond 0.05350 ( 303) hydrogen bonds : angle 5.12871 ( 870) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3987 (tmm) cc_final: 0.3062 (tmm) REVERT: A 155 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6932 (mt-10) REVERT: A 199 ASP cc_start: 0.8170 (m-30) cc_final: 0.7954 (m-30) REVERT: A 311 LYS cc_start: 0.7254 (mtpp) cc_final: 0.6729 (mptt) REVERT: B 69 GLU cc_start: 0.6918 (pt0) cc_final: 0.6130 (pm20) REVERT: B 108 GLU cc_start: 0.6824 (mm-30) cc_final: 0.6337 (tt0) REVERT: B 154 LYS cc_start: 0.8497 (mmtt) cc_final: 0.8142 (mmtm) REVERT: B 207 LEU cc_start: 0.8611 (mm) cc_final: 0.8323 (mm) REVERT: B 256 ASN cc_start: 0.7663 (t0) cc_final: 0.7420 (t0) REVERT: B 257 MET cc_start: 0.8400 (mmm) cc_final: 0.7397 (mmt) REVERT: B 412 GLU cc_start: 0.8342 (pt0) cc_final: 0.8056 (pt0) outliers start: 9 outliers final: 6 residues processed: 147 average time/residue: 0.0687 time to fit residues: 13.9232 Evaluate side-chains 138 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 193 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 30 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 4 optimal weight: 0.1980 chunk 62 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 35 optimal weight: 0.0570 chunk 20 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN A 358 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.165662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.141387 restraints weight = 10488.346| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.68 r_work: 0.3776 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6847 Z= 0.121 Angle : 0.556 7.453 9302 Z= 0.285 Chirality : 0.043 0.169 1021 Planarity : 0.005 0.063 1206 Dihedral : 12.253 165.294 942 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.95 % Allowed : 12.53 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.25 (0.29), residues: 834 helix: 1.25 (0.27), residues: 370 sheet: -0.49 (0.44), residues: 136 loop : -0.72 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 309 TYR 0.016 0.001 TYR A 210 PHE 0.016 0.001 PHE A 49 TRP 0.010 0.001 TRP B 101 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6847) covalent geometry : angle 0.55643 ( 9302) hydrogen bonds : bond 0.04265 ( 303) hydrogen bonds : angle 4.75637 ( 870) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.241 Fit side-chains REVERT: A 1 MET cc_start: 0.3796 (tmm) cc_final: 0.2781 (tmm) REVERT: A 76 ASP cc_start: 0.8045 (m-30) cc_final: 0.7816 (m-30) REVERT: A 155 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6945 (mt-10) REVERT: A 262 TYR cc_start: 0.7409 (m-80) cc_final: 0.7105 (m-80) REVERT: A 311 LYS cc_start: 0.7231 (mtpp) cc_final: 0.6772 (mptt) REVERT: B 37 HIS cc_start: 0.6798 (m-70) cc_final: 0.6598 (m-70) REVERT: B 69 GLU cc_start: 0.6910 (pt0) cc_final: 0.6092 (pm20) REVERT: B 108 GLU cc_start: 0.6852 (mm-30) cc_final: 0.6308 (tt0) REVERT: B 154 LYS cc_start: 0.8469 (mmtt) cc_final: 0.8129 (mmtm) REVERT: B 190 HIS cc_start: 0.8513 (t-170) cc_final: 0.8068 (t70) REVERT: B 194 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7569 (mm-30) REVERT: B 207 LEU cc_start: 0.8606 (mm) cc_final: 0.8278 (mm) REVERT: B 398 TYR cc_start: 0.7795 (m-80) cc_final: 0.7039 (m-80) REVERT: B 412 GLU cc_start: 0.8365 (pt0) cc_final: 0.8000 (pt0) outliers start: 14 outliers final: 7 residues processed: 157 average time/residue: 0.0674 time to fit residues: 14.7894 Evaluate side-chains 133 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 193 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 23 optimal weight: 0.0770 chunk 67 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.165936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.141672 restraints weight = 10639.078| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.70 r_work: 0.3777 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6847 Z= 0.126 Angle : 0.551 8.333 9302 Z= 0.283 Chirality : 0.043 0.173 1021 Planarity : 0.005 0.061 1206 Dihedral : 12.168 165.716 942 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.65 % Allowed : 13.23 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.29), residues: 834 helix: 1.30 (0.27), residues: 370 sheet: -0.38 (0.45), residues: 136 loop : -0.73 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 86 TYR 0.013 0.001 TYR A 210 PHE 0.015 0.001 PHE B 367 TRP 0.011 0.001 TRP B 101 HIS 0.005 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 6847) covalent geometry : angle 0.55088 ( 9302) hydrogen bonds : bond 0.04079 ( 303) hydrogen bonds : angle 4.65423 ( 870) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3549 (tmm) cc_final: 0.2587 (tmm) REVERT: A 76 ASP cc_start: 0.8038 (m-30) cc_final: 0.7790 (m-30) REVERT: A 155 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6922 (mt-10) REVERT: A 234 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8688 (mp) REVERT: A 262 TYR cc_start: 0.7300 (m-80) cc_final: 0.7050 (m-80) REVERT: A 311 LYS cc_start: 0.7210 (mtpp) cc_final: 0.6929 (mptt) REVERT: B 108 GLU cc_start: 0.6844 (mm-30) cc_final: 0.6311 (tt0) REVERT: B 154 LYS cc_start: 0.8463 (mmtt) cc_final: 0.8120 (mmtm) REVERT: B 207 LEU cc_start: 0.8629 (mm) cc_final: 0.8261 (mm) REVERT: B 412 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7997 (pt0) outliers start: 19 outliers final: 12 residues processed: 151 average time/residue: 0.0604 time to fit residues: 13.2734 Evaluate side-chains 139 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 412 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 76 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.162562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.138052 restraints weight = 10735.464| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.69 r_work: 0.3725 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6847 Z= 0.211 Angle : 0.625 9.692 9302 Z= 0.324 Chirality : 0.045 0.204 1021 Planarity : 0.005 0.068 1206 Dihedral : 12.483 167.558 942 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.48 % Allowed : 14.35 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.29), residues: 834 helix: 1.08 (0.27), residues: 366 sheet: -0.44 (0.47), residues: 132 loop : -0.79 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 86 TYR 0.014 0.002 TYR A 210 PHE 0.016 0.002 PHE B 20 TRP 0.013 0.001 TRP B 101 HIS 0.007 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 6847) covalent geometry : angle 0.62514 ( 9302) hydrogen bonds : bond 0.04617 ( 303) hydrogen bonds : angle 4.78119 ( 870) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3524 (tmm) cc_final: 0.2741 (tmm) REVERT: A 76 ASP cc_start: 0.8044 (m-30) cc_final: 0.7801 (m-30) REVERT: A 154 MET cc_start: 0.7879 (mmt) cc_final: 0.7573 (mmt) REVERT: A 155 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6987 (mt-10) REVERT: A 234 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8684 (mp) REVERT: A 255 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7518 (m-10) REVERT: A 262 TYR cc_start: 0.7353 (m-80) cc_final: 0.7147 (m-80) REVERT: A 311 LYS cc_start: 0.7378 (mtpp) cc_final: 0.6965 (mptt) REVERT: A 373 ARG cc_start: 0.7928 (ptp90) cc_final: 0.7684 (ptp90) REVERT: B 108 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6447 (mm-30) REVERT: B 154 LYS cc_start: 0.8489 (mmtt) cc_final: 0.8153 (mmtm) REVERT: B 207 LEU cc_start: 0.8649 (mm) cc_final: 0.8285 (mm) REVERT: B 293 MET cc_start: 0.7486 (ptm) cc_final: 0.7047 (ttp) REVERT: B 412 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7976 (pt0) outliers start: 25 outliers final: 17 residues processed: 147 average time/residue: 0.0699 time to fit residues: 14.4212 Evaluate side-chains 148 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 412 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 38 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 24 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.164110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.139721 restraints weight = 10622.987| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.71 r_work: 0.3748 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6847 Z= 0.152 Angle : 0.577 9.018 9302 Z= 0.298 Chirality : 0.044 0.175 1021 Planarity : 0.005 0.066 1206 Dihedral : 12.405 166.581 942 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.62 % Allowed : 15.32 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.12 (0.29), residues: 834 helix: 1.13 (0.27), residues: 367 sheet: -0.33 (0.46), residues: 136 loop : -0.87 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 79 TYR 0.014 0.001 TYR A 210 PHE 0.017 0.001 PHE B 367 TRP 0.014 0.001 TRP B 101 HIS 0.004 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6847) covalent geometry : angle 0.57683 ( 9302) hydrogen bonds : bond 0.04306 ( 303) hydrogen bonds : angle 4.68360 ( 870) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3486 (tmm) cc_final: 0.2721 (tmm) REVERT: A 76 ASP cc_start: 0.7998 (m-30) cc_final: 0.7736 (m-30) REVERT: A 154 MET cc_start: 0.7834 (mmt) cc_final: 0.7495 (mmt) REVERT: A 234 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8695 (mp) REVERT: A 255 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.7449 (m-10) REVERT: A 311 LYS cc_start: 0.7352 (mtpp) cc_final: 0.6944 (mptt) REVERT: A 373 ARG cc_start: 0.7946 (ptp90) cc_final: 0.7713 (ptp90) REVERT: B 108 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6409 (mm-30) REVERT: B 154 LYS cc_start: 0.8472 (mmtt) cc_final: 0.8131 (mmtm) REVERT: B 207 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8272 (mm) REVERT: B 412 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7969 (pt0) outliers start: 26 outliers final: 19 residues processed: 155 average time/residue: 0.0657 time to fit residues: 14.3840 Evaluate side-chains 154 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 412 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 1 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.163092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.138367 restraints weight = 10543.810| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.69 r_work: 0.3725 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6847 Z= 0.188 Angle : 0.613 9.468 9302 Z= 0.317 Chirality : 0.045 0.182 1021 Planarity : 0.005 0.069 1206 Dihedral : 12.544 167.336 942 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.62 % Allowed : 17.41 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.05 (0.29), residues: 834 helix: 0.99 (0.26), residues: 369 sheet: -0.33 (0.46), residues: 136 loop : -1.00 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 79 TYR 0.015 0.001 TYR A 210 PHE 0.016 0.002 PHE B 20 TRP 0.016 0.001 TRP B 101 HIS 0.006 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 6847) covalent geometry : angle 0.61349 ( 9302) hydrogen bonds : bond 0.04547 ( 303) hydrogen bonds : angle 4.78430 ( 870) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3493 (tmm) cc_final: 0.2739 (tmm) REVERT: A 76 ASP cc_start: 0.8021 (m-30) cc_final: 0.7764 (m-30) REVERT: A 234 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8676 (mp) REVERT: A 255 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.7430 (m-10) REVERT: A 311 LYS cc_start: 0.7412 (mtpp) cc_final: 0.7008 (mptt) REVERT: A 357 TYR cc_start: 0.6840 (m-80) cc_final: 0.6596 (m-80) REVERT: A 373 ARG cc_start: 0.7930 (ptp90) cc_final: 0.7673 (ptp90) REVERT: A 433 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: B 154 LYS cc_start: 0.8482 (mmtt) cc_final: 0.8133 (mmtm) REVERT: B 207 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8274 (mm) REVERT: B 293 MET cc_start: 0.7377 (ptm) cc_final: 0.7054 (ttp) REVERT: B 412 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8008 (pt0) outliers start: 26 outliers final: 18 residues processed: 149 average time/residue: 0.0674 time to fit residues: 14.0576 Evaluate side-chains 152 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 412 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 48 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 358 GLN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.166375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.141959 restraints weight = 10457.979| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.71 r_work: 0.3777 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6847 Z= 0.117 Angle : 0.566 9.215 9302 Z= 0.292 Chirality : 0.043 0.175 1021 Planarity : 0.005 0.061 1206 Dihedral : 12.242 165.265 942 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.79 % Allowed : 17.41 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.17 (0.29), residues: 834 helix: 1.25 (0.27), residues: 367 sheet: -0.35 (0.48), residues: 133 loop : -0.92 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 64 TYR 0.015 0.001 TYR A 210 PHE 0.013 0.001 PHE B 20 TRP 0.015 0.001 TRP B 101 HIS 0.005 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 6847) covalent geometry : angle 0.56631 ( 9302) hydrogen bonds : bond 0.03933 ( 303) hydrogen bonds : angle 4.63370 ( 870) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3355 (tmm) cc_final: 0.2659 (tmm) REVERT: A 76 ASP cc_start: 0.7903 (m-30) cc_final: 0.7631 (m-30) REVERT: A 234 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8695 (mp) REVERT: A 255 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7481 (m-10) REVERT: A 262 TYR cc_start: 0.7181 (m-80) cc_final: 0.6972 (m-10) REVERT: A 311 LYS cc_start: 0.7372 (mtpp) cc_final: 0.6981 (mptt) REVERT: A 357 TYR cc_start: 0.6814 (m-80) cc_final: 0.6521 (m-80) REVERT: A 373 ARG cc_start: 0.7916 (ptp90) cc_final: 0.7690 (ptp90) REVERT: A 433 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7137 (mp0) REVERT: B 154 LYS cc_start: 0.8472 (mmtt) cc_final: 0.8117 (mmtm) REVERT: B 207 LEU cc_start: 0.8637 (mm) cc_final: 0.8255 (mm) REVERT: B 412 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7959 (pt0) outliers start: 20 outliers final: 13 residues processed: 149 average time/residue: 0.0635 time to fit residues: 13.2872 Evaluate side-chains 149 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 412 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 81 optimal weight: 9.9990 chunk 35 optimal weight: 0.0970 chunk 56 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 266 HIS A 358 GLN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.164698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.139905 restraints weight = 10575.043| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.73 r_work: 0.3747 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6847 Z= 0.156 Angle : 0.606 10.568 9302 Z= 0.310 Chirality : 0.044 0.178 1021 Planarity : 0.005 0.065 1206 Dihedral : 12.320 166.318 942 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.20 % Allowed : 18.11 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.13 (0.29), residues: 834 helix: 1.18 (0.26), residues: 367 sheet: -0.33 (0.48), residues: 133 loop : -0.92 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 64 TYR 0.014 0.001 TYR A 210 PHE 0.015 0.001 PHE B 20 TRP 0.016 0.001 TRP B 101 HIS 0.004 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 6847) covalent geometry : angle 0.60580 ( 9302) hydrogen bonds : bond 0.04153 ( 303) hydrogen bonds : angle 4.62069 ( 870) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3432 (tmm) cc_final: 0.2729 (tmm) REVERT: A 76 ASP cc_start: 0.7936 (m-30) cc_final: 0.7657 (m-30) REVERT: A 234 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8696 (mp) REVERT: A 255 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7514 (m-10) REVERT: A 262 TYR cc_start: 0.7141 (m-80) cc_final: 0.6927 (m-10) REVERT: A 311 LYS cc_start: 0.7366 (mtpp) cc_final: 0.6988 (mptt) REVERT: A 357 TYR cc_start: 0.6867 (m-80) cc_final: 0.6602 (m-80) REVERT: A 373 ARG cc_start: 0.7948 (ptp90) cc_final: 0.7699 (ptp90) REVERT: A 433 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: B 154 LYS cc_start: 0.8506 (mmtt) cc_final: 0.8158 (mmtm) REVERT: B 207 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8238 (mm) REVERT: B 412 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8019 (pt0) outliers start: 23 outliers final: 16 residues processed: 149 average time/residue: 0.0669 time to fit residues: 13.9389 Evaluate side-chains 153 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 412 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 15 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 266 HIS A 358 GLN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.166579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.141755 restraints weight = 10569.965| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.71 r_work: 0.3775 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6847 Z= 0.126 Angle : 0.601 10.308 9302 Z= 0.307 Chirality : 0.043 0.178 1021 Planarity : 0.005 0.064 1206 Dihedral : 12.208 165.411 942 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.06 % Allowed : 17.97 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.20 (0.29), residues: 834 helix: 1.27 (0.27), residues: 367 sheet: -0.30 (0.48), residues: 132 loop : -0.91 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 264 TYR 0.013 0.001 TYR A 210 PHE 0.029 0.001 PHE A 267 TRP 0.014 0.001 TRP B 101 HIS 0.005 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 6847) covalent geometry : angle 0.60113 ( 9302) hydrogen bonds : bond 0.03910 ( 303) hydrogen bonds : angle 4.56535 ( 870) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3404 (tmm) cc_final: 0.2735 (tmm) REVERT: A 76 ASP cc_start: 0.7884 (m-30) cc_final: 0.7619 (m-30) REVERT: A 234 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8668 (mp) REVERT: A 255 PHE cc_start: 0.7799 (OUTLIER) cc_final: 0.7509 (m-10) REVERT: A 311 LYS cc_start: 0.7355 (mtpp) cc_final: 0.7004 (mptt) REVERT: A 357 TYR cc_start: 0.6805 (m-80) cc_final: 0.6535 (m-80) REVERT: A 373 ARG cc_start: 0.7922 (ptp90) cc_final: 0.7692 (ptp90) REVERT: A 433 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: B 154 LYS cc_start: 0.8497 (mmtt) cc_final: 0.8160 (mmtm) REVERT: B 207 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8260 (mm) REVERT: B 412 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7964 (pt0) outliers start: 22 outliers final: 14 residues processed: 149 average time/residue: 0.0701 time to fit residues: 14.6188 Evaluate side-chains 152 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 412 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 52 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 266 HIS ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.164756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.139920 restraints weight = 10558.138| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.69 r_work: 0.3749 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 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 0.064 6847 Z= 0.176 Angle : 0.646 11.649 9302 Z= 0.332 Chirality : 0.046 0.191 1021 Planarity : 0.005 0.067 1206 Dihedral : 12.339 166.441 942 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.79 % Allowed : 17.83 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.29), residues: 834 helix: 1.10 (0.26), residues: 371 sheet: -0.29 (0.48), residues: 132 loop : -0.92 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 320 TYR 0.013 0.001 TYR A 210 PHE 0.017 0.002 PHE A 267 TRP 0.014 0.001 TRP B 101 HIS 0.010 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 6847) covalent geometry : angle 0.64572 ( 9302) hydrogen bonds : bond 0.04202 ( 303) hydrogen bonds : angle 4.66122 ( 870) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1485.94 seconds wall clock time: 26 minutes 12.56 seconds (1572.56 seconds total)