Starting phenix.real_space_refine on Thu May 15 22:33:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ag5_15416/05_2025/8ag5_15416.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ag5_15416/05_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_15416/05_2025/8ag5_15416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ag5_15416/05_2025/8ag5_15416.map" model { file = "/net/cci-nas-00/data/ceres_data/8ag5_15416/05_2025/8ag5_15416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ag5_15416/05_2025/8ag5_15416.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.46, per 1000 atoms: 0.54 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: 2.89 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.68 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: 3.94 Time building geometry restraints manager: 3.45 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.540 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.300 ------------------------------------------------------------------------------- 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 : 6.46 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (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 TRP 0.008 0.001 TRP C 91 HIS 0.004 0.001 HIS B 246 PHE 0.026 0.001 PHE C 287 TYR 0.012 0.001 TYR D 98 ARG 0.011 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.14352 ( 562) hydrogen bonds : angle 6.11552 ( 1647) covalent geometry : bond 0.00272 (14033) covalent geometry : angle 0.48692 (18948) *********************** 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 : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 337 average time/residue: 0.3207 time to fit residues: 145.4859 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 : 1.481 ------------------------------------------------------------------------------- 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 142 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 68 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 B 43 GLN C 10 GLN C 120 HIS D 52 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.131728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.102632 restraints weight = 19859.861| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.16 r_work: 0.2944 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 14033 Z= 0.281 Angle : 0.584 7.164 18948 Z= 0.312 Chirality : 0.046 0.148 2131 Planarity : 0.004 0.049 2432 Dihedral : 5.036 61.156 1842 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.94 % Allowed : 25.14 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.20), residues: 1691 helix: 1.62 (0.25), residues: 455 sheet: 0.64 (0.26), residues: 372 loop : -1.02 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 276 HIS 0.006 0.001 HIS B 511 PHE 0.024 0.002 PHE B 409 TYR 0.017 0.002 TYR D 98 ARG 0.008 0.001 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.05452 ( 562) hydrogen bonds : angle 5.02641 ( 1647) covalent geometry : bond 0.00688 (14033) covalent geometry : angle 0.58424 (18948) *********************** 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 401 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 355 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 VAL cc_start: 0.8609 (p) cc_final: 0.8274 (m) REVERT: A 195 ASP cc_start: 0.7396 (m-30) cc_final: 0.7169 (m-30) REVERT: A 200 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7767 (mt) REVERT: A 516 LYS cc_start: 0.7731 (mptt) cc_final: 0.7498 (mptt) REVERT: B 258 SER cc_start: 0.8212 (OUTLIER) cc_final: 0.7866 (t) REVERT: B 510 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7094 (tm-30) REVERT: C 23 ARG cc_start: 0.7808 (mtm-85) cc_final: 0.7583 (mtt90) REVERT: C 164 MET cc_start: 0.7198 (tmm) cc_final: 0.6954 (tmm) REVERT: D 31 LYS cc_start: 0.7853 (pttt) cc_final: 0.7586 (pttt) REVERT: D 58 TYR cc_start: 0.7725 (m-80) cc_final: 0.7486 (m-80) REVERT: D 68 ASP cc_start: 0.6875 (t0) cc_final: 0.6594 (t0) REVERT: D 241 ASP cc_start: 0.7596 (m-30) cc_final: 0.7257 (m-30) outliers start: 46 outliers final: 26 residues processed: 371 average time/residue: 0.3008 time to fit residues: 152.3521 Evaluate side-chains 382 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 353 time to evaluate : 1.446 ------------------------------------------------------------------------------- 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 196 THR Chi-restraints excluded: chain A residue 200 LEU 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 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 275 THR Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 510 GLN 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 D residue 72 THR Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 203 THR 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 19 optimal weight: 0.0170 chunk 96 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 161 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 163 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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 17 ASN C 120 HIS C 178 HIS C 262 ASN 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 = 0.3589 r_free = 0.3589 target = 0.133578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.104458 restraints weight = 19877.852| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.17 r_work: 0.2974 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14033 Z= 0.120 Angle : 0.480 5.524 18948 Z= 0.259 Chirality : 0.042 0.147 2131 Planarity : 0.004 0.053 2432 Dihedral : 4.704 58.653 1840 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.87 % Allowed : 25.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.21), residues: 1691 helix: 1.87 (0.25), residues: 455 sheet: 0.68 (0.27), residues: 372 loop : -0.93 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 247 HIS 0.006 0.001 HIS D 220 PHE 0.017 0.001 PHE B 409 TYR 0.012 0.001 TYR D 98 ARG 0.007 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 562) hydrogen bonds : angle 4.67360 ( 1647) covalent geometry : bond 0.00276 (14033) covalent geometry : angle 0.48006 (18948) *********************** 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 403 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 358 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 VAL cc_start: 0.8628 (p) cc_final: 0.8307 (m) REVERT: A 195 ASP cc_start: 0.7487 (m-30) cc_final: 0.7230 (m-30) REVERT: A 381 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7445 (tt) REVERT: A 516 LYS cc_start: 0.7770 (mptt) cc_final: 0.7492 (mptt) REVERT: A 528 LEU cc_start: 0.7822 (mt) cc_final: 0.7465 (mp) REVERT: B 258 SER cc_start: 0.8196 (OUTLIER) cc_final: 0.7826 (t) REVERT: C 1 MET cc_start: 0.7967 (mmt) cc_final: 0.7713 (mmm) REVERT: C 18 GLU cc_start: 0.7690 (mp0) cc_final: 0.7142 (mp0) REVERT: C 164 MET cc_start: 0.7130 (tmm) cc_final: 0.6845 (tmm) REVERT: D 31 LYS cc_start: 0.7874 (pttt) cc_final: 0.7594 (pttt) REVERT: D 169 TYR cc_start: 0.8211 (t80) cc_final: 0.7852 (t80) outliers start: 45 outliers final: 28 residues processed: 376 average time/residue: 0.3002 time to fit residues: 154.5878 Evaluate side-chains 390 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 360 time to evaluate : 1.472 ------------------------------------------------------------------------------- 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 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 123 ILE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 258 SER 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 240 MET Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain D residue 98 TYR 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 21 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 71 optimal weight: 0.2980 chunk 66 optimal weight: 0.7980 chunk 101 optimal weight: 0.0870 chunk 154 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 54 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 C 262 ASN D 52 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.134476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.105306 restraints weight = 19786.136| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.17 r_work: 0.3002 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14033 Z= 0.097 Angle : 0.454 5.483 18948 Z= 0.245 Chirality : 0.041 0.148 2131 Planarity : 0.003 0.049 2432 Dihedral : 4.140 18.770 1837 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.94 % Allowed : 25.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.21), residues: 1691 helix: 2.07 (0.25), residues: 455 sheet: 0.73 (0.27), residues: 370 loop : -0.87 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 247 HIS 0.007 0.001 HIS D 220 PHE 0.015 0.001 PHE B 409 TYR 0.012 0.001 TYR D 98 ARG 0.006 0.000 ARG C 59 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 562) hydrogen bonds : angle 4.46433 ( 1647) covalent geometry : bond 0.00220 (14033) covalent geometry : angle 0.45374 (18948) *********************** 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 401 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 355 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASP cc_start: 0.7486 (t0) cc_final: 0.7089 (t0) REVERT: A 195 ASP cc_start: 0.7501 (m-30) cc_final: 0.7230 (m-30) REVERT: A 247 ARG cc_start: 0.7975 (mmm160) cc_final: 0.7651 (mmm160) REVERT: A 381 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7422 (tt) REVERT: A 516 LYS cc_start: 0.7824 (mptt) cc_final: 0.7533 (mptt) REVERT: A 528 LEU cc_start: 0.7747 (mt) cc_final: 0.7385 (mp) REVERT: B 32 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7220 (mm-30) REVERT: B 258 SER cc_start: 0.8166 (OUTLIER) cc_final: 0.7797 (t) REVERT: D 31 LYS cc_start: 0.7904 (pttt) cc_final: 0.7601 (pttm) REVERT: D 58 TYR cc_start: 0.7628 (m-80) cc_final: 0.7308 (m-80) REVERT: D 140 LYS cc_start: 0.8173 (tptt) cc_final: 0.7686 (tppt) REVERT: D 169 TYR cc_start: 0.8186 (t80) cc_final: 0.7859 (t80) outliers start: 46 outliers final: 33 residues processed: 372 average time/residue: 0.3185 time to fit residues: 164.0478 Evaluate side-chains 387 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 352 time to evaluate : 1.476 ------------------------------------------------------------------------------- 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 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 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 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 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 203 THR Chi-restraints excluded: chain D residue 269 LYS Chi-restraints excluded: chain D residue 293 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 144 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 17 ASN C 120 HIS C 262 ASN 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 = 0.3584 r_free = 0.3584 target = 0.133131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.103909 restraints weight = 19952.930| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.18 r_work: 0.2973 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14033 Z= 0.166 Angle : 0.498 6.435 18948 Z= 0.267 Chirality : 0.043 0.150 2131 Planarity : 0.004 0.051 2432 Dihedral : 4.307 19.024 1837 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.70 % Allowed : 24.76 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.21), residues: 1691 helix: 2.06 (0.25), residues: 449 sheet: 0.68 (0.27), residues: 371 loop : -0.89 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 247 HIS 0.008 0.001 HIS D 220 PHE 0.026 0.002 PHE C 287 TYR 0.014 0.001 TYR D 98 ARG 0.006 0.000 ARG D 27 Details of bonding type rmsd hydrogen bonds : bond 0.04245 ( 562) hydrogen bonds : angle 4.57339 ( 1647) covalent geometry : bond 0.00401 (14033) covalent geometry : angle 0.49761 (18948) *********************** 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 412 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 354 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ASP cc_start: 0.7468 (t0) cc_final: 0.7158 (t0) REVERT: A 195 ASP cc_start: 0.7533 (m-30) cc_final: 0.7240 (m-30) REVERT: A 247 ARG cc_start: 0.8032 (mmm160) cc_final: 0.7715 (mmm160) REVERT: A 381 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7469 (tt) REVERT: A 516 LYS cc_start: 0.7778 (mptt) cc_final: 0.7444 (mptt) REVERT: A 528 LEU cc_start: 0.7763 (mt) cc_final: 0.7401 (mp) REVERT: B 32 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7275 (mm-30) REVERT: B 258 SER cc_start: 0.8154 (OUTLIER) cc_final: 0.7789 (t) REVERT: C 164 MET cc_start: 0.7186 (tmm) cc_final: 0.6864 (tmm) REVERT: D 31 LYS cc_start: 0.7909 (pttt) cc_final: 0.7650 (pttt) REVERT: D 58 TYR cc_start: 0.7692 (m-80) cc_final: 0.7367 (m-80) REVERT: D 169 TYR cc_start: 0.8196 (t80) cc_final: 0.7875 (t80) outliers start: 58 outliers final: 37 residues processed: 379 average time/residue: 0.2953 time to fit residues: 153.5297 Evaluate side-chains 398 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 359 time to evaluate : 1.618 ------------------------------------------------------------------------------- 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 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 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 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 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 203 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 269 LYS Chi-restraints excluded: chain D residue 293 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 120 HIS C 262 ASN D 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.132362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.103328 restraints weight = 19968.868| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.17 r_work: 0.2960 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14033 Z= 0.209 Angle : 0.530 6.525 18948 Z= 0.283 Chirality : 0.044 0.170 2131 Planarity : 0.004 0.059 2432 Dihedral : 4.468 19.421 1837 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.45 % Allowed : 24.89 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.21), residues: 1691 helix: 1.95 (0.25), residues: 449 sheet: 0.64 (0.27), residues: 371 loop : -0.94 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 247 HIS 0.008 0.001 HIS D 220 PHE 0.025 0.002 PHE C 287 TYR 0.015 0.002 TYR D 98 ARG 0.007 0.000 ARG C 59 Details of bonding type rmsd hydrogen bonds : bond 0.04619 ( 562) hydrogen bonds : angle 4.66433 ( 1647) covalent geometry : bond 0.00512 (14033) covalent geometry : angle 0.52995 (18948) *********************** 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 417 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 363 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 VAL cc_start: 0.8655 (p) cc_final: 0.8355 (m) REVERT: A 195 ASP cc_start: 0.7544 (m-30) cc_final: 0.7242 (m-30) REVERT: A 381 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7469 (tt) REVERT: A 516 LYS cc_start: 0.7752 (mptt) cc_final: 0.7428 (mptt) REVERT: A 528 LEU cc_start: 0.7893 (mt) cc_final: 0.7536 (mp) REVERT: B 137 ASP cc_start: 0.7709 (p0) cc_final: 0.7455 (p0) REVERT: C 65 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7431 (tm-30) REVERT: C 176 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.7164 (p0) REVERT: D 31 LYS cc_start: 0.7940 (pttt) cc_final: 0.7652 (pttt) REVERT: D 58 TYR cc_start: 0.7730 (m-80) cc_final: 0.7404 (m-80) REVERT: D 169 TYR cc_start: 0.8221 (t80) cc_final: 0.7846 (t80) outliers start: 54 outliers final: 42 residues processed: 382 average time/residue: 0.3131 time to fit residues: 160.9721 Evaluate side-chains 401 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 357 time to evaluate : 1.417 ------------------------------------------------------------------------------- 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 129 LYS Chi-restraints excluded: chain B residue 229 GLU 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 490 LEU Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 536 LEU 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 138 ASP Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 269 LYS Chi-restraints excluded: chain D residue 293 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 128 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 67 optimal weight: 20.0000 chunk 138 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 262 ASN D 10 GLN D 52 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.132660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.103593 restraints weight = 19913.403| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.18 r_work: 0.2965 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14033 Z= 0.180 Angle : 0.515 6.062 18948 Z= 0.276 Chirality : 0.043 0.169 2131 Planarity : 0.004 0.062 2432 Dihedral : 4.438 19.309 1837 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.57 % Allowed : 24.89 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.21), residues: 1691 helix: 1.97 (0.25), residues: 449 sheet: 0.64 (0.27), residues: 371 loop : -0.93 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 247 HIS 0.009 0.001 HIS D 220 PHE 0.027 0.002 PHE C 287 TYR 0.013 0.001 TYR D 98 ARG 0.008 0.000 ARG C 59 Details of bonding type rmsd hydrogen bonds : bond 0.04341 ( 562) hydrogen bonds : angle 4.61794 ( 1647) covalent geometry : bond 0.00439 (14033) covalent geometry : angle 0.51518 (18948) *********************** 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 424 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 368 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 VAL cc_start: 0.8666 (p) cc_final: 0.8401 (m) REVERT: A 381 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7484 (tt) REVERT: A 516 LYS cc_start: 0.7747 (mptt) cc_final: 0.7413 (mptt) REVERT: A 528 LEU cc_start: 0.7855 (mt) cc_final: 0.7505 (mp) REVERT: B 137 ASP cc_start: 0.7703 (p0) cc_final: 0.7441 (p0) REVERT: B 258 SER cc_start: 0.8136 (OUTLIER) cc_final: 0.7818 (t) REVERT: C 52 ASN cc_start: 0.8368 (m-40) cc_final: 0.7882 (m110) REVERT: C 65 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7423 (tm-30) REVERT: C 175 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7411 (pt) REVERT: C 176 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7076 (p0) REVERT: D 58 TYR cc_start: 0.7723 (m-80) cc_final: 0.7389 (m-80) REVERT: D 169 TYR cc_start: 0.8212 (t80) cc_final: 0.7839 (t80) outliers start: 56 outliers final: 41 residues processed: 392 average time/residue: 0.3180 time to fit residues: 168.7841 Evaluate side-chains 412 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 367 time to evaluate : 1.564 ------------------------------------------------------------------------------- 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 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 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 275 THR Chi-restraints excluded: chain B residue 323 PHE 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 207 ILE 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 175 ILE Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 269 LYS Chi-restraints excluded: chain D residue 293 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 163 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 137 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 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 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 GLN C 17 ASN C 120 HIS D 52 ASN D 90 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.133331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.104206 restraints weight = 19933.154| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.18 r_work: 0.2977 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14033 Z= 0.145 Angle : 0.500 6.012 18948 Z= 0.268 Chirality : 0.042 0.168 2131 Planarity : 0.004 0.059 2432 Dihedral : 4.371 19.271 1837 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.38 % Allowed : 25.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.21), residues: 1691 helix: 2.06 (0.25), residues: 449 sheet: 0.65 (0.27), residues: 371 loop : -0.91 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 247 HIS 0.009 0.001 HIS D 220 PHE 0.026 0.001 PHE C 287 TYR 0.012 0.001 TYR A 88 ARG 0.007 0.000 ARG C 59 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 562) hydrogen bonds : angle 4.54382 ( 1647) covalent geometry : bond 0.00347 (14033) covalent geometry : angle 0.49975 (18948) *********************** 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 422 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 369 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 VAL cc_start: 0.8658 (p) cc_final: 0.8399 (m) REVERT: A 231 VAL cc_start: 0.6335 (OUTLIER) cc_final: 0.6134 (t) REVERT: A 247 ARG cc_start: 0.8031 (mmm160) cc_final: 0.7709 (mmm-85) REVERT: A 381 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7473 (tt) REVERT: A 516 LYS cc_start: 0.7751 (mptt) cc_final: 0.7422 (mptt) REVERT: A 528 LEU cc_start: 0.7864 (mt) cc_final: 0.7496 (mp) REVERT: B 32 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7254 (mm-30) REVERT: B 137 ASP cc_start: 0.7715 (p0) cc_final: 0.7452 (p0) REVERT: B 258 SER cc_start: 0.8122 (OUTLIER) cc_final: 0.7789 (t) REVERT: C 52 ASN cc_start: 0.8356 (m-40) cc_final: 0.7912 (m110) REVERT: C 65 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7436 (tm-30) REVERT: C 175 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.7400 (pt) REVERT: C 176 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.7132 (p0) REVERT: D 58 TYR cc_start: 0.7726 (m-80) cc_final: 0.7374 (m-80) REVERT: D 169 TYR cc_start: 0.8224 (t80) cc_final: 0.7852 (t80) outliers start: 53 outliers final: 44 residues processed: 389 average time/residue: 0.3358 time to fit residues: 179.2238 Evaluate side-chains 416 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 367 time to evaluate : 1.559 ------------------------------------------------------------------------------- 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 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 231 VAL 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 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 207 ILE 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 175 ILE Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 269 LYS Chi-restraints excluded: chain D residue 293 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 140 optimal weight: 0.0770 chunk 82 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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 D 90 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.133352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.104290 restraints weight = 19817.933| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.16 r_work: 0.2983 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14033 Z= 0.129 Angle : 0.495 5.982 18948 Z= 0.266 Chirality : 0.042 0.168 2131 Planarity : 0.004 0.059 2432 Dihedral : 4.306 19.132 1837 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.21), residues: 1691 helix: 2.10 (0.25), residues: 449 sheet: 0.67 (0.27), residues: 371 loop : -0.90 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 247 HIS 0.009 0.001 HIS D 220 PHE 0.028 0.001 PHE C 287 TYR 0.011 0.001 TYR D 98 ARG 0.007 0.000 ARG C 59 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 562) hydrogen bonds : angle 4.49340 ( 1647) covalent geometry : bond 0.00305 (14033) covalent geometry : angle 0.49515 (18948) *********************** 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 416 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 365 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 VAL cc_start: 0.8680 (p) cc_final: 0.8406 (m) REVERT: A 231 VAL cc_start: 0.6316 (OUTLIER) cc_final: 0.6110 (t) REVERT: A 247 ARG cc_start: 0.8035 (mmm160) cc_final: 0.7713 (mmm-85) REVERT: A 381 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7463 (tt) REVERT: A 516 LYS cc_start: 0.7777 (mptt) cc_final: 0.7441 (mptt) REVERT: A 528 LEU cc_start: 0.7864 (mt) cc_final: 0.7643 (mp) REVERT: B 32 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7255 (mm-30) REVERT: B 137 ASP cc_start: 0.7714 (p0) cc_final: 0.7450 (p0) REVERT: B 258 SER cc_start: 0.8134 (OUTLIER) cc_final: 0.7786 (t) REVERT: C 52 ASN cc_start: 0.8337 (m-40) cc_final: 0.7883 (m110) REVERT: C 175 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.7413 (pt) REVERT: C 176 ASP cc_start: 0.7489 (OUTLIER) cc_final: 0.7150 (p0) REVERT: D 58 TYR cc_start: 0.7712 (m-80) cc_final: 0.7356 (m-80) REVERT: D 169 TYR cc_start: 0.8224 (t80) cc_final: 0.7781 (t80) outliers start: 51 outliers final: 39 residues processed: 388 average time/residue: 0.3141 time to fit residues: 164.5537 Evaluate side-chains 408 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 364 time to evaluate : 1.448 ------------------------------------------------------------------------------- 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 153 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 231 VAL 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 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 275 THR Chi-restraints excluded: chain B residue 323 PHE 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 138 ASP Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 293 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 153 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 140 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 163 optimal weight: 0.0980 chunk 115 optimal weight: 0.0870 chunk 41 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN 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 = 0.3593 r_free = 0.3593 target = 0.133833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.104660 restraints weight = 19785.246| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.16 r_work: 0.2990 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14033 Z= 0.118 Angle : 0.488 6.338 18948 Z= 0.262 Chirality : 0.042 0.168 2131 Planarity : 0.004 0.060 2432 Dihedral : 4.226 18.894 1837 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.87 % Allowed : 26.16 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.21), residues: 1691 helix: 2.15 (0.25), residues: 449 sheet: 0.83 (0.27), residues: 360 loop : -0.90 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 91 HIS 0.009 0.001 HIS D 220 PHE 0.028 0.001 PHE C 287 TYR 0.011 0.001 TYR D 98 ARG 0.010 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 562) hydrogen bonds : angle 4.44414 ( 1647) covalent geometry : bond 0.00275 (14033) covalent geometry : angle 0.48843 (18948) ********************** 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 409 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 364 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASP cc_start: 0.7374 (t0) cc_final: 0.7085 (t0) REVERT: A 97 VAL cc_start: 0.8679 (p) cc_final: 0.8417 (m) REVERT: A 231 VAL cc_start: 0.6324 (OUTLIER) cc_final: 0.6122 (t) REVERT: A 247 ARG cc_start: 0.8006 (mmm160) cc_final: 0.7680 (mmm-85) REVERT: A 381 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7448 (tt) REVERT: A 516 LYS cc_start: 0.7754 (mptt) cc_final: 0.7436 (mptt) REVERT: A 528 LEU cc_start: 0.7809 (mt) cc_final: 0.7432 (mp) REVERT: B 32 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7206 (mm-30) REVERT: B 137 ASP cc_start: 0.7701 (p0) cc_final: 0.7449 (p0) REVERT: B 258 SER cc_start: 0.8151 (OUTLIER) cc_final: 0.7795 (t) REVERT: C 52 ASN cc_start: 0.8320 (m-40) cc_final: 0.7889 (m-40) REVERT: C 175 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7387 (pt) REVERT: C 176 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.6797 (p0) REVERT: D 58 TYR cc_start: 0.7700 (m-80) cc_final: 0.7349 (m-80) REVERT: D 169 TYR cc_start: 0.8174 (t80) cc_final: 0.7745 (t80) outliers start: 45 outliers final: 38 residues processed: 385 average time/residue: 0.3134 time to fit residues: 162.6034 Evaluate side-chains 406 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 363 time to evaluate : 1.516 ------------------------------------------------------------------------------- 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 153 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 231 VAL 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 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 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 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 138 ASP Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 293 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 114 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 144 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 158 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 D 90 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 = 0.133096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.103930 restraints weight = 20031.027| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.18 r_work: 0.2977 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14033 Z= 0.150 Angle : 0.514 8.385 18948 Z= 0.275 Chirality : 0.043 0.168 2131 Planarity : 0.004 0.059 2432 Dihedral : 4.304 18.839 1837 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.94 % Allowed : 26.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.21), residues: 1691 helix: 2.08 (0.25), residues: 449 sheet: 0.79 (0.27), residues: 359 loop : -0.91 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 91 HIS 0.004 0.001 HIS B 511 PHE 0.029 0.002 PHE C 287 TYR 0.012 0.001 TYR D 98 ARG 0.011 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 562) hydrogen bonds : angle 4.48667 ( 1647) covalent geometry : bond 0.00360 (14033) covalent geometry : angle 0.51447 (18948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7718.92 seconds wall clock time: 134 minutes 2.26 seconds (8042.26 seconds total)