Starting phenix.real_space_refine on Thu Jun 5 20:39:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qud_14148/06_2025/7qud_14148.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qud_14148/06_2025/7qud_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_14148/06_2025/7qud_14148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qud_14148/06_2025/7qud_14148.map" model { file = "/net/cci-nas-00/data/ceres_data/7qud_14148/06_2025/7qud_14148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qud_14148/06_2025/7qud_14148.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.11, per 1000 atoms: 0.91 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: 1.65 Conformation dependent library (CDL) restraints added in 876.8 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: 0.80 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: 2.02 Time building geometry restraints manager: 1.93 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: 1.710 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 21.420 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.680 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP B 21 HIS 0.006 0.001 HIS A 266 PHE 0.011 0.002 PHE A 138 TYR 0.017 0.002 TYR B 36 ARG 0.003 0.000 ARG A 79 Details of bonding type rmsd hydrogen bonds : bond 0.15859 ( 303) hydrogen bonds : angle 6.76406 ( 870) covalent geometry : bond 0.00410 ( 6847) covalent geometry : angle 0.61567 ( 9302) *********************** 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 : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3969 (tmm) cc_final: 0.3313 (tmm) REVERT: A 27 GLU cc_start: 0.6970 (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: 0.7642 (t160) cc_final: 0.7439 (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: 0.1833 time to fit residues: 43.6212 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 : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 39 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.163879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.139524 restraints weight = 10475.982| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.67 r_work: 0.3750 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6847 Z= 0.161 Angle : 0.607 6.376 9302 Z= 0.313 Chirality : 0.045 0.220 1021 Planarity : 0.005 0.067 1206 Dihedral : 12.453 165.904 942 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.67 % Allowed : 10.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.29), residues: 834 helix: 1.03 (0.27), residues: 365 sheet: -0.64 (0.45), residues: 132 loop : -0.58 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 346 HIS 0.006 0.001 HIS A 309 PHE 0.021 0.002 PHE A 49 TYR 0.015 0.001 TYR A 262 ARG 0.004 0.000 ARG B 309 Details of bonding type rmsd hydrogen bonds : bond 0.05059 ( 303) hydrogen bonds : angle 5.07350 ( 870) covalent geometry : bond 0.00362 ( 6847) covalent geometry : angle 0.60676 ( 9302) *********************** 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 156 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3967 (tmm) cc_final: 0.3047 (tmm) REVERT: A 76 ASP cc_start: 0.8135 (m-30) cc_final: 0.7907 (m-30) REVERT: A 155 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6920 (mt-10) REVERT: A 311 LYS cc_start: 0.7266 (mtpp) cc_final: 0.6665 (mmtm) REVERT: B 69 GLU cc_start: 0.6911 (pt0) cc_final: 0.6127 (pm20) REVERT: B 108 GLU cc_start: 0.6830 (mm-30) cc_final: 0.6337 (tt0) REVERT: B 154 LYS cc_start: 0.8496 (mmtt) cc_final: 0.8142 (mmtm) REVERT: B 207 LEU cc_start: 0.8614 (mm) cc_final: 0.8336 (mm) REVERT: B 256 ASN cc_start: 0.7653 (t0) cc_final: 0.7411 (t0) REVERT: B 257 MET cc_start: 0.8397 (mmm) cc_final: 0.7387 (mmt) REVERT: B 412 GLU cc_start: 0.8361 (pt0) cc_final: 0.8044 (pt0) outliers start: 12 outliers final: 7 residues processed: 151 average time/residue: 0.1617 time to fit residues: 33.4474 Evaluate side-chains 138 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 0.1980 chunk 51 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 ** 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 = 0.4203 r_free = 0.4203 target = 0.167274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.142919 restraints weight = 10509.158| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.72 r_work: 0.3792 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6847 Z= 0.110 Angle : 0.543 7.242 9302 Z= 0.278 Chirality : 0.042 0.174 1021 Planarity : 0.005 0.059 1206 Dihedral : 12.150 164.851 942 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.53 % Allowed : 12.67 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.29), residues: 834 helix: 1.32 (0.27), residues: 370 sheet: -0.46 (0.45), residues: 136 loop : -0.65 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 101 HIS 0.004 0.001 HIS A 283 PHE 0.015 0.001 PHE A 49 TYR 0.010 0.001 TYR A 210 ARG 0.002 0.000 ARG B 309 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 303) hydrogen bonds : angle 4.72970 ( 870) covalent geometry : bond 0.00236 ( 6847) covalent geometry : angle 0.54343 ( 9302) *********************** 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 163 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3749 (tmm) cc_final: 0.2727 (tmm) REVERT: A 76 ASP cc_start: 0.8043 (m-30) cc_final: 0.7804 (m-30) REVERT: A 155 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6921 (mt-10) REVERT: A 311 LYS cc_start: 0.7234 (mtpp) cc_final: 0.6767 (mptt) REVERT: B 37 HIS cc_start: 0.6800 (m-70) cc_final: 0.6566 (m-70) REVERT: B 69 GLU cc_start: 0.6877 (pt0) cc_final: 0.5805 (pm20) REVERT: B 108 GLU cc_start: 0.6818 (mm-30) cc_final: 0.6286 (tt0) REVERT: B 154 LYS cc_start: 0.8455 (mmtt) cc_final: 0.8106 (mmtm) REVERT: B 190 HIS cc_start: 0.8522 (t-170) cc_final: 0.8059 (t70) REVERT: B 194 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7543 (mm-30) REVERT: B 207 LEU cc_start: 0.8599 (mm) cc_final: 0.8265 (mm) REVERT: B 293 MET cc_start: 0.7436 (ptm) cc_final: 0.7098 (ttp) REVERT: B 398 TYR cc_start: 0.7755 (m-80) cc_final: 0.7011 (m-80) REVERT: B 412 GLU cc_start: 0.8403 (pt0) cc_final: 0.8036 (pt0) outliers start: 11 outliers final: 6 residues processed: 160 average time/residue: 0.1822 time to fit residues: 38.9369 Evaluate side-chains 136 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 24 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 32 optimal weight: 20.0000 chunk 6 optimal weight: 0.0570 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.165299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.140979 restraints weight = 10592.635| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 2.73 r_work: 0.3768 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6847 Z= 0.139 Angle : 0.565 9.122 9302 Z= 0.288 Chirality : 0.043 0.173 1021 Planarity : 0.005 0.062 1206 Dihedral : 12.159 166.169 942 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.23 % Allowed : 13.37 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.29), residues: 834 helix: 1.31 (0.27), residues: 370 sheet: -0.38 (0.45), residues: 136 loop : -0.68 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 101 HIS 0.004 0.001 HIS A 8 PHE 0.020 0.001 PHE B 367 TYR 0.009 0.001 TYR A 210 ARG 0.012 0.000 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.04107 ( 303) hydrogen bonds : angle 4.62247 ( 870) covalent geometry : bond 0.00315 ( 6847) covalent geometry : angle 0.56532 ( 9302) *********************** 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 152 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3578 (tmm) cc_final: 0.2607 (tmm) REVERT: A 76 ASP cc_start: 0.8062 (m-30) cc_final: 0.7812 (m-30) REVERT: A 155 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6945 (mt-10) REVERT: A 234 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8667 (mp) REVERT: A 262 TYR cc_start: 0.7343 (m-80) cc_final: 0.7067 (m-80) REVERT: A 311 LYS cc_start: 0.7253 (mtpp) cc_final: 0.6950 (mptt) REVERT: B 108 GLU cc_start: 0.6855 (mm-30) cc_final: 0.6310 (tt0) REVERT: B 154 LYS cc_start: 0.8473 (mmtt) cc_final: 0.8135 (mmtm) REVERT: B 207 LEU cc_start: 0.8612 (mm) cc_final: 0.8247 (mm) REVERT: B 412 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8020 (pt0) outliers start: 16 outliers final: 11 residues processed: 145 average time/residue: 0.1556 time to fit residues: 31.6530 Evaluate side-chains 138 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 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 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 412 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 30 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN ** 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** ** B 332 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 = 0.4182 r_free = 0.4182 target = 0.165422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.141007 restraints weight = 10543.330| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.69 r_work: 0.3769 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6847 Z= 0.142 Angle : 0.562 8.473 9302 Z= 0.289 Chirality : 0.043 0.191 1021 Planarity : 0.005 0.062 1206 Dihedral : 12.186 166.346 942 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.79 % Allowed : 15.32 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.29), residues: 834 helix: 1.24 (0.27), residues: 370 sheet: -0.33 (0.45), residues: 136 loop : -0.67 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 101 HIS 0.003 0.001 HIS A 8 PHE 0.015 0.001 PHE B 20 TYR 0.010 0.001 TYR A 210 ARG 0.005 0.000 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 303) hydrogen bonds : angle 4.63176 ( 870) covalent geometry : bond 0.00323 ( 6847) covalent geometry : angle 0.56223 ( 9302) *********************** 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 153 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3465 (tmm) cc_final: 0.2503 (tmm) REVERT: A 76 ASP cc_start: 0.7978 (m-30) cc_final: 0.7724 (m-30) REVERT: A 155 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6905 (mt-10) REVERT: A 234 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8669 (mp) REVERT: A 262 TYR cc_start: 0.7310 (m-80) cc_final: 0.7075 (m-80) REVERT: A 311 LYS cc_start: 0.7346 (mtpp) cc_final: 0.6932 (mptt) REVERT: B 108 GLU cc_start: 0.6855 (mm-30) cc_final: 0.6450 (mm-30) REVERT: B 154 LYS cc_start: 0.8479 (mmtt) cc_final: 0.8140 (mmtm) REVERT: B 207 LEU cc_start: 0.8606 (mm) cc_final: 0.8260 (mm) REVERT: B 412 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7961 (pt0) outliers start: 20 outliers final: 15 residues processed: 145 average time/residue: 0.1561 time to fit residues: 31.7155 Evaluate side-chains 138 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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 207 GLU Chi-restraints excluded: chain A residue 234 ILE 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 68 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.166702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.142271 restraints weight = 10449.398| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.72 r_work: 0.3783 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2215 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= 0.122 Angle : 0.544 9.064 9302 Z= 0.280 Chirality : 0.043 0.173 1021 Planarity : 0.005 0.060 1206 Dihedral : 12.089 165.946 942 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.79 % Allowed : 16.57 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.29), residues: 834 helix: 1.32 (0.27), residues: 370 sheet: -0.16 (0.46), residues: 136 loop : -0.73 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 101 HIS 0.003 0.001 HIS A 8 PHE 0.015 0.001 PHE B 20 TYR 0.010 0.001 TYR A 210 ARG 0.004 0.000 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.03919 ( 303) hydrogen bonds : angle 4.57397 ( 870) covalent geometry : bond 0.00273 ( 6847) covalent geometry : angle 0.54415 ( 9302) *********************** 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 156 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3428 (tmm) cc_final: 0.2678 (tmm) REVERT: A 76 ASP cc_start: 0.7959 (m-30) cc_final: 0.7711 (m-30) REVERT: A 155 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6933 (mt-10) REVERT: A 234 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8654 (mp) REVERT: A 255 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.7479 (m-10) REVERT: A 262 TYR cc_start: 0.7195 (m-80) cc_final: 0.6957 (m-80) REVERT: A 311 LYS cc_start: 0.7348 (mtpp) cc_final: 0.6936 (mptt) REVERT: B 108 GLU cc_start: 0.6851 (mm-30) cc_final: 0.6437 (mm-30) REVERT: B 154 LYS cc_start: 0.8464 (mmtt) cc_final: 0.8120 (mmtm) REVERT: B 194 GLU cc_start: 0.8216 (tt0) cc_final: 0.8013 (tt0) REVERT: B 207 LEU cc_start: 0.8615 (mm) cc_final: 0.8247 (mm) REVERT: B 412 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7966 (pt0) outliers start: 20 outliers final: 13 residues processed: 149 average time/residue: 0.1655 time to fit residues: 33.9134 Evaluate side-chains 142 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 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 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 412 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 38 optimal weight: 5.9990 chunk 80 optimal weight: 0.0170 chunk 31 optimal weight: 0.6980 chunk 77 optimal weight: 9.9990 chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 HIS ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 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 = 0.4224 r_free = 0.4224 target = 0.169179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.144744 restraints weight = 10390.101| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.73 r_work: 0.3816 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6847 Z= 0.106 Angle : 0.539 9.593 9302 Z= 0.277 Chirality : 0.043 0.175 1021 Planarity : 0.005 0.059 1206 Dihedral : 11.850 165.261 942 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.92 % Allowed : 16.71 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.29), residues: 834 helix: 1.50 (0.27), residues: 368 sheet: -0.18 (0.47), residues: 133 loop : -0.71 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 101 HIS 0.003 0.001 HIS A 8 PHE 0.013 0.001 PHE B 20 TYR 0.009 0.001 TYR A 210 ARG 0.004 0.000 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.03646 ( 303) hydrogen bonds : angle 4.50463 ( 870) covalent geometry : bond 0.00225 ( 6847) covalent geometry : angle 0.53871 ( 9302) *********************** 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: 21 poor density : 139 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3392 (tmm) cc_final: 0.2707 (tmm) REVERT: A 76 ASP cc_start: 0.7863 (m-30) cc_final: 0.7618 (m-30) REVERT: A 155 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6939 (mt-10) REVERT: A 234 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8639 (mp) REVERT: A 255 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.7470 (m-10) REVERT: A 262 TYR cc_start: 0.6964 (m-80) cc_final: 0.6531 (m-10) REVERT: A 311 LYS cc_start: 0.7338 (mtpp) cc_final: 0.6955 (mptt) REVERT: A 433 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: B 108 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6425 (mm-30) REVERT: B 154 LYS cc_start: 0.8463 (mmtt) cc_final: 0.8116 (mmtm) REVERT: B 207 LEU cc_start: 0.8575 (mm) cc_final: 0.8197 (mm) REVERT: B 412 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7947 (pt0) outliers start: 21 outliers final: 13 residues processed: 153 average time/residue: 0.1771 time to fit residues: 36.7236 Evaluate side-chains 145 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL 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 271 THR 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 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 28 optimal weight: 0.0970 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 35 optimal weight: 0.0770 chunk 82 optimal weight: 10.0000 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN ** 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 = 0.4231 r_free = 0.4231 target = 0.169599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.145175 restraints weight = 10446.753| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.69 r_work: 0.3825 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 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 : 0.002 0.045 6847 Z= 0.106 Angle : 0.555 8.660 9302 Z= 0.280 Chirality : 0.042 0.177 1021 Planarity : 0.005 0.061 1206 Dihedral : 11.747 165.942 942 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.65 % Allowed : 17.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.30), residues: 834 helix: 1.42 (0.27), residues: 375 sheet: -0.14 (0.48), residues: 132 loop : -0.70 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 101 HIS 0.004 0.001 HIS A 8 PHE 0.015 0.001 PHE B 20 TYR 0.006 0.001 TYR B 340 ARG 0.003 0.000 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 303) hydrogen bonds : angle 4.54642 ( 870) covalent geometry : bond 0.00234 ( 6847) covalent geometry : angle 0.55529 ( 9302) *********************** 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 153 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3331 (tmm) cc_final: 0.2696 (tmm) REVERT: A 76 ASP cc_start: 0.7814 (m-30) cc_final: 0.7571 (m-30) REVERT: A 155 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6859 (mt-10) REVERT: A 228 ASN cc_start: 0.7926 (m110) cc_final: 0.7713 (m110) REVERT: A 234 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8672 (mp) REVERT: A 255 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.7488 (m-10) REVERT: A 262 TYR cc_start: 0.6908 (m-80) cc_final: 0.6695 (m-10) REVERT: A 311 LYS cc_start: 0.7285 (mtpp) cc_final: 0.6933 (mptt) REVERT: A 433 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: B 108 GLU cc_start: 0.6897 (mm-30) cc_final: 0.6483 (mm-30) REVERT: B 154 LYS cc_start: 0.8482 (mmtt) cc_final: 0.8151 (mmtm) REVERT: B 207 LEU cc_start: 0.8564 (mm) cc_final: 0.8196 (mm) REVERT: B 412 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7940 (pt0) outliers start: 19 outliers final: 15 residues processed: 147 average time/residue: 0.1661 time to fit residues: 34.0326 Evaluate side-chains 149 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 271 THR 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 335 ASN 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 78 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 25 optimal weight: 0.0570 chunk 70 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 34 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.169217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.144545 restraints weight = 10490.124| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 2.74 r_work: 0.3812 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6847 Z= 0.116 Angle : 0.569 10.609 9302 Z= 0.286 Chirality : 0.044 0.301 1021 Planarity : 0.005 0.056 1206 Dihedral : 11.672 160.762 942 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.20 % Allowed : 16.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.29), residues: 834 helix: 1.38 (0.27), residues: 375 sheet: -0.12 (0.48), residues: 131 loop : -0.69 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 101 HIS 0.003 0.001 HIS A 8 PHE 0.024 0.001 PHE B 367 TYR 0.034 0.001 TYR A 224 ARG 0.003 0.000 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.03647 ( 303) hydrogen bonds : angle 4.57859 ( 870) covalent geometry : bond 0.00265 ( 6847) covalent geometry : angle 0.56897 ( 9302) *********************** 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 155 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3377 (tmm) cc_final: 0.2663 (tmm) REVERT: A 16 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7626 (mt) REVERT: A 76 ASP cc_start: 0.7820 (m-30) cc_final: 0.7572 (m-30) REVERT: A 155 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6913 (mt-10) REVERT: A 234 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8659 (mp) REVERT: A 255 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.7496 (m-10) REVERT: A 262 TYR cc_start: 0.6818 (m-80) cc_final: 0.6588 (m-10) REVERT: A 311 LYS cc_start: 0.7297 (mtpp) cc_final: 0.6948 (mptt) REVERT: A 433 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: B 108 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6497 (mm-30) REVERT: B 154 LYS cc_start: 0.8495 (mmtt) cc_final: 0.8168 (mmtm) REVERT: B 207 LEU cc_start: 0.8572 (mm) cc_final: 0.8197 (mm) REVERT: B 412 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7954 (pt0) outliers start: 23 outliers final: 15 residues processed: 146 average time/residue: 0.1513 time to fit residues: 30.5984 Evaluate side-chains 150 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE 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 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 335 ASN 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 61 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 17 optimal weight: 0.0970 chunk 28 optimal weight: 0.0980 chunk 66 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.169810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.145025 restraints weight = 10603.817| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.75 r_work: 0.3818 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2722 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= 0.111 Angle : 0.565 9.242 9302 Z= 0.285 Chirality : 0.043 0.262 1021 Planarity : 0.005 0.056 1206 Dihedral : 11.604 160.651 942 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.92 % Allowed : 17.41 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.30), residues: 834 helix: 1.37 (0.27), residues: 377 sheet: -0.17 (0.48), residues: 134 loop : -0.60 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 101 HIS 0.003 0.001 HIS A 8 PHE 0.014 0.001 PHE B 20 TYR 0.024 0.001 TYR A 224 ARG 0.003 0.000 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 303) hydrogen bonds : angle 4.55436 ( 870) covalent geometry : bond 0.00252 ( 6847) covalent geometry : angle 0.56530 ( 9302) ********************** 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: 21 poor density : 136 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3355 (tmm) cc_final: 0.2614 (tmm) REVERT: A 16 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7501 (mt) REVERT: A 76 ASP cc_start: 0.7821 (m-30) cc_final: 0.7571 (m-30) REVERT: A 155 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6941 (mt-10) REVERT: A 234 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8642 (mp) REVERT: A 255 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.7501 (m-10) REVERT: A 262 TYR cc_start: 0.6886 (m-80) cc_final: 0.6619 (m-10) REVERT: A 311 LYS cc_start: 0.7280 (mtpp) cc_final: 0.6927 (mptt) REVERT: A 433 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: B 108 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6494 (mm-30) REVERT: B 154 LYS cc_start: 0.8483 (mmtt) cc_final: 0.8142 (mmtm) REVERT: B 207 LEU cc_start: 0.8573 (mm) cc_final: 0.8198 (mm) REVERT: B 412 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7975 (pt0) outliers start: 21 outliers final: 15 residues processed: 149 average time/residue: 0.1614 time to fit residues: 33.3459 Evaluate side-chains 149 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 26 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 HIS A 216 ASN ** 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 = 0.4189 r_free = 0.4189 target = 0.166264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.141577 restraints weight = 10480.472| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.72 r_work: 0.3776 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6847 Z= 0.161 Angle : 0.606 9.681 9302 Z= 0.309 Chirality : 0.045 0.229 1021 Planarity : 0.005 0.059 1206 Dihedral : 11.836 162.115 942 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.92 % Allowed : 17.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.30), residues: 834 helix: 1.30 (0.27), residues: 371 sheet: -0.00 (0.48), residues: 135 loop : -0.65 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 101 HIS 0.006 0.001 HIS A 266 PHE 0.026 0.002 PHE B 367 TYR 0.035 0.002 TYR A 224 ARG 0.003 0.000 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.04109 ( 303) hydrogen bonds : angle 4.67001 ( 870) covalent geometry : bond 0.00371 ( 6847) covalent geometry : angle 0.60552 ( 9302) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3421.82 seconds wall clock time: 59 minutes 44.17 seconds (3584.17 seconds total)