Starting phenix.real_space_refine on Thu Jun 12 07:44:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ag5_15416/06_2025/8ag5_15416.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ag5_15416/06_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_15416/06_2025/8ag5_15416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ag5_15416/06_2025/8ag5_15416.map" model { file = "/net/cci-nas-00/data/ceres_data/8ag5_15416/06_2025/8ag5_15416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ag5_15416/06_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-5710/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: 8.66, per 1000 atoms: 0.63 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: 3.63 Conformation dependent library (CDL) restraints added in 2.1 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: 1.63 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: 4.70 Time building geometry restraints manager: 4.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4489 1.34 - 1.46: 2813 1.46 - 1.58: 6610 1.58 - 1.69: 0 1.69 - 1.81: 121 Bond restraints: 14033 Sorted by residual: bond pdb=" CB ASP B 65 " pdb=" CG ASP B 65 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.13e+00 bond pdb=" CB ASP C 5 " pdb=" CG ASP C 5 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 9.75e-01 bond pdb=" CB PHE B 142 " pdb=" CG PHE B 142 " ideal model delta sigma weight residual 1.502 1.519 -0.017 2.30e-02 1.89e+03 5.60e-01 bond pdb=" CB LYS A 516 " pdb=" CG LYS A 516 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.48e-01 bond pdb=" C ILE C 175 " pdb=" O ILE C 175 " ideal model delta sigma weight residual 1.229 1.236 -0.008 1.03e-02 9.43e+03 5.36e-01 ... (remaining 14028 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 18455 1.26 - 2.51: 371 2.51 - 3.77: 94 3.77 - 5.03: 24 5.03 - 6.28: 4 Bond angle restraints: 18948 Sorted by residual: angle pdb=" C LYS D 85 " pdb=" N ARG D 86 " pdb=" CA ARG D 86 " ideal model delta sigma weight residual 121.54 126.77 -5.23 1.91e+00 2.74e-01 7.49e+00 angle pdb=" N ARG A 218 " pdb=" CA ARG A 218 " pdb=" C ARG A 218 " ideal model delta sigma weight residual 113.72 109.66 4.06 1.52e+00 4.33e-01 7.14e+00 angle pdb=" C ARG D 86 " pdb=" N THR D 87 " pdb=" CA THR D 87 " ideal model delta sigma weight residual 121.54 126.26 -4.72 1.91e+00 2.74e-01 6.11e+00 angle pdb=" CA ILE D 49 " pdb=" CB ILE D 49 " pdb=" CG1 ILE D 49 " ideal model delta sigma weight residual 110.40 114.18 -3.78 1.70e+00 3.46e-01 4.95e+00 angle pdb=" CA ARG A 218 " pdb=" C ARG A 218 " pdb=" N ASP A 219 " ideal model delta sigma weight residual 118.87 116.33 2.54 1.18e+00 7.18e-01 4.62e+00 ... (remaining 18943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 7262 17.44 - 34.89: 947 34.89 - 52.33: 294 52.33 - 69.77: 74 69.77 - 87.21: 21 Dihedral angle restraints: 8598 sinusoidal: 3580 harmonic: 5018 Sorted by residual: dihedral pdb=" CG ARG A 488 " pdb=" CD ARG A 488 " pdb=" NE ARG A 488 " pdb=" CZ ARG A 488 " ideal model delta sinusoidal sigma weight residual -90.00 -36.49 -53.51 2 1.50e+01 4.44e-03 1.38e+01 dihedral pdb=" CA ASP D 20 " pdb=" CB ASP D 20 " pdb=" CG ASP D 20 " pdb=" OD1 ASP D 20 " ideal model delta sinusoidal sigma weight residual -30.00 -88.14 58.14 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA PRO D 121 " pdb=" C PRO D 121 " pdb=" N THR D 122 " pdb=" CA THR D 122 " ideal model delta harmonic sigma weight residual 180.00 163.23 16.77 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 8595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1325 0.030 - 0.060: 525 0.060 - 0.090: 147 0.090 - 0.120: 120 0.120 - 0.151: 14 Chirality restraints: 2131 Sorted by residual: chirality pdb=" CA ILE D 73 " pdb=" N ILE D 73 " pdb=" C ILE D 73 " pdb=" CB ILE D 73 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA ILE D 12 " pdb=" N ILE D 12 " pdb=" C ILE D 12 " pdb=" CB ILE D 12 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA ILE A 166 " pdb=" N ILE A 166 " pdb=" C ILE A 166 " pdb=" CB ILE A 166 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 2128 not shown) Planarity restraints: 2432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 65 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.71e+00 pdb=" C ASP B 65 " -0.033 2.00e-02 2.50e+03 pdb=" O ASP B 65 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN B 66 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 120 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO C 121 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 369 " 0.028 5.00e-02 4.00e+02 4.30e-02 2.95e+00 pdb=" N PRO A 370 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " 0.024 5.00e-02 4.00e+02 ... (remaining 2429 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 837 2.74 - 3.28: 12553 3.28 - 3.82: 21616 3.82 - 4.36: 26188 4.36 - 4.90: 45209 Nonbonded interactions: 106403 Sorted by model distance: nonbonded pdb=" OG SER B 378 " pdb=" OE2 GLU B 417 " model vdw 2.194 3.040 nonbonded pdb=" O GLN C 10 " pdb=" OH TYR C 101 " model vdw 2.199 3.040 nonbonded pdb=" OG1 THR C 281 " pdb=" OD1 ASP C 283 " model vdw 2.226 3.040 nonbonded pdb=" OG1 THR C 312 " pdb=" O PRO C 314 " model vdw 2.231 3.040 nonbonded pdb=" OE1 GLU D 28 " pdb=" NZ LYS D 31 " model vdw 2.236 3.120 ... (remaining 106398 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 35.750 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.430 ------------------------------------------------------------------------------- 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 : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 337 average time/residue: 0.3274 time to fit residues: 149.4060 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 : 1.819 ------------------------------------------------------------------------------- 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 = 46)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.102629 restraints weight = 19859.861| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.16 r_work: 0.2951 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 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 : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 VAL cc_start: 0.8610 (p) cc_final: 0.8276 (m) REVERT: A 195 ASP cc_start: 0.7396 (m-30) cc_final: 0.7168 (m-30) REVERT: A 200 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7771 (mt) REVERT: A 516 LYS cc_start: 0.7731 (mptt) cc_final: 0.7499 (mptt) REVERT: B 258 SER cc_start: 0.8212 (OUTLIER) cc_final: 0.7867 (t) REVERT: B 510 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7096 (tm-30) REVERT: C 23 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7581 (mtt90) REVERT: C 164 MET cc_start: 0.7197 (tmm) cc_final: 0.6954 (tmm) REVERT: D 31 LYS cc_start: 0.7854 (pttt) cc_final: 0.7588 (pttt) REVERT: D 58 TYR cc_start: 0.7728 (m-80) cc_final: 0.7491 (m-80) REVERT: D 68 ASP cc_start: 0.6873 (t0) cc_final: 0.6593 (t0) REVERT: D 241 ASP cc_start: 0.7599 (m-30) cc_final: 0.7261 (m-30) outliers start: 46 outliers final: 26 residues processed: 371 average time/residue: 0.3063 time to fit residues: 156.2257 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 : 1.669 ------------------------------------------------------------------------------- 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: 0.0970 chunk 96 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 161 optimal weight: 0.0670 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 163 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- 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 17 ASN C 120 HIS C 178 HIS C 262 ASN D 10 GLN D 52 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.133931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.104776 restraints weight = 19860.090| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.18 r_work: 0.2984 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 14033 Z= 0.102 Angle : 0.467 5.472 18948 Z= 0.252 Chirality : 0.041 0.149 2131 Planarity : 0.004 0.053 2432 Dihedral : 4.624 57.926 1840 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.62 % Allowed : 25.65 % 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: 0.37 (0.21), residues: 1691 helix: 1.92 (0.25), residues: 455 sheet: 0.69 (0.27), residues: 372 loop : -0.91 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 247 HIS 0.007 0.001 HIS D 220 PHE 0.016 0.001 PHE B 409 TYR 0.011 0.001 TYR D 98 ARG 0.007 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.03758 ( 562) hydrogen bonds : angle 4.61562 ( 1647) covalent geometry : bond 0.00230 (14033) covalent geometry : angle 0.46743 (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 401 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 360 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASP cc_start: 0.7482 (m-30) cc_final: 0.7198 (m-30) REVERT: A 381 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7392 (tt) REVERT: A 516 LYS cc_start: 0.7812 (mptt) cc_final: 0.7559 (mptt) REVERT: A 528 LEU cc_start: 0.7765 (mt) cc_final: 0.7402 (mp) REVERT: B 258 SER cc_start: 0.8182 (OUTLIER) cc_final: 0.7810 (t) REVERT: C 18 GLU cc_start: 0.7688 (mp0) cc_final: 0.7142 (mp0) REVERT: C 164 MET cc_start: 0.7122 (tmm) cc_final: 0.6840 (tmm) REVERT: D 31 LYS cc_start: 0.7857 (pttt) cc_final: 0.7567 (pttt) REVERT: D 169 TYR cc_start: 0.8197 (t80) cc_final: 0.7843 (t80) outliers start: 41 outliers final: 23 residues processed: 377 average time/residue: 0.3041 time to fit residues: 157.2736 Evaluate side-chains 388 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 363 time to evaluate : 1.487 ------------------------------------------------------------------------------- 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 240 GLU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 281 LEU 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 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: 1.9990 chunk 117 optimal weight: 7.9990 chunk 71 optimal weight: 0.2980 chunk 66 optimal weight: 0.9980 chunk 101 optimal weight: 0.0370 chunk 154 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 chunk 25 optimal weight: 3.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.133455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.104213 restraints weight = 19793.561| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.20 r_work: 0.2967 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14033 Z= 0.132 Angle : 0.476 5.947 18948 Z= 0.256 Chirality : 0.042 0.146 2131 Planarity : 0.004 0.050 2432 Dihedral : 4.249 19.025 1837 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.06 % Allowed : 25.21 % 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: 0.41 (0.21), residues: 1691 helix: 2.00 (0.25), residues: 455 sheet: 0.69 (0.27), residues: 371 loop : -0.89 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 247 HIS 0.007 0.001 HIS D 220 PHE 0.017 0.001 PHE B 409 TYR 0.013 0.001 TYR D 98 ARG 0.006 0.000 ARG C 59 Details of bonding type rmsd hydrogen bonds : bond 0.03947 ( 562) hydrogen bonds : angle 4.55605 ( 1647) covalent geometry : bond 0.00314 (14033) covalent geometry : angle 0.47601 (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 405 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 357 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASP cc_start: 0.7494 (t0) cc_final: 0.7113 (t0) REVERT: A 195 ASP cc_start: 0.7522 (m-30) cc_final: 0.7252 (m-30) REVERT: A 247 ARG cc_start: 0.8020 (mmm160) cc_final: 0.7692 (mmm160) REVERT: A 333 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7153 (mt-10) REVERT: A 381 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7445 (tt) REVERT: A 516 LYS cc_start: 0.7819 (mptt) cc_final: 0.7523 (mptt) REVERT: A 528 LEU cc_start: 0.7760 (mt) cc_final: 0.7401 (mp) REVERT: B 32 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7270 (mm-30) REVERT: B 258 SER cc_start: 0.8187 (OUTLIER) cc_final: 0.7810 (t) REVERT: C 164 MET cc_start: 0.7201 (tmm) cc_final: 0.6892 (tmm) REVERT: D 31 LYS cc_start: 0.7898 (pttt) cc_final: 0.7595 (pttm) REVERT: D 58 TYR cc_start: 0.7680 (m-80) cc_final: 0.7367 (m-80) REVERT: D 140 LYS cc_start: 0.8215 (tptt) cc_final: 0.7722 (tppt) REVERT: D 169 TYR cc_start: 0.8194 (t80) cc_final: 0.7858 (t80) outliers start: 48 outliers final: 38 residues processed: 374 average time/residue: 0.3136 time to fit residues: 160.9629 Evaluate side-chains 395 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 355 time to evaluate : 1.657 ------------------------------------------------------------------------------- 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 A residue 427 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 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 53 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 226 VAL 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: 0.9990 chunk 103 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 89 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 chunk 17 optimal weight: 2.9990 chunk 92 optimal weight: 0.2980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 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 = 0.3602 r_free = 0.3602 target = 0.134380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.105213 restraints weight = 19922.748| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.17 r_work: 0.2995 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14033 Z= 0.100 Angle : 0.450 5.505 18948 Z= 0.243 Chirality : 0.041 0.149 2131 Planarity : 0.003 0.049 2432 Dihedral : 4.103 18.579 1837 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.70 % Allowed : 24.31 % Favored : 71.98 % 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: 0.50 (0.21), residues: 1691 helix: 2.11 (0.25), residues: 455 sheet: 0.82 (0.27), residues: 357 loop : -0.86 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 247 HIS 0.009 0.001 HIS D 220 PHE 0.016 0.001 PHE C 303 TYR 0.011 0.001 TYR D 98 ARG 0.008 0.000 ARG C 59 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 562) hydrogen bonds : angle 4.41741 ( 1647) covalent geometry : bond 0.00228 (14033) covalent geometry : angle 0.45029 (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 415 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 357 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASP cc_start: 0.7490 (t0) cc_final: 0.7173 (t0) REVERT: A 195 ASP cc_start: 0.7531 (m-30) cc_final: 0.7266 (m-30) REVERT: A 247 ARG cc_start: 0.7994 (mmm160) cc_final: 0.7651 (mmm160) REVERT: A 333 GLU cc_start: 0.7379 (mt-10) cc_final: 0.7112 (mt-10) REVERT: A 381 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7435 (tt) REVERT: A 516 LYS cc_start: 0.7811 (mptt) cc_final: 0.7514 (mptt) REVERT: A 528 LEU cc_start: 0.7738 (mt) cc_final: 0.7374 (mp) REVERT: B 32 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7197 (mm-30) REVERT: B 258 SER cc_start: 0.8135 (OUTLIER) cc_final: 0.7795 (t) REVERT: C 164 MET cc_start: 0.7112 (tmm) cc_final: 0.6840 (tmm) REVERT: D 27 ARG cc_start: 0.7695 (mtt180) cc_final: 0.7329 (mtt180) REVERT: D 31 LYS cc_start: 0.7903 (pttt) cc_final: 0.7648 (pttt) REVERT: D 58 TYR cc_start: 0.7650 (m-80) cc_final: 0.7322 (m-80) REVERT: D 140 LYS cc_start: 0.8192 (tptt) cc_final: 0.7699 (tppt) REVERT: D 169 TYR cc_start: 0.8174 (t80) cc_final: 0.7863 (t80) outliers start: 58 outliers final: 39 residues processed: 384 average time/residue: 0.3519 time to fit residues: 189.3459 Evaluate side-chains 396 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 355 time to evaluate : 1.688 ------------------------------------------------------------------------------- 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 108 LEU 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 221 LEU 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 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 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 53 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 98 TYR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 151 optimal weight: 0.0670 chunk 64 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 120 HIS D 10 GLN D 52 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.133700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.104407 restraints weight = 19953.801| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.20 r_work: 0.2984 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.0974 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= 0.124 Angle : 0.470 5.923 18948 Z= 0.252 Chirality : 0.042 0.169 2131 Planarity : 0.003 0.050 2432 Dihedral : 4.143 18.700 1837 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.25 % Allowed : 25.02 % 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: 0.51 (0.21), residues: 1691 helix: 2.17 (0.25), residues: 449 sheet: 0.82 (0.28), residues: 357 loop : -0.87 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 247 HIS 0.009 0.001 HIS D 220 PHE 0.017 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 0.03756 ( 562) hydrogen bonds : angle 4.44703 ( 1647) covalent geometry : bond 0.00295 (14033) covalent geometry : angle 0.46967 (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 408 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 357 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASP cc_start: 0.7493 (t0) cc_final: 0.7161 (t0) REVERT: A 195 ASP cc_start: 0.7549 (m-30) cc_final: 0.7297 (m-30) REVERT: A 247 ARG cc_start: 0.7977 (mmm160) cc_final: 0.7616 (mmm-85) REVERT: A 258 ARG cc_start: 0.7958 (mtt180) cc_final: 0.7626 (mtt180) REVERT: A 333 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7150 (mt-10) REVERT: A 381 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7471 (tt) REVERT: A 516 LYS cc_start: 0.7813 (mptt) cc_final: 0.7472 (mptt) REVERT: A 528 LEU cc_start: 0.7745 (mt) cc_final: 0.7383 (mp) REVERT: B 32 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7238 (mm-30) REVERT: B 142 PHE cc_start: 0.8287 (p90) cc_final: 0.8078 (p90) REVERT: B 258 SER cc_start: 0.8165 (OUTLIER) cc_final: 0.7794 (t) REVERT: C 164 MET cc_start: 0.7166 (tmm) cc_final: 0.6889 (tmm) REVERT: D 31 LYS cc_start: 0.7935 (pttt) cc_final: 0.7668 (pttt) REVERT: D 58 TYR cc_start: 0.7678 (m-80) cc_final: 0.7353 (m-80) REVERT: D 140 LYS cc_start: 0.8217 (tptt) cc_final: 0.8011 (tttp) REVERT: D 169 TYR cc_start: 0.8184 (t80) cc_final: 0.7808 (t80) outliers start: 51 outliers final: 40 residues processed: 378 average time/residue: 0.3218 time to fit residues: 165.0607 Evaluate side-chains 398 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 356 time to evaluate : 1.673 ------------------------------------------------------------------------------- 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 A residue 427 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 323 PHE 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 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 53 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 165 THR 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 293 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 128 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 140 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 20.0000 chunk 138 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 GLN C 17 ASN C 120 HIS D 10 GLN D 52 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.133268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.104100 restraints weight = 19904.358| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.18 r_work: 0.2974 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14033 Z= 0.152 Angle : 0.490 6.235 18948 Z= 0.262 Chirality : 0.042 0.171 2131 Planarity : 0.004 0.053 2432 Dihedral : 4.241 18.749 1837 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.13 % Allowed : 24.95 % 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: 0.47 (0.21), residues: 1691 helix: 2.12 (0.25), residues: 449 sheet: 0.70 (0.27), residues: 371 loop : -0.86 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 247 HIS 0.009 0.001 HIS D 220 PHE 0.029 0.002 PHE C 287 TYR 0.012 0.001 TYR D 98 ARG 0.007 0.000 ARG C 59 Details of bonding type rmsd hydrogen bonds : bond 0.04010 ( 562) hydrogen bonds : angle 4.49955 ( 1647) covalent geometry : bond 0.00366 (14033) covalent geometry : angle 0.48952 (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 410 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 361 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ASP cc_start: 0.7492 (t0) cc_final: 0.7180 (t0) REVERT: A 247 ARG cc_start: 0.8018 (mmm160) cc_final: 0.7662 (mmm-85) REVERT: A 333 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7147 (mt-10) REVERT: A 381 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7451 (tt) REVERT: A 516 LYS cc_start: 0.7818 (mptt) cc_final: 0.7473 (mptt) REVERT: A 528 LEU cc_start: 0.7800 (mt) cc_final: 0.7433 (mp) REVERT: B 32 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7261 (mm-30) REVERT: B 137 ASP cc_start: 0.7716 (p0) cc_final: 0.7445 (p0) REVERT: B 142 PHE cc_start: 0.8336 (p90) cc_final: 0.8132 (p90) REVERT: B 258 SER cc_start: 0.8163 (OUTLIER) cc_final: 0.7788 (t) REVERT: C 1 MET cc_start: 0.8102 (mmt) cc_final: 0.7890 (mmt) REVERT: C 164 MET cc_start: 0.7137 (tmm) cc_final: 0.6809 (tmm) REVERT: C 175 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.7375 (pt) REVERT: C 176 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.7043 (p0) REVERT: C 329 MET cc_start: 0.5313 (mmm) cc_final: 0.5095 (mmm) REVERT: D 31 LYS cc_start: 0.7948 (pttt) cc_final: 0.7671 (pttt) REVERT: D 58 TYR cc_start: 0.7723 (m-80) cc_final: 0.7395 (m-80) REVERT: D 140 LYS cc_start: 0.8195 (tptt) cc_final: 0.7994 (tttp) REVERT: D 169 TYR cc_start: 0.8190 (t80) cc_final: 0.7819 (t80) outliers start: 49 outliers final: 38 residues processed: 380 average time/residue: 0.3326 time to fit residues: 172.0507 Evaluate side-chains 401 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 359 time to evaluate : 1.530 ------------------------------------------------------------------------------- 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 A residue 427 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 323 PHE 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 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 53 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 98 TYR 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: 2.9990 chunk 58 optimal weight: 0.1980 chunk 163 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 100 optimal weight: 0.3980 chunk 137 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 164 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 120 HIS D 10 GLN D 52 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.133495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.104236 restraints weight = 19978.222| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.20 r_work: 0.2982 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14033 Z= 0.138 Angle : 0.484 5.906 18948 Z= 0.260 Chirality : 0.042 0.171 2131 Planarity : 0.004 0.056 2432 Dihedral : 4.227 18.722 1837 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.25 % Allowed : 24.63 % Favored : 72.11 % 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: 2.13 (0.25), residues: 449 sheet: 0.78 (0.27), residues: 359 loop : -0.87 (0.21), residues: 883 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 0.026 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 0.03869 ( 562) hydrogen bonds : angle 4.47299 ( 1647) covalent geometry : bond 0.00329 (14033) covalent geometry : angle 0.48437 (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 418 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 367 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ASP cc_start: 0.7500 (t0) cc_final: 0.7172 (t0) REVERT: A 97 VAL cc_start: 0.8689 (p) cc_final: 0.8407 (m) REVERT: A 247 ARG cc_start: 0.7997 (mmm160) cc_final: 0.7649 (mmm-85) REVERT: A 333 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7122 (mt-10) REVERT: A 381 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7465 (tt) REVERT: A 516 LYS cc_start: 0.7750 (mptt) cc_final: 0.7419 (mptt) REVERT: A 528 LEU cc_start: 0.7784 (mt) cc_final: 0.7412 (mp) REVERT: B 32 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7258 (mm-30) REVERT: B 137 ASP cc_start: 0.7691 (p0) cc_final: 0.7426 (p0) REVERT: B 142 PHE cc_start: 0.8341 (p90) cc_final: 0.8108 (p90) REVERT: B 258 SER cc_start: 0.8150 (OUTLIER) cc_final: 0.7795 (t) REVERT: C 1 MET cc_start: 0.8097 (mmt) cc_final: 0.7885 (mmt) REVERT: C 30 PHE cc_start: 0.7811 (t80) cc_final: 0.7611 (t80) REVERT: C 52 ASN cc_start: 0.8333 (m-40) cc_final: 0.7897 (m110) REVERT: C 164 MET cc_start: 0.7132 (tmm) cc_final: 0.6800 (tmm) REVERT: C 175 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.7405 (pt) REVERT: C 176 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7035 (p0) REVERT: C 329 MET cc_start: 0.5265 (mmm) cc_final: 0.4987 (mmm) REVERT: D 31 LYS cc_start: 0.7970 (pttt) cc_final: 0.7674 (pttt) REVERT: D 58 TYR cc_start: 0.7718 (m-80) cc_final: 0.7385 (m-80) REVERT: D 169 TYR cc_start: 0.8171 (t80) cc_final: 0.7799 (t80) outliers start: 51 outliers final: 38 residues processed: 391 average time/residue: 0.3272 time to fit residues: 173.8570 Evaluate side-chains 408 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 366 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 532 LYS 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 53 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 165 THR 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: 1.9990 chunk 1 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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** B 33 GLN C 17 ASN C 120 HIS D 10 GLN D 52 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.131962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.102904 restraints weight = 19855.549| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.17 r_work: 0.2927 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 14033 Z= 0.258 Angle : 0.568 6.823 18948 Z= 0.304 Chirality : 0.046 0.171 2131 Planarity : 0.004 0.058 2432 Dihedral : 4.551 19.531 1837 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.94 % Allowed : 25.46 % 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: 0.30 (0.21), residues: 1691 helix: 1.93 (0.25), residues: 449 sheet: 0.64 (0.27), residues: 375 loop : -0.96 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 276 HIS 0.007 0.001 HIS D 220 PHE 0.026 0.002 PHE C 287 TYR 0.016 0.002 TYR D 101 ARG 0.011 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.04910 ( 562) hydrogen bonds : angle 4.69722 ( 1647) covalent geometry : bond 0.00635 (14033) covalent geometry : angle 0.56755 (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 413 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 367 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 VAL cc_start: 0.8640 (p) cc_final: 0.8406 (m) REVERT: A 244 ARG cc_start: 0.7986 (mtm-85) cc_final: 0.7679 (mtp180) REVERT: A 247 ARG cc_start: 0.8036 (mmm160) cc_final: 0.7713 (mmm160) REVERT: A 333 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7181 (mt-10) REVERT: A 381 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7455 (tt) REVERT: A 516 LYS cc_start: 0.7755 (mptt) cc_final: 0.7415 (mptt) REVERT: A 528 LEU cc_start: 0.7830 (mt) cc_final: 0.7482 (mp) REVERT: B 137 ASP cc_start: 0.7737 (p0) cc_final: 0.7474 (p0) REVERT: C 52 ASN cc_start: 0.8414 (m-40) cc_final: 0.7906 (m110) REVERT: C 175 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7393 (pt) REVERT: C 176 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.6807 (p0) REVERT: C 329 MET cc_start: 0.5251 (mmm) cc_final: 0.5042 (mmm) REVERT: D 58 TYR cc_start: 0.7798 (m-80) cc_final: 0.7483 (m-80) REVERT: D 169 TYR cc_start: 0.8223 (t80) cc_final: 0.7853 (t80) outliers start: 46 outliers final: 35 residues processed: 387 average time/residue: 0.3352 time to fit residues: 181.4885 Evaluate side-chains 401 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 363 time to evaluate : 1.739 ------------------------------------------------------------------------------- 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 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 123 ILE 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 490 LEU Chi-restraints excluded: chain B residue 532 LYS 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 312 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 53 ILE 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 267 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: 0.9980 chunk 165 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 140 optimal weight: 0.1980 chunk 99 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 163 optimal weight: 0.1980 chunk 115 optimal weight: 0.1980 chunk 41 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN A 416 GLN C 17 ASN C 120 HIS 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 = 0.3598 r_free = 0.3598 target = 0.134071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.105016 restraints weight = 19769.296| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.17 r_work: 0.2969 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14033 Z= 0.111 Angle : 0.488 6.547 18948 Z= 0.262 Chirality : 0.042 0.175 2131 Planarity : 0.004 0.059 2432 Dihedral : 4.267 18.835 1837 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.30 % Allowed : 26.23 % Favored : 71.47 % 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: 2.13 (0.25), residues: 449 sheet: 0.69 (0.27), residues: 371 loop : -0.87 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 247 HIS 0.008 0.001 HIS D 220 PHE 0.029 0.001 PHE C 287 TYR 0.013 0.001 TYR D 98 ARG 0.010 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 562) hydrogen bonds : angle 4.46949 ( 1647) covalent geometry : bond 0.00257 (14033) covalent geometry : angle 0.48812 (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 402 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 366 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 ARG cc_start: 0.7997 (mmm160) cc_final: 0.7656 (mmm-85) REVERT: A 381 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7391 (tt) REVERT: A 516 LYS cc_start: 0.7817 (mptt) cc_final: 0.7476 (mptt) REVERT: A 528 LEU cc_start: 0.7812 (mt) cc_final: 0.7591 (mp) REVERT: B 32 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7220 (mm-30) REVERT: B 137 ASP cc_start: 0.7689 (p0) cc_final: 0.7434 (p0) REVERT: B 142 PHE cc_start: 0.8376 (p90) cc_final: 0.8052 (p90) REVERT: C 52 ASN cc_start: 0.8307 (m-40) cc_final: 0.7875 (m-40) REVERT: C 164 MET cc_start: 0.7073 (tmm) cc_final: 0.6816 (tmm) REVERT: C 175 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7387 (pt) REVERT: C 176 ASP cc_start: 0.7442 (OUTLIER) cc_final: 0.6753 (p0) REVERT: C 184 LYS cc_start: 0.8030 (mmtp) cc_final: 0.7616 (mmtm) REVERT: D 58 TYR cc_start: 0.7737 (m-80) cc_final: 0.7420 (m-80) REVERT: D 140 LYS cc_start: 0.8134 (tttp) cc_final: 0.7815 (tptt) REVERT: D 169 TYR cc_start: 0.8169 (t80) cc_final: 0.7803 (t80) outliers start: 36 outliers final: 32 residues processed: 380 average time/residue: 0.3172 time to fit residues: 162.9521 Evaluate side-chains 398 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 363 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 332 GLU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 409 TYR 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 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 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 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 312 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 53 ILE 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 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: 0.8980 chunk 90 optimal weight: 0.9990 chunk 144 optimal weight: 0.0570 chunk 119 optimal weight: 0.3980 chunk 115 optimal weight: 2.9990 chunk 158 optimal weight: 0.0980 chunk 132 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 ASN C 120 HIS D 90 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.134273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.105434 restraints weight = 19943.292| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.13 r_work: 0.2989 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 14033 Z= 0.144 Angle : 0.743 59.154 18948 Z= 0.439 Chirality : 0.047 1.017 2131 Planarity : 0.004 0.057 2432 Dihedral : 4.347 37.605 1837 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.23 % Allowed : 26.68 % Favored : 71.09 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 2.14 (0.25), residues: 449 sheet: 0.70 (0.27), residues: 371 loop : -0.86 (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 0.027 0.001 PHE C 287 TYR 0.013 0.001 TYR D 98 ARG 0.009 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.03556 ( 562) hydrogen bonds : angle 4.47200 ( 1647) covalent geometry : bond 0.00295 (14033) covalent geometry : angle 0.74305 (18948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8089.68 seconds wall clock time: 138 minutes 49.43 seconds (8329.43 seconds total)