Starting phenix.real_space_refine on Sat Aug 23 17:40:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ag5_15416/08_2025/8ag5_15416.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ag5_15416/08_2025/8ag5_15416.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/8ag5_15416/08_2025/8ag5_15416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ag5_15416/08_2025/8ag5_15416.map" model { file = "/net/cci-nas-00/data/ceres_data/8ag5_15416/08_2025/8ag5_15416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ag5_15416/08_2025/8ag5_15416.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= 0.010 sd= 1.052 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: 4 Type Number sf(0) Gaussians S 76 5.16 5 C 8770 2.51 5 N 2293 2.21 5 O 2623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13762 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 4054 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 27, 'TRANS': 474} Chain: "B" Number of atoms: 4302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4302 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 25, 'TRANS': 513} Chain breaks: 2 Chain: "C" Number of atoms: 2703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2703 Classifications: {'peptide': 331} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 321} Chain: "D" Number of atoms: 2703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2703 Classifications: {'peptide': 331} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 321} Time building chain proxies: 2.66, per 1000 atoms: 0.19 Number of scatterers: 13762 At special positions: 0 Unit cell: (141.95, 135.27, 113.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 76 16.00 O 2623 8.00 N 2293 7.00 C 8770 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: 0.84 Conformation dependent library (CDL) restraints added in 448.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 19 sheets defined 29.6% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 58 through 78 Processing helix chain 'A' and resid 112 through 121 Processing helix chain 'A' and resid 123 through 135 Processing helix chain 'A' and resid 142 through 156 Processing helix chain 'A' and resid 179 through 197 Processing helix chain 'A' and resid 238 through 251 removed outlier: 3.743A pdb=" N LEU A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 314 No H-bonds generated for 'chain 'A' and resid 312 through 314' Processing helix chain 'A' and resid 330 through 337 Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 377 through 393 removed outlier: 3.640A pdb=" N LEU A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 480 through 495 Processing helix chain 'A' and resid 510 through 519 Processing helix chain 'A' and resid 520 through 530 Processing helix chain 'B' and resid 29 through 48 Processing helix chain 'B' and resid 87 through 97 removed outlier: 3.522A pdb=" N LEU B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 122 removed outlier: 3.535A pdb=" N THR B 122 " --> pdb=" O ILE B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 157 Processing helix chain 'B' and resid 198 through 216 Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'B' and resid 232 through 233 No H-bonds generated for 'chain 'B' and resid 232 through 233' Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 285 through 289 removed outlier: 3.754A pdb=" N ASP B 288 " --> pdb=" O LYS B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 326 No H-bonds generated for 'chain 'B' and resid 324 through 326' Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 352 through 356 removed outlier: 3.555A pdb=" N PHE B 355 " --> pdb=" O GLN B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 447 through 461 Processing helix chain 'B' and resid 478 through 482 removed outlier: 3.647A pdb=" N LYS B 481 " --> pdb=" O PRO B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 500 removed outlier: 4.154A pdb=" N GLN B 488 " --> pdb=" O ASN B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 516 removed outlier: 3.591A pdb=" N TRP B 513 " --> pdb=" O GLN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 526 removed outlier: 3.710A pdb=" N THR B 523 " --> pdb=" O PRO B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 537 Processing helix chain 'C' and resid 22 through 30 Processing helix chain 'C' and resid 47 through 60 Processing helix chain 'C' and resid 223 through 229 removed outlier: 3.584A pdb=" N ASP C 228 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 242 Processing helix chain 'C' and resid 282 through 298 removed outlier: 4.102A pdb=" N LYS C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 31 Processing helix chain 'D' and resid 47 through 61 Processing helix chain 'D' and resid 223 through 228 Processing helix chain 'D' and resid 234 through 243 Processing helix chain 'D' and resid 281 through 299 Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 109 removed outlier: 6.505A pdb=" N VAL A 85 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLU A 107 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LEU A 83 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N SER A 37 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N MET A 167 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE A 39 " --> pdb=" O MET A 167 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N PHE A 169 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU A 41 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N PHE A 199 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LYS A 164 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ASP A 201 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE A 166 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 262 removed outlier: 7.989A pdb=" N VAL A 394 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA A 395 " --> pdb=" O PHE A 350 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N PHE A 350 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU A 397 " --> pdb=" O MET A 348 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LYS A 260 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEU A 347 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LYS A 262 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N GLY A 349 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 299 through 303 Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 329 Processing sheet with id=AA5, first strand: chain 'A' and resid 375 through 376 Processing sheet with id=AA6, first strand: chain 'A' and resid 419 through 420 removed outlier: 6.443A pdb=" N GLU A 419 " --> pdb=" O VAL A 427 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 84 removed outlier: 6.292A pdb=" N LEU B 56 " --> pdb=" O HIS B 80 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N HIS B 82 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE B 54 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA B 9 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N GLU B 133 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL B 11 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N PHE B 135 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N CYS B 13 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ARG B 130 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N GLN B 162 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE B 132 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N PHE B 164 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE B 134 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N TYR B 225 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE B 163 " --> pdb=" O TYR B 225 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 247 through 252 removed outlier: 6.644A pdb=" N VAL B 361 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N GLN B 360 " --> pdb=" O GLN B 423 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLN B 423 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ALA B 366 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N GLU B 417 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL B 405 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N MET B 389 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL B 390 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N PHE B 345 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE B 392 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N PHE B 340 " --> pdb=" O PRO B 248 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ARG B 250 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL B 342 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N THR B 252 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLY B 344 " --> pdb=" O THR B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 313 through 315 Processing sheet with id=AB1, first strand: chain 'B' and resid 464 through 466 Processing sheet with id=AB2, first strand: chain 'C' and resid 2 through 4 removed outlier: 7.055A pdb=" N ILE C 3 " --> pdb=" O THR C 11 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N THR C 11 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP C 130 " --> pdb=" O PHE C 15 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N THR C 150 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS C 149 " --> pdb=" O TYR C 78 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 2 through 4 removed outlier: 7.055A pdb=" N ILE C 3 " --> pdb=" O THR C 11 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N THR C 11 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP C 130 " --> pdb=" O PHE C 15 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N THR C 150 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS C 66 " --> pdb=" O SER C 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 85 through 86 removed outlier: 3.737A pdb=" N PHE C 139 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP C 138 " --> pdb=" O TYR C 119 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ASN C 124 " --> pdb=" O LYS D 126 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LYS D 126 " --> pdb=" O ASN C 124 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS C 126 " --> pdb=" O ASN D 124 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN D 124 " --> pdb=" O LYS C 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 165 through 167 Processing sheet with id=AB6, first strand: chain 'C' and resid 231 through 232 removed outlier: 5.698A pdb=" N LEU C 216 " --> pdb=" O ILE C 207 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ILE C 207 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN C 218 " --> pdb=" O GLY C 205 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 2 through 4 removed outlier: 7.216A pdb=" N ILE D 3 " --> pdb=" O THR D 11 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N THR D 11 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP D 130 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR D 150 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASP D 155 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR D 72 " --> pdb=" O ASP D 155 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 2 through 4 removed outlier: 7.216A pdb=" N ILE D 3 " --> pdb=" O THR D 11 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N THR D 11 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP D 130 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR D 150 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 164 through 168 Processing sheet with id=AC1, first strand: chain 'D' and resid 231 through 232 removed outlier: 6.682A pdb=" N GLY D 205 " --> pdb=" O VAL D 217 " (cutoff:3.500A) 598 hydrogen bonds defined for protein. 1647 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: 1.83 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4489 1.34 - 1.46: 2813 1.46 - 1.58: 6610 1.58 - 1.69: 0 1.69 - 1.81: 121 Bond restraints: 14033 Sorted by residual: bond pdb=" CB ASP B 65 " pdb=" CG ASP B 65 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.13e+00 bond pdb=" CB ASP C 5 " pdb=" CG ASP C 5 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 9.75e-01 bond pdb=" CB PHE B 142 " pdb=" CG PHE B 142 " ideal model delta sigma weight residual 1.502 1.519 -0.017 2.30e-02 1.89e+03 5.60e-01 bond pdb=" CB LYS A 516 " pdb=" CG LYS A 516 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.48e-01 bond pdb=" C ILE C 175 " pdb=" O ILE C 175 " ideal model delta sigma weight residual 1.229 1.236 -0.008 1.03e-02 9.43e+03 5.36e-01 ... (remaining 14028 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 18455 1.26 - 2.51: 371 2.51 - 3.77: 94 3.77 - 5.03: 24 5.03 - 6.28: 4 Bond angle restraints: 18948 Sorted by residual: angle pdb=" C LYS D 85 " pdb=" N ARG D 86 " pdb=" CA ARG D 86 " ideal model delta sigma weight residual 121.54 126.77 -5.23 1.91e+00 2.74e-01 7.49e+00 angle pdb=" N ARG A 218 " pdb=" CA ARG A 218 " pdb=" C ARG A 218 " ideal model delta sigma weight residual 113.72 109.66 4.06 1.52e+00 4.33e-01 7.14e+00 angle pdb=" C ARG D 86 " pdb=" N THR D 87 " pdb=" CA THR D 87 " ideal model delta sigma weight residual 121.54 126.26 -4.72 1.91e+00 2.74e-01 6.11e+00 angle pdb=" CA ILE D 49 " pdb=" CB ILE D 49 " pdb=" CG1 ILE D 49 " ideal model delta sigma weight residual 110.40 114.18 -3.78 1.70e+00 3.46e-01 4.95e+00 angle pdb=" CA ARG A 218 " pdb=" C ARG A 218 " pdb=" N ASP A 219 " ideal model delta sigma weight residual 118.87 116.33 2.54 1.18e+00 7.18e-01 4.62e+00 ... (remaining 18943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 7262 17.44 - 34.89: 947 34.89 - 52.33: 294 52.33 - 69.77: 74 69.77 - 87.21: 21 Dihedral angle restraints: 8598 sinusoidal: 3580 harmonic: 5018 Sorted by residual: dihedral pdb=" CG ARG A 488 " pdb=" CD ARG A 488 " pdb=" NE ARG A 488 " pdb=" CZ ARG A 488 " ideal model delta sinusoidal sigma weight residual -90.00 -36.49 -53.51 2 1.50e+01 4.44e-03 1.38e+01 dihedral pdb=" CA ASP D 20 " pdb=" CB ASP D 20 " pdb=" CG ASP D 20 " pdb=" OD1 ASP D 20 " ideal model delta sinusoidal sigma weight residual -30.00 -88.14 58.14 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA PRO D 121 " pdb=" C PRO D 121 " pdb=" N THR D 122 " pdb=" CA THR D 122 " ideal model delta harmonic sigma weight residual 180.00 163.23 16.77 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 8595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1325 0.030 - 0.060: 525 0.060 - 0.090: 147 0.090 - 0.120: 120 0.120 - 0.151: 14 Chirality restraints: 2131 Sorted by residual: chirality pdb=" CA ILE D 73 " pdb=" N ILE D 73 " pdb=" C ILE D 73 " pdb=" CB ILE D 73 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA ILE D 12 " pdb=" N ILE D 12 " pdb=" C ILE D 12 " pdb=" CB ILE D 12 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA ILE A 166 " pdb=" N ILE A 166 " pdb=" C ILE A 166 " pdb=" CB ILE A 166 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 2128 not shown) Planarity restraints: 2432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 65 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.71e+00 pdb=" C ASP B 65 " -0.033 2.00e-02 2.50e+03 pdb=" O ASP B 65 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN B 66 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 120 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO C 121 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 369 " 0.028 5.00e-02 4.00e+02 4.30e-02 2.95e+00 pdb=" N PRO A 370 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " 0.024 5.00e-02 4.00e+02 ... (remaining 2429 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 837 2.74 - 3.28: 12553 3.28 - 3.82: 21616 3.82 - 4.36: 26188 4.36 - 4.90: 45209 Nonbonded interactions: 106403 Sorted by model distance: nonbonded pdb=" OG SER B 378 " pdb=" OE2 GLU B 417 " model vdw 2.194 3.040 nonbonded pdb=" O GLN C 10 " pdb=" OH TYR C 101 " model vdw 2.199 3.040 nonbonded pdb=" OG1 THR C 281 " pdb=" OD1 ASP C 283 " model vdw 2.226 3.040 nonbonded pdb=" OG1 THR C 312 " pdb=" O PRO C 314 " model vdw 2.231 3.040 nonbonded pdb=" OE1 GLU D 28 " pdb=" NZ LYS D 31 " model vdw 2.236 3.120 ... (remaining 106398 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.430 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.300 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14033 Z= 0.119 Angle : 0.487 6.284 18948 Z= 0.261 Chirality : 0.041 0.151 2131 Planarity : 0.004 0.047 2432 Dihedral : 17.817 87.212 5338 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.26 % Allowed : 27.50 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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 aren not related in a simple way. whole: 0.35 (0.21), residues: 1691 helix: 1.86 (0.26), residues: 445 sheet: 0.71 (0.27), residues: 379 loop : -0.88 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 488 TYR 0.012 0.001 TYR D 98 PHE 0.026 0.001 PHE C 287 TRP 0.008 0.001 TRP C 91 HIS 0.004 0.001 HIS B 246 Details of bonding type rmsd covalent geometry : bond 0.00272 (14033) covalent geometry : angle 0.48692 (18948) hydrogen bonds : bond 0.14352 ( 562) hydrogen bonds : angle 6.11552 ( 1647) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 336 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 337 average time/residue: 0.1254 time to fit residues: 57.3213 Evaluate side-chains 332 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 330 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 219 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 163 HIS ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN C 10 GLN C 120 HIS D 52 ASN D 124 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.133702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.104390 restraints weight = 19921.279| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.18 r_work: 0.2971 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.0585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14033 Z= 0.157 Angle : 0.503 6.257 18948 Z= 0.271 Chirality : 0.043 0.148 2131 Planarity : 0.004 0.045 2432 Dihedral : 4.750 60.116 1842 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.68 % Allowed : 24.89 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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 aren not related in a simple way. whole: 0.36 (0.21), residues: 1691 helix: 1.96 (0.25), residues: 447 sheet: 0.68 (0.27), residues: 372 loop : -0.90 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 488 TYR 0.014 0.001 TYR D 98 PHE 0.018 0.001 PHE B 409 TRP 0.008 0.001 TRP B 247 HIS 0.004 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00376 (14033) covalent geometry : angle 0.50262 (18948) hydrogen bonds : bond 0.04422 ( 562) hydrogen bonds : angle 4.82487 ( 1647) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 355 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 516 LYS cc_start: 0.7802 (mptt) cc_final: 0.7596 (mptt) REVERT: B 258 SER cc_start: 0.8196 (OUTLIER) cc_final: 0.7825 (t) REVERT: C 17 ASN cc_start: 0.8127 (m-40) cc_final: 0.7837 (m110) REVERT: C 18 GLU cc_start: 0.7693 (mp0) cc_final: 0.7092 (mp0) REVERT: C 52 ASN cc_start: 0.8307 (m-40) cc_final: 0.7816 (m-40) REVERT: D 31 LYS cc_start: 0.7830 (pttt) cc_final: 0.7583 (pttt) REVERT: D 58 TYR cc_start: 0.7681 (m-80) cc_final: 0.7333 (m-80) REVERT: D 241 ASP cc_start: 0.7597 (m-30) cc_final: 0.7261 (m-30) outliers start: 42 outliers final: 26 residues processed: 370 average time/residue: 0.1220 time to fit residues: 62.0929 Evaluate side-chains 374 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 347 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 269 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 105 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 73 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 158 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS A 278 GLN C 120 HIS D 10 GLN D 52 ASN D 124 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.133021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.103820 restraints weight = 20064.866| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.18 r_work: 0.2972 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.0766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14033 Z= 0.167 Angle : 0.498 6.247 18948 Z= 0.268 Chirality : 0.043 0.145 2131 Planarity : 0.004 0.047 2432 Dihedral : 4.727 59.325 1840 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.13 % Allowed : 25.02 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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 aren not related in a simple way. whole: 0.33 (0.21), residues: 1691 helix: 1.86 (0.25), residues: 455 sheet: 0.67 (0.27), residues: 372 loop : -0.92 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 488 TYR 0.013 0.001 TYR D 98 PHE 0.019 0.001 PHE B 409 TRP 0.008 0.001 TRP B 247 HIS 0.006 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00404 (14033) covalent geometry : angle 0.49809 (18948) hydrogen bonds : bond 0.04388 ( 562) hydrogen bonds : angle 4.69928 ( 1647) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 351 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 VAL cc_start: 0.8606 (p) cc_final: 0.8258 (m) REVERT: A 195 ASP cc_start: 0.7472 (m-30) cc_final: 0.7225 (m-30) REVERT: A 381 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7468 (tt) REVERT: A 516 LYS cc_start: 0.7773 (mptt) cc_final: 0.7488 (mptt) REVERT: A 528 LEU cc_start: 0.7780 (mt) cc_final: 0.7419 (mp) REVERT: B 258 SER cc_start: 0.8143 (OUTLIER) cc_final: 0.7795 (t) REVERT: C 17 ASN cc_start: 0.8119 (m-40) cc_final: 0.7777 (m110) REVERT: C 18 GLU cc_start: 0.7683 (mp0) cc_final: 0.7151 (mp0) REVERT: C 52 ASN cc_start: 0.8352 (m-40) cc_final: 0.7840 (m110) REVERT: C 164 MET cc_start: 0.7177 (tmm) cc_final: 0.6862 (tmm) REVERT: D 31 LYS cc_start: 0.7872 (pttt) cc_final: 0.7589 (pttt) REVERT: D 58 TYR cc_start: 0.7698 (m-80) cc_final: 0.7412 (m-80) outliers start: 49 outliers final: 32 residues processed: 372 average time/residue: 0.1255 time to fit residues: 64.5325 Evaluate side-chains 384 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 350 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 269 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 39 optimal weight: 0.0980 chunk 103 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 97 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS A 278 GLN C 10 GLN C 120 HIS D 52 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.104123 restraints weight = 20019.934| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.20 r_work: 0.2969 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14033 Z= 0.142 Angle : 0.484 5.882 18948 Z= 0.260 Chirality : 0.042 0.147 2131 Planarity : 0.004 0.050 2432 Dihedral : 4.282 19.155 1837 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.19 % Allowed : 25.21 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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 aren not related in a simple way. whole: 0.37 (0.21), residues: 1691 helix: 1.94 (0.25), residues: 455 sheet: 0.67 (0.27), residues: 372 loop : -0.90 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 59 TYR 0.012 0.001 TYR D 98 PHE 0.018 0.001 PHE B 409 TRP 0.008 0.001 TRP B 247 HIS 0.007 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00339 (14033) covalent geometry : angle 0.48381 (18948) hydrogen bonds : bond 0.04026 ( 562) hydrogen bonds : angle 4.59174 ( 1647) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 364 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASP cc_start: 0.7515 (t0) cc_final: 0.7125 (t0) REVERT: A 97 VAL cc_start: 0.8607 (p) cc_final: 0.8275 (m) REVERT: A 195 ASP cc_start: 0.7514 (m-30) cc_final: 0.7243 (m-30) REVERT: A 247 ARG cc_start: 0.8041 (mmm160) cc_final: 0.7710 (mmm160) REVERT: A 516 LYS cc_start: 0.7779 (mptt) cc_final: 0.7478 (mptt) REVERT: A 528 LEU cc_start: 0.7770 (mt) cc_final: 0.7416 (mp) REVERT: B 32 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7267 (mm-30) REVERT: B 258 SER cc_start: 0.8157 (OUTLIER) cc_final: 0.7794 (t) REVERT: C 52 ASN cc_start: 0.8339 (m-40) cc_final: 0.7852 (m-40) REVERT: C 164 MET cc_start: 0.7146 (tmm) cc_final: 0.6832 (tmm) REVERT: C 176 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.7233 (p0) REVERT: D 31 LYS cc_start: 0.7890 (pttt) cc_final: 0.7597 (pttm) REVERT: D 58 TYR cc_start: 0.7699 (m-80) cc_final: 0.7386 (m-80) REVERT: D 140 LYS cc_start: 0.8239 (tptt) cc_final: 0.7726 (tppt) outliers start: 50 outliers final: 35 residues processed: 384 average time/residue: 0.1209 time to fit residues: 64.3111 Evaluate side-chains 397 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 360 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 226 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 108 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS A 278 GLN C 10 GLN C 17 ASN C 120 HIS D 10 GLN D 52 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.132498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.103298 restraints weight = 20038.433| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.18 r_work: 0.2935 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 14033 Z= 0.194 Angle : 0.520 6.448 18948 Z= 0.278 Chirality : 0.043 0.150 2131 Planarity : 0.004 0.055 2432 Dihedral : 4.426 19.308 1837 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.57 % Allowed : 24.70 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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 aren not related in a simple way. whole: 0.33 (0.21), residues: 1691 helix: 1.95 (0.25), residues: 449 sheet: 0.65 (0.27), residues: 371 loop : -0.93 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 59 TYR 0.014 0.002 TYR D 98 PHE 0.021 0.002 PHE B 409 TRP 0.009 0.001 TRP B 247 HIS 0.007 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00473 (14033) covalent geometry : angle 0.51986 (18948) hydrogen bonds : bond 0.04515 ( 562) hydrogen bonds : angle 4.66674 ( 1647) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 369 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 VAL cc_start: 0.8641 (p) cc_final: 0.8349 (m) REVERT: A 107 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7823 (mt-10) REVERT: A 195 ASP cc_start: 0.7526 (m-30) cc_final: 0.7259 (m-30) REVERT: A 247 ARG cc_start: 0.8044 (mmm160) cc_final: 0.7732 (mmm160) REVERT: A 381 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7456 (tt) REVERT: A 516 LYS cc_start: 0.7781 (mptt) cc_final: 0.7443 (mptt) REVERT: A 528 LEU cc_start: 0.7815 (mt) cc_final: 0.7463 (mp) REVERT: B 137 ASP cc_start: 0.7731 (p0) cc_final: 0.7478 (p0) REVERT: C 52 ASN cc_start: 0.8374 (m-40) cc_final: 0.7877 (m110) REVERT: C 65 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7436 (tm-30) REVERT: C 176 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7228 (p0) REVERT: C 262 ASN cc_start: 0.7876 (t0) cc_final: 0.7669 (t0) REVERT: D 31 LYS cc_start: 0.7923 (pttt) cc_final: 0.7666 (pttt) REVERT: D 58 TYR cc_start: 0.7734 (m-80) cc_final: 0.7420 (m-80) REVERT: D 140 LYS cc_start: 0.8265 (tptt) cc_final: 0.8063 (tttp) outliers start: 56 outliers final: 38 residues processed: 393 average time/residue: 0.1292 time to fit residues: 70.1093 Evaluate side-chains 405 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 365 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 6 ASP Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 269 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 85 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 GLN C 17 ASN C 120 HIS D 52 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.133206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.103928 restraints weight = 19809.277| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.19 r_work: 0.2972 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14033 Z= 0.149 Angle : 0.490 5.823 18948 Z= 0.263 Chirality : 0.042 0.150 2131 Planarity : 0.004 0.053 2432 Dihedral : 4.332 19.158 1837 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.51 % Allowed : 25.21 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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 aren not related in a simple way. whole: 0.38 (0.21), residues: 1691 helix: 2.02 (0.25), residues: 449 sheet: 0.65 (0.27), residues: 371 loop : -0.90 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 59 TYR 0.012 0.001 TYR D 98 PHE 0.028 0.001 PHE C 287 TRP 0.009 0.001 TRP B 247 HIS 0.008 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00359 (14033) covalent geometry : angle 0.49027 (18948) hydrogen bonds : bond 0.04061 ( 562) hydrogen bonds : angle 4.56211 ( 1647) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 374 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 VAL cc_start: 0.8677 (p) cc_final: 0.8378 (m) REVERT: A 107 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7803 (mt-10) REVERT: A 195 ASP cc_start: 0.7528 (m-30) cc_final: 0.7234 (m-30) REVERT: A 247 ARG cc_start: 0.8024 (mmm160) cc_final: 0.7690 (mmm-85) REVERT: A 381 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7441 (tt) REVERT: A 516 LYS cc_start: 0.7756 (mptt) cc_final: 0.7425 (mptt) REVERT: A 528 LEU cc_start: 0.7773 (mt) cc_final: 0.7435 (mp) REVERT: B 32 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7247 (mm-30) REVERT: B 137 ASP cc_start: 0.7714 (p0) cc_final: 0.7463 (p0) REVERT: B 258 SER cc_start: 0.8117 (OUTLIER) cc_final: 0.7789 (t) REVERT: C 1 MET cc_start: 0.8095 (mmt) cc_final: 0.7876 (mmt) REVERT: C 52 ASN cc_start: 0.8347 (m-40) cc_final: 0.7897 (m110) REVERT: C 65 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7439 (tm-30) REVERT: C 164 MET cc_start: 0.7131 (tmm) cc_final: 0.6792 (tmm) REVERT: C 176 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7292 (p0) REVERT: C 184 LYS cc_start: 0.8279 (mmtt) cc_final: 0.7836 (mmtm) REVERT: C 262 ASN cc_start: 0.7858 (t0) cc_final: 0.7648 (t0) REVERT: D 31 LYS cc_start: 0.7919 (pttt) cc_final: 0.7629 (pttt) REVERT: D 58 TYR cc_start: 0.7714 (m-80) cc_final: 0.7368 (m-80) REVERT: D 140 LYS cc_start: 0.8226 (tptt) cc_final: 0.8022 (tttp) outliers start: 55 outliers final: 37 residues processed: 397 average time/residue: 0.1226 time to fit residues: 67.1723 Evaluate side-chains 415 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 375 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 226 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 91 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 125 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 GLN C 17 ASN C 120 HIS D 10 GLN D 52 ASN D 90 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.132665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.103925 restraints weight = 19885.635| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.32 r_work: 0.2965 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14033 Z= 0.173 Angle : 0.509 6.093 18948 Z= 0.273 Chirality : 0.043 0.168 2131 Planarity : 0.004 0.059 2432 Dihedral : 4.383 19.308 1837 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.51 % Allowed : 25.14 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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 aren not related in a simple way. whole: 0.34 (0.21), residues: 1691 helix: 1.97 (0.25), residues: 449 sheet: 0.64 (0.27), residues: 371 loop : -0.92 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 59 TYR 0.013 0.001 TYR D 98 PHE 0.024 0.002 PHE C 287 TRP 0.009 0.001 TRP C 91 HIS 0.009 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00420 (14033) covalent geometry : angle 0.50918 (18948) hydrogen bonds : bond 0.04280 ( 562) hydrogen bonds : angle 4.60190 ( 1647) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 373 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 VAL cc_start: 0.8714 (p) cc_final: 0.8455 (m) REVERT: A 130 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7047 (mtm180) REVERT: A 247 ARG cc_start: 0.8067 (mmm160) cc_final: 0.7750 (mmm-85) REVERT: A 333 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7182 (mt-10) REVERT: A 381 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7541 (tt) REVERT: A 516 LYS cc_start: 0.7802 (mptt) cc_final: 0.7466 (mptt) REVERT: A 528 LEU cc_start: 0.7860 (mt) cc_final: 0.7522 (mp) REVERT: B 32 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7298 (mm-30) REVERT: B 137 ASP cc_start: 0.7727 (p0) cc_final: 0.7468 (p0) REVERT: B 258 SER cc_start: 0.8142 (OUTLIER) cc_final: 0.7813 (t) REVERT: C 1 MET cc_start: 0.8091 (mmt) cc_final: 0.7873 (mmt) REVERT: C 52 ASN cc_start: 0.8351 (m-40) cc_final: 0.7923 (m110) REVERT: C 176 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7264 (p0) REVERT: D 31 LYS cc_start: 0.7971 (pttt) cc_final: 0.7673 (pttt) REVERT: D 58 TYR cc_start: 0.7786 (m-80) cc_final: 0.7467 (m-80) outliers start: 55 outliers final: 41 residues processed: 394 average time/residue: 0.1274 time to fit residues: 68.5734 Evaluate side-chains 410 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 365 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 269 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 77 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 58 optimal weight: 0.0970 chunk 59 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 GLN C 17 ASN C 120 HIS D 52 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.133033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.103892 restraints weight = 19816.508| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.17 r_work: 0.2976 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14033 Z= 0.152 Angle : 0.505 5.925 18948 Z= 0.271 Chirality : 0.043 0.172 2131 Planarity : 0.004 0.059 2432 Dihedral : 4.348 19.227 1837 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.25 % Allowed : 25.65 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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 aren not related in a simple way. whole: 0.38 (0.21), residues: 1691 helix: 2.02 (0.25), residues: 449 sheet: 0.65 (0.27), residues: 372 loop : -0.90 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 59 TYR 0.012 0.001 TYR D 98 PHE 0.027 0.001 PHE C 287 TRP 0.010 0.001 TRP C 91 HIS 0.008 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00364 (14033) covalent geometry : angle 0.50463 (18948) hydrogen bonds : bond 0.04066 ( 562) hydrogen bonds : angle 4.55532 ( 1647) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 372 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 VAL cc_start: 0.8651 (p) cc_final: 0.8365 (m) REVERT: A 130 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.6968 (mtm180) REVERT: A 247 ARG cc_start: 0.7992 (mmm160) cc_final: 0.7657 (mmm-85) REVERT: A 333 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7145 (mt-10) REVERT: A 381 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7452 (tt) REVERT: A 516 LYS cc_start: 0.7750 (mptt) cc_final: 0.7414 (mptt) REVERT: A 528 LEU cc_start: 0.7783 (mt) cc_final: 0.7440 (mp) REVERT: B 32 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7242 (mm-30) REVERT: B 137 ASP cc_start: 0.7709 (p0) cc_final: 0.7452 (p0) REVERT: B 258 SER cc_start: 0.8127 (OUTLIER) cc_final: 0.7787 (t) REVERT: C 1 MET cc_start: 0.8064 (mmt) cc_final: 0.7843 (mmt) REVERT: C 52 ASN cc_start: 0.8345 (m-40) cc_final: 0.7906 (m110) REVERT: C 176 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7247 (p0) REVERT: D 58 TYR cc_start: 0.7712 (m-80) cc_final: 0.7354 (m-80) REVERT: D 169 TYR cc_start: 0.8224 (t80) cc_final: 0.7906 (t80) outliers start: 51 outliers final: 40 residues processed: 392 average time/residue: 0.1242 time to fit residues: 66.3415 Evaluate side-chains 414 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 370 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 269 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 26 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 140 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 GLN C 17 ASN C 120 HIS D 10 GLN D 52 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.133636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.104740 restraints weight = 19855.665| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.12 r_work: 0.2981 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14033 Z= 0.128 Angle : 0.492 5.812 18948 Z= 0.264 Chirality : 0.042 0.170 2131 Planarity : 0.004 0.059 2432 Dihedral : 4.266 18.995 1837 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.13 % Allowed : 25.85 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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 aren not related in a simple way. whole: 0.43 (0.21), residues: 1691 helix: 2.07 (0.25), residues: 449 sheet: 0.67 (0.27), residues: 372 loop : -0.88 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 59 TYR 0.011 0.001 TYR D 98 PHE 0.027 0.001 PHE C 287 TRP 0.010 0.001 TRP B 247 HIS 0.008 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00303 (14033) covalent geometry : angle 0.49170 (18948) hydrogen bonds : bond 0.03803 ( 562) hydrogen bonds : angle 4.49670 ( 1647) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 365 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 VAL cc_start: 0.8655 (p) cc_final: 0.8391 (m) REVERT: A 130 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.6973 (mtm180) REVERT: A 247 ARG cc_start: 0.7983 (mmm160) cc_final: 0.7649 (mmm-85) REVERT: A 333 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7113 (mt-10) REVERT: A 381 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7455 (tt) REVERT: A 516 LYS cc_start: 0.7756 (mptt) cc_final: 0.7441 (mptt) REVERT: A 528 LEU cc_start: 0.7798 (mt) cc_final: 0.7442 (mp) REVERT: B 32 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7230 (mm-30) REVERT: B 137 ASP cc_start: 0.7710 (p0) cc_final: 0.7448 (p0) REVERT: B 258 SER cc_start: 0.8135 (OUTLIER) cc_final: 0.7776 (t) REVERT: C 1 MET cc_start: 0.8053 (mmt) cc_final: 0.7831 (mmt) REVERT: C 52 ASN cc_start: 0.8324 (m-40) cc_final: 0.7897 (m110) REVERT: C 175 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.7343 (pt) REVERT: C 176 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7200 (p0) REVERT: D 58 TYR cc_start: 0.7710 (m-80) cc_final: 0.7358 (m-80) REVERT: D 169 TYR cc_start: 0.8215 (t80) cc_final: 0.7846 (t80) outliers start: 49 outliers final: 40 residues processed: 387 average time/residue: 0.1326 time to fit residues: 69.9772 Evaluate side-chains 408 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 363 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 269 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 109 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 GLN C 17 ASN C 120 HIS D 10 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.133146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.104042 restraints weight = 19847.590| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.17 r_work: 0.2957 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14033 Z= 0.152 Angle : 0.511 6.056 18948 Z= 0.273 Chirality : 0.043 0.171 2131 Planarity : 0.004 0.060 2432 Dihedral : 4.319 19.010 1837 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.87 % Allowed : 26.04 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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 aren not related in a simple way. whole: 0.40 (0.21), residues: 1691 helix: 2.01 (0.25), residues: 449 sheet: 0.70 (0.27), residues: 372 loop : -0.90 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 488 TYR 0.012 0.001 TYR D 98 PHE 0.027 0.002 PHE C 287 TRP 0.010 0.001 TRP C 91 HIS 0.008 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00364 (14033) covalent geometry : angle 0.51099 (18948) hydrogen bonds : bond 0.04040 ( 562) hydrogen bonds : angle 4.53391 ( 1647) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 362 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 VAL cc_start: 0.8621 (p) cc_final: 0.8373 (m) REVERT: A 130 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.6972 (mtm180) REVERT: A 247 ARG cc_start: 0.7993 (mmm160) cc_final: 0.7650 (mmm-85) REVERT: A 333 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7140 (mt-10) REVERT: A 381 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7440 (tt) REVERT: A 516 LYS cc_start: 0.7768 (mptt) cc_final: 0.7445 (mptt) REVERT: A 528 LEU cc_start: 0.7764 (mt) cc_final: 0.7400 (mp) REVERT: B 32 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7233 (mm-30) REVERT: B 137 ASP cc_start: 0.7712 (p0) cc_final: 0.7453 (p0) REVERT: B 258 SER cc_start: 0.8150 (OUTLIER) cc_final: 0.7792 (t) REVERT: C 1 MET cc_start: 0.8060 (mmt) cc_final: 0.7855 (mmt) REVERT: C 52 ASN cc_start: 0.8349 (m-40) cc_final: 0.7927 (m110) REVERT: C 175 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7363 (pt) REVERT: C 176 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7205 (p0) REVERT: D 58 TYR cc_start: 0.7714 (m-80) cc_final: 0.7351 (m-80) REVERT: D 169 TYR cc_start: 0.8196 (t80) cc_final: 0.7842 (t80) outliers start: 45 outliers final: 38 residues processed: 383 average time/residue: 0.1304 time to fit residues: 68.4441 Evaluate side-chains 404 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 361 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 123 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 12 optimal weight: 0.0270 chunk 150 optimal weight: 0.9990 chunk 151 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 GLN C 17 ASN C 120 HIS C 182 ASN D 10 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.133020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.103867 restraints weight = 19973.154| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.19 r_work: 0.2974 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14033 Z= 0.152 Angle : 0.517 6.790 18948 Z= 0.276 Chirality : 0.043 0.240 2131 Planarity : 0.004 0.059 2432 Dihedral : 4.333 19.028 1837 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.06 % Allowed : 26.10 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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 aren not related in a simple way. whole: 0.39 (0.21), residues: 1691 helix: 1.98 (0.25), residues: 449 sheet: 0.71 (0.27), residues: 372 loop : -0.90 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 488 TYR 0.012 0.001 TYR D 98 PHE 0.028 0.002 PHE C 287 TRP 0.010 0.001 TRP C 91 HIS 0.009 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00366 (14033) covalent geometry : angle 0.51726 (18948) hydrogen bonds : bond 0.04028 ( 562) hydrogen bonds : angle 4.53136 ( 1647) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3291.54 seconds wall clock time: 56 minutes 58.35 seconds (3418.35 seconds total)