Starting phenix.real_space_refine on Wed Mar 4 03:39:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e4e_47507/03_2026/9e4e_47507.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e4e_47507/03_2026/9e4e_47507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e4e_47507/03_2026/9e4e_47507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e4e_47507/03_2026/9e4e_47507.map" model { file = "/net/cci-nas-00/data/ceres_data/9e4e_47507/03_2026/9e4e_47507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e4e_47507/03_2026/9e4e_47507.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 87 5.16 5 C 6495 2.51 5 N 1667 2.21 5 O 1909 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10158 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3440 Classifications: {'peptide': 428} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 409} Chain: "B" Number of atoms: 3413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3413 Classifications: {'peptide': 425} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 406} Chain: "C" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3305 Classifications: {'peptide': 413} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 394} Time building chain proxies: 2.54, per 1000 atoms: 0.25 Number of scatterers: 10158 At special positions: 0 Unit cell: (98.2345, 95.758, 142.812, 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 87 16.00 O 1909 8.00 N 1667 7.00 C 6495 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 314 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 345 " distance=2.03 Simple disulfide: pdb=" SG CYS A 325 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 310 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 314 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 345 " distance=2.03 Simple disulfide: pdb=" SG CYS B 325 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 310 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 314 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 345 " distance=2.03 Simple disulfide: pdb=" SG CYS C 325 " - pdb=" SG CYS C 337 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 596.0 milliseconds 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2376 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 12 sheets defined 44.5% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 37 through 69 removed outlier: 3.726A pdb=" N LYS A 42 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 103 Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 153 through 162 Processing helix chain 'A' and resid 164 through 168 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.875A pdb=" N ASP A 202 " --> pdb=" O SER A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 225 through 229 Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.503A pdb=" N GLY A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 299 Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 338 through 345 removed outlier: 3.567A pdb=" N LYS A 343 " --> pdb=" O PRO A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 355 Processing helix chain 'A' and resid 386 through 394 Processing helix chain 'A' and resid 397 through 404 removed outlier: 3.722A pdb=" N GLY A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 452 removed outlier: 3.621A pdb=" N GLY A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 460 removed outlier: 3.665A pdb=" N ALA A 457 " --> pdb=" O LEU A 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 69 removed outlier: 4.306A pdb=" N TRP B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL B 56 " --> pdb=" O GLY B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 103 Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 126 through 130 removed outlier: 3.612A pdb=" N ALA B 130 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 153 through 162 Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 199 through 203 removed outlier: 3.808A pdb=" N ASP B 202 " --> pdb=" O SER B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 216 Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 306 through 324 Processing helix chain 'B' and resid 338 through 345 removed outlier: 3.552A pdb=" N LYS B 343 " --> pdb=" O PRO B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 355 Processing helix chain 'B' and resid 386 through 395 Processing helix chain 'B' and resid 397 through 404 removed outlier: 3.567A pdb=" N GLY B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU B 403 " --> pdb=" O GLN B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 453 removed outlier: 3.903A pdb=" N VAL B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 451 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU B 452 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 453 " --> pdb=" O THR B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 462 removed outlier: 3.876A pdb=" N GLU B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL B 460 " --> pdb=" O TYR B 456 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 70 removed outlier: 3.599A pdb=" N LEU C 45 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLU C 63 " --> pdb=" O CYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.564A pdb=" N ALA C 130 " --> pdb=" O THR C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 142 removed outlier: 3.511A pdb=" N ASP C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 162 Processing helix chain 'C' and resid 164 through 168 Processing helix chain 'C' and resid 180 through 182 No H-bonds generated for 'chain 'C' and resid 180 through 182' Processing helix chain 'C' and resid 199 through 203 removed outlier: 4.207A pdb=" N ASP C 202 " --> pdb=" O SER C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 216 Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'C' and resid 257 through 262 removed outlier: 3.545A pdb=" N GLY C 262 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 299 Processing helix chain 'C' and resid 306 through 324 Processing helix chain 'C' and resid 338 through 345 removed outlier: 3.700A pdb=" N LYS C 343 " --> pdb=" O PRO C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 355 Processing helix chain 'C' and resid 386 through 394 Processing helix chain 'C' and resid 397 through 404 removed outlier: 3.668A pdb=" N GLY C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU C 403 " --> pdb=" O GLN C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 450 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 78 removed outlier: 9.332A pdb=" N GLU A 418 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLU A 277 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ILE A 420 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ARG A 279 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N GLN A 422 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE A 281 " --> pdb=" O GLN A 422 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N LYS A 424 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE A 269 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLU A 219 " --> pdb=" O CYS A 172 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N CYS A 172 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N MET A 221 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 78 removed outlier: 9.332A pdb=" N GLU A 418 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLU A 277 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ILE A 420 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ARG A 279 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N GLN A 422 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE A 281 " --> pdb=" O GLN A 422 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N LYS A 424 " --> pdb=" O ILE A 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 189 removed outlier: 7.049A pdb=" N LYS A 193 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ASN A 94 " --> pdb=" O LYS A 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 73 through 80 removed outlier: 3.771A pdb=" N GLU B 421 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N GLU B 418 " --> pdb=" O CYS B 275 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLU B 277 " --> pdb=" O GLU B 418 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ILE B 420 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG B 279 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLN B 422 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE B 281 " --> pdb=" O GLN B 422 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N LYS B 424 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N PHE B 269 " --> pdb=" O ILE B 405 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASP B 223 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU B 169 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 80 removed outlier: 3.771A pdb=" N GLU B 421 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N GLU B 418 " --> pdb=" O CYS B 275 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLU B 277 " --> pdb=" O GLU B 418 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ILE B 420 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG B 279 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLN B 422 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE B 281 " --> pdb=" O GLN B 422 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N LYS B 424 " --> pdb=" O ILE B 281 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA8, first strand: chain 'B' and resid 184 through 189 removed outlier: 6.997A pdb=" N LYS B 193 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASN B 94 " --> pdb=" O LYS B 193 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 73 through 78 removed outlier: 6.938A pdb=" N GLU C 219 " --> pdb=" O CYS C 172 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N CYS C 172 " --> pdb=" O GLU C 219 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N MET C 221 " --> pdb=" O LEU C 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 73 through 78 removed outlier: 4.318A pdb=" N PHE C 269 " --> pdb=" O ILE C 405 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 407 " --> pdb=" O PHE C 269 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU C 413 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 9.984A pdb=" N GLU C 277 " --> pdb=" O GLU C 413 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N LEU C 415 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 12.398A pdb=" N ARG C 279 " --> pdb=" O LEU C 415 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N TYR C 417 " --> pdb=" O ARG C 279 " (cutoff:3.500A) removed outlier: 10.842A pdb=" N ILE C 281 " --> pdb=" O TYR C 417 " (cutoff:3.500A) removed outlier: 9.935A pdb=" N THR C 419 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AB3, first strand: chain 'C' and resid 184 through 189 removed outlier: 7.132A pdb=" N LYS C 193 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ASN C 94 " --> pdb=" O LYS C 193 " (cutoff:3.500A) 507 hydrogen bonds defined for protein. 1383 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.33 Time building geometry restraints manager: 0.87 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: 3306 1.34 - 1.46: 2462 1.46 - 1.58: 4506 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 10394 Sorted by residual: bond pdb=" CA VAL A 80 " pdb=" CB VAL A 80 " ideal model delta sigma weight residual 1.532 1.540 -0.007 1.47e-02 4.63e+03 2.57e-01 bond pdb=" CA GLY C 192 " pdb=" C GLY C 192 " ideal model delta sigma weight residual 1.514 1.521 -0.007 1.41e-02 5.03e+03 2.49e-01 bond pdb=" CA TYR A 36 " pdb=" CB TYR A 36 " ideal model delta sigma weight residual 1.530 1.538 -0.008 1.69e-02 3.50e+03 2.31e-01 bond pdb=" N VAL A 450 " pdb=" CA VAL A 450 " ideal model delta sigma weight residual 1.459 1.453 0.006 1.25e-02 6.40e+03 2.28e-01 bond pdb=" CG1 ILE B 258 " pdb=" CD1 ILE B 258 " ideal model delta sigma weight residual 1.513 1.495 0.018 3.90e-02 6.57e+02 2.06e-01 ... (remaining 10389 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 13638 0.99 - 1.98: 323 1.98 - 2.97: 61 2.97 - 3.96: 26 3.96 - 4.95: 4 Bond angle restraints: 14052 Sorted by residual: angle pdb=" C SER A 35 " pdb=" N TYR A 36 " pdb=" CA TYR A 36 " ideal model delta sigma weight residual 121.54 124.91 -3.37 1.91e+00 2.74e-01 3.11e+00 angle pdb=" C PHE C 257 " pdb=" N ILE C 258 " pdb=" CA ILE C 258 " ideal model delta sigma weight residual 120.86 123.59 -2.73 1.67e+00 3.59e-01 2.68e+00 angle pdb=" C GLU A 79 " pdb=" N VAL A 80 " pdb=" CA VAL A 80 " ideal model delta sigma weight residual 120.77 123.15 -2.38 1.46e+00 4.69e-01 2.65e+00 angle pdb=" N PHE C 257 " pdb=" CA PHE C 257 " pdb=" CB PHE C 257 " ideal model delta sigma weight residual 111.53 108.41 3.12 1.93e+00 2.68e-01 2.62e+00 angle pdb=" C PHE C 257 " pdb=" CA PHE C 257 " pdb=" CB PHE C 257 " ideal model delta sigma weight residual 111.97 115.16 -3.19 1.99e+00 2.53e-01 2.57e+00 ... (remaining 14047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 5709 17.17 - 34.34: 475 34.34 - 51.51: 87 51.51 - 68.68: 24 68.68 - 85.85: 3 Dihedral angle restraints: 6298 sinusoidal: 2594 harmonic: 3704 Sorted by residual: dihedral pdb=" CB CYS C 323 " pdb=" SG CYS C 323 " pdb=" SG CYS C 345 " pdb=" CB CYS C 345 " ideal model delta sinusoidal sigma weight residual 93.00 49.15 43.85 1 1.00e+01 1.00e-02 2.68e+01 dihedral pdb=" CB CYS B 323 " pdb=" SG CYS B 323 " pdb=" SG CYS B 345 " pdb=" CB CYS B 345 " ideal model delta sinusoidal sigma weight residual 93.00 56.84 36.16 1 1.00e+01 1.00e-02 1.85e+01 dihedral pdb=" CB CYS A 314 " pdb=" SG CYS A 314 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 61.75 31.25 1 1.00e+01 1.00e-02 1.39e+01 ... (remaining 6295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 907 0.028 - 0.056: 422 0.056 - 0.084: 105 0.084 - 0.111: 62 0.111 - 0.139: 14 Chirality restraints: 1510 Sorted by residual: chirality pdb=" CB VAL C 450 " pdb=" CA VAL C 450 " pdb=" CG1 VAL C 450 " pdb=" CG2 VAL C 450 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA ILE B 124 " pdb=" N ILE B 124 " pdb=" C ILE B 124 " pdb=" CB ILE B 124 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE A 410 " pdb=" N ILE A 410 " pdb=" C ILE A 410 " pdb=" CB ILE A 410 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 1507 not shown) Planarity restraints: 1829 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 257 " -0.014 2.00e-02 2.50e+03 1.34e-02 3.13e+00 pdb=" CG PHE C 257 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE C 257 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 257 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 257 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 257 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE C 257 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 284 " 0.019 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO C 285 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO C 285 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 285 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 284 " 0.016 5.00e-02 4.00e+02 2.49e-02 9.91e-01 pdb=" N PRO A 285 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 285 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 285 " 0.014 5.00e-02 4.00e+02 ... (remaining 1826 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2490 2.79 - 3.32: 9255 3.32 - 3.85: 15965 3.85 - 4.37: 19276 4.37 - 4.90: 33451 Nonbonded interactions: 80437 Sorted by model distance: nonbonded pdb=" OH TYR A 282 " pdb=" OE1 GLU B 79 " model vdw 2.267 3.040 nonbonded pdb=" O LEU A 77 " pdb=" OG1 THR C 75 " model vdw 2.292 3.040 nonbonded pdb=" OD2 ASP B 126 " pdb=" NE2 GLN B 128 " model vdw 2.301 3.120 nonbonded pdb=" OH TYR A 426 " pdb=" OD2 ASP A 434 " model vdw 2.317 3.040 nonbonded pdb=" OG1 THR C 236 " pdb=" OG1 THR C 239 " model vdw 2.321 3.040 ... (remaining 80432 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 'A' and resid 40 through 452) selection = (chain 'B' and resid 40 through 452) selection = chain 'C' } 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: 3.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.520 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 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 : 0.002 0.023 10415 Z= 0.087 Angle : 0.417 4.955 14094 Z= 0.217 Chirality : 0.037 0.139 1510 Planarity : 0.002 0.030 1829 Dihedral : 13.113 85.848 3859 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.25), residues: 1260 helix: 1.15 (0.27), residues: 391 sheet: 0.77 (0.29), residues: 307 loop : 1.06 (0.29), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 279 TYR 0.012 0.001 TYR C 342 PHE 0.030 0.001 PHE C 257 TRP 0.003 0.001 TRP B 46 HIS 0.002 0.000 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00194 (10394) covalent geometry : angle 0.41362 (14052) SS BOND : bond 0.00171 ( 21) SS BOND : angle 1.00258 ( 42) hydrogen bonds : bond 0.22853 ( 488) hydrogen bonds : angle 8.35697 ( 1383) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 418 GLU cc_start: 0.8077 (pt0) cc_final: 0.7693 (mm-30) REVERT: B 458 TYR cc_start: 0.8026 (t80) cc_final: 0.7799 (t80) REVERT: C 46 TRP cc_start: 0.8829 (t60) cc_final: 0.8433 (t60) REVERT: C 66 GLN cc_start: 0.8987 (mm110) cc_final: 0.8618 (mt0) REVERT: C 259 ASP cc_start: 0.8488 (t0) cc_final: 0.8201 (t0) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1186 time to fit residues: 23.7455 Evaluate side-chains 93 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN B 329 HIS B 416 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.082912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.063962 restraints weight = 24387.546| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.31 r_work: 0.2910 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10415 Z= 0.220 Angle : 0.595 10.757 14094 Z= 0.311 Chirality : 0.042 0.201 1510 Planarity : 0.003 0.028 1829 Dihedral : 4.245 25.905 1383 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.35 % Allowed : 6.95 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.24), residues: 1260 helix: 1.44 (0.25), residues: 423 sheet: 0.75 (0.28), residues: 303 loop : 1.06 (0.30), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 201 TYR 0.016 0.001 TYR C 342 PHE 0.023 0.001 PHE C 257 TRP 0.010 0.001 TRP B 46 HIS 0.003 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00503 (10394) covalent geometry : angle 0.58900 (14052) SS BOND : bond 0.00392 ( 21) SS BOND : angle 1.64480 ( 42) hydrogen bonds : bond 0.04914 ( 488) hydrogen bonds : angle 5.81565 ( 1383) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8725 (t0) cc_final: 0.8513 (t0) REVERT: A 133 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.9190 (ptpp) REVERT: B 418 GLU cc_start: 0.8079 (pt0) cc_final: 0.7872 (pt0) REVERT: B 434 ASP cc_start: 0.8461 (m-30) cc_final: 0.8242 (m-30) REVERT: C 66 GLN cc_start: 0.9031 (mm110) cc_final: 0.8700 (mt0) REVERT: C 259 ASP cc_start: 0.8650 (t0) cc_final: 0.8435 (t0) REVERT: C 327 MET cc_start: 0.8537 (mtp) cc_final: 0.8321 (mtt) REVERT: C 418 GLU cc_start: 0.8283 (pm20) cc_final: 0.7974 (pm20) outliers start: 15 outliers final: 9 residues processed: 102 average time/residue: 0.0827 time to fit residues: 12.5660 Evaluate side-chains 95 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 61 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 58 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 52 optimal weight: 0.0170 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN B 128 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.083321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.064568 restraints weight = 24315.826| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.31 r_work: 0.2956 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10415 Z= 0.134 Angle : 0.525 10.457 14094 Z= 0.265 Chirality : 0.040 0.164 1510 Planarity : 0.003 0.027 1829 Dihedral : 4.117 23.135 1383 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.53 % Allowed : 8.94 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.24), residues: 1260 helix: 1.76 (0.25), residues: 423 sheet: 0.75 (0.29), residues: 287 loop : 1.00 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 201 TYR 0.012 0.001 TYR B 458 PHE 0.022 0.001 PHE A 50 TRP 0.014 0.001 TRP B 46 HIS 0.003 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00304 (10394) covalent geometry : angle 0.52178 (14052) SS BOND : bond 0.00372 ( 21) SS BOND : angle 1.15025 ( 42) hydrogen bonds : bond 0.04142 ( 488) hydrogen bonds : angle 5.35407 ( 1383) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8719 (t0) cc_final: 0.8506 (t0) REVERT: A 133 LYS cc_start: 0.9410 (OUTLIER) cc_final: 0.9194 (ptpp) REVERT: A 295 MET cc_start: 0.4498 (mmm) cc_final: 0.4293 (mtm) REVERT: A 439 MET cc_start: 0.8196 (mmt) cc_final: 0.7887 (mmp) REVERT: B 330 MET cc_start: 0.9598 (mtt) cc_final: 0.9328 (mtt) REVERT: B 418 GLU cc_start: 0.8106 (pt0) cc_final: 0.7859 (pt0) REVERT: C 66 GLN cc_start: 0.9022 (mm110) cc_final: 0.8679 (mt0) REVERT: C 259 ASP cc_start: 0.8634 (t0) cc_final: 0.8419 (t0) REVERT: C 418 GLU cc_start: 0.8175 (pm20) cc_final: 0.7873 (pm20) outliers start: 17 outliers final: 7 residues processed: 99 average time/residue: 0.0912 time to fit residues: 13.2496 Evaluate side-chains 96 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 58 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 51 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.082871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.063924 restraints weight = 24384.738| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.33 r_work: 0.2923 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10415 Z= 0.148 Angle : 0.531 15.207 14094 Z= 0.266 Chirality : 0.040 0.183 1510 Planarity : 0.003 0.026 1829 Dihedral : 4.172 29.612 1383 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.53 % Allowed : 9.93 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.24), residues: 1260 helix: 1.86 (0.26), residues: 423 sheet: 0.68 (0.29), residues: 289 loop : 0.92 (0.29), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 145 TYR 0.011 0.001 TYR C 342 PHE 0.023 0.001 PHE B 50 TRP 0.026 0.002 TRP C 46 HIS 0.008 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00340 (10394) covalent geometry : angle 0.52468 (14052) SS BOND : bond 0.00397 ( 21) SS BOND : angle 1.55696 ( 42) hydrogen bonds : bond 0.03694 ( 488) hydrogen bonds : angle 5.11465 ( 1383) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8705 (t0) cc_final: 0.8493 (t0) REVERT: A 439 MET cc_start: 0.8188 (mmt) cc_final: 0.7871 (mmp) REVERT: B 45 LEU cc_start: 0.9277 (mm) cc_final: 0.8670 (tp) REVERT: B 330 MET cc_start: 0.9564 (mtt) cc_final: 0.9311 (mtt) REVERT: B 418 GLU cc_start: 0.8135 (pt0) cc_final: 0.7860 (pt0) REVERT: C 66 GLN cc_start: 0.9029 (mm110) cc_final: 0.8682 (mt0) REVERT: C 259 ASP cc_start: 0.8656 (t0) cc_final: 0.8433 (t0) REVERT: C 418 GLU cc_start: 0.8185 (pm20) cc_final: 0.7884 (pm20) outliers start: 17 outliers final: 9 residues processed: 99 average time/residue: 0.0964 time to fit residues: 14.2296 Evaluate side-chains 95 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 432 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 107 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 56 optimal weight: 0.2980 chunk 103 optimal weight: 0.8980 chunk 68 optimal weight: 0.0570 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.084036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.065052 restraints weight = 24255.464| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.33 r_work: 0.2944 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10415 Z= 0.104 Angle : 0.518 15.157 14094 Z= 0.256 Chirality : 0.039 0.166 1510 Planarity : 0.002 0.026 1829 Dihedral : 4.110 29.360 1383 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.35 % Allowed : 9.84 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.24), residues: 1260 helix: 1.88 (0.26), residues: 429 sheet: 0.75 (0.29), residues: 283 loop : 0.96 (0.29), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 201 TYR 0.008 0.001 TYR A 342 PHE 0.024 0.001 PHE B 50 TRP 0.015 0.001 TRP C 46 HIS 0.004 0.000 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00231 (10394) covalent geometry : angle 0.51149 (14052) SS BOND : bond 0.00348 ( 21) SS BOND : angle 1.54514 ( 42) hydrogen bonds : bond 0.03386 ( 488) hydrogen bonds : angle 5.01196 ( 1383) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8700 (t0) cc_final: 0.8474 (t0) REVERT: A 439 MET cc_start: 0.8152 (mmt) cc_final: 0.7827 (mmp) REVERT: B 45 LEU cc_start: 0.9193 (mm) cc_final: 0.8659 (tp) REVERT: B 330 MET cc_start: 0.9551 (mtt) cc_final: 0.9299 (mtt) REVERT: B 418 GLU cc_start: 0.8168 (pt0) cc_final: 0.7878 (pt0) REVERT: C 58 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8506 (pp) REVERT: C 66 GLN cc_start: 0.9032 (mm110) cc_final: 0.8646 (mt0) REVERT: C 136 GLU cc_start: 0.9450 (tp30) cc_final: 0.9236 (tm-30) REVERT: C 259 ASP cc_start: 0.8639 (t0) cc_final: 0.8413 (t0) REVERT: C 418 GLU cc_start: 0.8189 (pm20) cc_final: 0.7889 (pm20) outliers start: 15 outliers final: 11 residues processed: 99 average time/residue: 0.0794 time to fit residues: 12.0711 Evaluate side-chains 101 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 69 PHE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 432 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 22 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.083633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.064652 restraints weight = 24307.982| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.34 r_work: 0.2943 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10415 Z= 0.129 Angle : 0.524 15.012 14094 Z= 0.256 Chirality : 0.039 0.153 1510 Planarity : 0.002 0.025 1829 Dihedral : 4.034 28.805 1383 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.44 % Allowed : 11.10 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.24), residues: 1260 helix: 1.95 (0.26), residues: 430 sheet: 0.71 (0.29), residues: 283 loop : 0.96 (0.29), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 145 TYR 0.009 0.001 TYR A 342 PHE 0.028 0.001 PHE C 50 TRP 0.013 0.001 TRP C 46 HIS 0.002 0.000 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00296 (10394) covalent geometry : angle 0.51919 (14052) SS BOND : bond 0.00301 ( 21) SS BOND : angle 1.37955 ( 42) hydrogen bonds : bond 0.03234 ( 488) hydrogen bonds : angle 4.89315 ( 1383) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8566 (tttm) cc_final: 0.8211 (ttmm) REVERT: A 78 ASP cc_start: 0.8703 (t0) cc_final: 0.8485 (t0) REVERT: A 242 GLU cc_start: 0.8759 (mp0) cc_final: 0.8541 (mp0) REVERT: A 439 MET cc_start: 0.8135 (mmt) cc_final: 0.7811 (mmp) REVERT: B 45 LEU cc_start: 0.9211 (mm) cc_final: 0.8644 (tp) REVERT: B 129 MET cc_start: 0.8730 (mmt) cc_final: 0.8463 (mmt) REVERT: B 330 MET cc_start: 0.9558 (mtt) cc_final: 0.9305 (mtt) REVERT: B 418 GLU cc_start: 0.8134 (pt0) cc_final: 0.7840 (pt0) REVERT: C 58 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8492 (pp) REVERT: C 66 GLN cc_start: 0.9035 (mm110) cc_final: 0.8645 (mt0) REVERT: C 76 LYS cc_start: 0.8603 (tttm) cc_final: 0.8240 (mmtm) REVERT: C 259 ASP cc_start: 0.8654 (t0) cc_final: 0.8425 (t0) REVERT: C 418 GLU cc_start: 0.8194 (pm20) cc_final: 0.7891 (pm20) outliers start: 16 outliers final: 13 residues processed: 100 average time/residue: 0.0862 time to fit residues: 13.0812 Evaluate side-chains 102 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 69 PHE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 432 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 82 optimal weight: 1.9990 chunk 104 optimal weight: 0.0980 chunk 121 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 36 optimal weight: 0.4980 chunk 98 optimal weight: 0.0980 chunk 61 optimal weight: 4.9990 chunk 71 optimal weight: 0.0470 chunk 43 optimal weight: 4.9990 chunk 18 optimal weight: 0.0670 chunk 4 optimal weight: 2.9990 overall best weight: 0.1616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.085259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.066426 restraints weight = 24135.010| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.37 r_work: 0.2985 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10415 Z= 0.084 Angle : 0.499 14.720 14094 Z= 0.247 Chirality : 0.038 0.145 1510 Planarity : 0.002 0.026 1829 Dihedral : 3.957 28.246 1383 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.17 % Allowed : 11.82 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.24), residues: 1260 helix: 1.92 (0.26), residues: 436 sheet: 0.92 (0.30), residues: 271 loop : 0.90 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 201 TYR 0.006 0.001 TYR B 195 PHE 0.029 0.001 PHE A 454 TRP 0.018 0.001 TRP C 46 HIS 0.009 0.001 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00178 (10394) covalent geometry : angle 0.49481 (14052) SS BOND : bond 0.00239 ( 21) SS BOND : angle 1.30195 ( 42) hydrogen bonds : bond 0.02952 ( 488) hydrogen bonds : angle 4.80467 ( 1383) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 PHE cc_start: 0.8969 (t80) cc_final: 0.8534 (t80) REVERT: A 78 ASP cc_start: 0.8703 (t0) cc_final: 0.8478 (t0) REVERT: A 242 GLU cc_start: 0.8734 (mp0) cc_final: 0.8486 (mp0) REVERT: A 439 MET cc_start: 0.8109 (mmt) cc_final: 0.7794 (mmp) REVERT: B 43 ARG cc_start: 0.7888 (tmm160) cc_final: 0.6711 (mtm180) REVERT: B 45 LEU cc_start: 0.9139 (mm) cc_final: 0.8574 (tp) REVERT: B 129 MET cc_start: 0.8715 (mmt) cc_final: 0.8481 (mmt) REVERT: B 330 MET cc_start: 0.9530 (mtt) cc_final: 0.9297 (mtt) REVERT: B 418 GLU cc_start: 0.8109 (pt0) cc_final: 0.7357 (mm-30) REVERT: C 58 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8411 (pp) REVERT: C 66 GLN cc_start: 0.9010 (mm110) cc_final: 0.8609 (mt0) REVERT: C 76 LYS cc_start: 0.8515 (tttm) cc_final: 0.8157 (mmtm) REVERT: C 259 ASP cc_start: 0.8601 (t0) cc_final: 0.8344 (t0) REVERT: C 418 GLU cc_start: 0.8144 (pm20) cc_final: 0.7849 (pm20) outliers start: 13 outliers final: 8 residues processed: 104 average time/residue: 0.0934 time to fit residues: 14.4531 Evaluate side-chains 98 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 69 PHE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 342 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 21 optimal weight: 0.6980 chunk 25 optimal weight: 0.0000 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 329 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.084532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.063782 restraints weight = 24235.957| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.33 r_work: 0.2905 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10415 Z= 0.099 Angle : 0.504 15.638 14094 Z= 0.247 Chirality : 0.039 0.143 1510 Planarity : 0.002 0.026 1829 Dihedral : 3.911 27.968 1383 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.08 % Allowed : 11.82 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.24), residues: 1260 helix: 1.89 (0.26), residues: 437 sheet: 0.74 (0.30), residues: 280 loop : 0.92 (0.29), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 201 TYR 0.007 0.001 TYR A 36 PHE 0.038 0.001 PHE C 442 TRP 0.021 0.001 TRP C 46 HIS 0.002 0.000 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00224 (10394) covalent geometry : angle 0.50003 (14052) SS BOND : bond 0.00254 ( 21) SS BOND : angle 1.29985 ( 42) hydrogen bonds : bond 0.02886 ( 488) hydrogen bonds : angle 4.70747 ( 1383) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8543 (tttm) cc_final: 0.8220 (ttmm) REVERT: A 50 PHE cc_start: 0.8959 (t80) cc_final: 0.8548 (t80) REVERT: A 78 ASP cc_start: 0.8760 (t0) cc_final: 0.8554 (t0) REVERT: A 242 GLU cc_start: 0.8704 (mp0) cc_final: 0.8489 (mp0) REVERT: A 439 MET cc_start: 0.8131 (mmt) cc_final: 0.7816 (mmp) REVERT: B 43 ARG cc_start: 0.7953 (tmm160) cc_final: 0.6772 (mtm180) REVERT: B 45 LEU cc_start: 0.9136 (mm) cc_final: 0.8575 (tp) REVERT: B 129 MET cc_start: 0.8772 (mmt) cc_final: 0.8490 (mmt) REVERT: B 330 MET cc_start: 0.9558 (mtt) cc_final: 0.9354 (mtt) REVERT: B 418 GLU cc_start: 0.8154 (pt0) cc_final: 0.7832 (pt0) REVERT: C 58 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8415 (pp) REVERT: C 66 GLN cc_start: 0.9035 (mm110) cc_final: 0.8620 (mt0) REVERT: C 76 LYS cc_start: 0.8642 (tttm) cc_final: 0.8309 (mmtm) REVERT: C 259 ASP cc_start: 0.8570 (t0) cc_final: 0.8312 (t0) REVERT: C 418 GLU cc_start: 0.8209 (pm20) cc_final: 0.7931 (pm20) outliers start: 12 outliers final: 9 residues processed: 94 average time/residue: 0.0880 time to fit residues: 12.4941 Evaluate side-chains 99 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 69 PHE Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 342 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 0.2980 chunk 33 optimal weight: 0.0470 chunk 120 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.084969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.065996 restraints weight = 24030.014| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.33 r_work: 0.2872 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10415 Z= 0.102 Angle : 0.511 16.139 14094 Z= 0.247 Chirality : 0.039 0.145 1510 Planarity : 0.002 0.026 1829 Dihedral : 3.883 27.244 1383 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.08 % Allowed : 11.82 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.24), residues: 1260 helix: 2.00 (0.26), residues: 431 sheet: 0.74 (0.29), residues: 285 loop : 0.87 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 201 TYR 0.009 0.001 TYR A 342 PHE 0.036 0.001 PHE A 454 TRP 0.022 0.001 TRP C 46 HIS 0.002 0.000 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00234 (10394) covalent geometry : angle 0.50703 (14052) SS BOND : bond 0.00246 ( 21) SS BOND : angle 1.21654 ( 42) hydrogen bonds : bond 0.02842 ( 488) hydrogen bonds : angle 4.65380 ( 1383) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8547 (tttm) cc_final: 0.8236 (ttmm) REVERT: A 50 PHE cc_start: 0.8973 (t80) cc_final: 0.8592 (t80) REVERT: A 439 MET cc_start: 0.8169 (mmt) cc_final: 0.7849 (mmp) REVERT: B 43 ARG cc_start: 0.7999 (tmm160) cc_final: 0.6748 (mtm180) REVERT: B 45 LEU cc_start: 0.9141 (mm) cc_final: 0.8588 (tp) REVERT: B 129 MET cc_start: 0.8756 (mmt) cc_final: 0.8487 (mmt) REVERT: B 330 MET cc_start: 0.9564 (mtt) cc_final: 0.9356 (mtt) REVERT: B 418 GLU cc_start: 0.8158 (pt0) cc_final: 0.7830 (pt0) REVERT: C 58 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8400 (pp) REVERT: C 66 GLN cc_start: 0.9056 (mm110) cc_final: 0.8638 (mt0) REVERT: C 76 LYS cc_start: 0.8632 (tttm) cc_final: 0.8299 (mmtm) REVERT: C 259 ASP cc_start: 0.8587 (t0) cc_final: 0.8334 (t0) outliers start: 12 outliers final: 11 residues processed: 94 average time/residue: 0.0819 time to fit residues: 11.6895 Evaluate side-chains 99 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 69 PHE Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 342 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 4 optimal weight: 5.9990 chunk 77 optimal weight: 0.0670 chunk 18 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 6 optimal weight: 0.0670 chunk 70 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 GLN C 278 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.085120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.066090 restraints weight = 23959.821| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.34 r_work: 0.3108 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10415 Z= 0.095 Angle : 0.514 15.912 14094 Z= 0.246 Chirality : 0.039 0.142 1510 Planarity : 0.002 0.026 1829 Dihedral : 3.846 26.958 1383 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.08 % Allowed : 12.18 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.24), residues: 1260 helix: 1.96 (0.26), residues: 436 sheet: 0.78 (0.29), residues: 280 loop : 0.86 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 201 TYR 0.008 0.001 TYR A 342 PHE 0.036 0.001 PHE A 454 TRP 0.020 0.001 TRP C 46 HIS 0.002 0.000 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00216 (10394) covalent geometry : angle 0.51128 (14052) SS BOND : bond 0.00236 ( 21) SS BOND : angle 1.13623 ( 42) hydrogen bonds : bond 0.02790 ( 488) hydrogen bonds : angle 4.62763 ( 1383) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8456 (tttm) cc_final: 0.8144 (ttmm) REVERT: A 50 PHE cc_start: 0.8964 (t80) cc_final: 0.8616 (t80) REVERT: A 439 MET cc_start: 0.8151 (mmt) cc_final: 0.7841 (mmp) REVERT: B 43 ARG cc_start: 0.7866 (tmm160) cc_final: 0.6571 (mtm180) REVERT: B 45 LEU cc_start: 0.9084 (mm) cc_final: 0.8507 (tp) REVERT: B 129 MET cc_start: 0.8629 (mmt) cc_final: 0.8308 (mmt) REVERT: B 330 MET cc_start: 0.9467 (mtt) cc_final: 0.9193 (mtt) REVERT: B 418 GLU cc_start: 0.8021 (pt0) cc_final: 0.7674 (pt0) REVERT: C 58 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8358 (pp) REVERT: C 66 GLN cc_start: 0.9015 (mm110) cc_final: 0.8637 (mt0) REVERT: C 76 LYS cc_start: 0.8367 (tttm) cc_final: 0.8026 (mmtm) REVERT: C 259 ASP cc_start: 0.8596 (t0) cc_final: 0.8352 (t0) outliers start: 12 outliers final: 10 residues processed: 93 average time/residue: 0.0883 time to fit residues: 12.1669 Evaluate side-chains 100 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 69 PHE Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 342 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 63 optimal weight: 0.0000 chunk 53 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.084926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.065813 restraints weight = 24218.270| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.37 r_work: 0.3072 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10415 Z= 0.107 Angle : 0.536 15.833 14094 Z= 0.255 Chirality : 0.039 0.143 1510 Planarity : 0.002 0.026 1829 Dihedral : 3.860 26.629 1383 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.26 % Allowed : 11.82 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.24), residues: 1260 helix: 2.08 (0.26), residues: 431 sheet: 0.76 (0.29), residues: 285 loop : 0.87 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 201 TYR 0.007 0.001 TYR A 36 PHE 0.038 0.001 PHE A 454 TRP 0.023 0.001 TRP C 46 HIS 0.002 0.000 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00248 (10394) covalent geometry : angle 0.53282 (14052) SS BOND : bond 0.00249 ( 21) SS BOND : angle 1.13316 ( 42) hydrogen bonds : bond 0.02782 ( 488) hydrogen bonds : angle 4.60986 ( 1383) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2187.76 seconds wall clock time: 38 minutes 12.69 seconds (2292.69 seconds total)