Starting phenix.real_space_refine on Sun May 3 02:28:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ya7_72723/05_2026/9ya7_72723.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ya7_72723/05_2026/9ya7_72723.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ya7_72723/05_2026/9ya7_72723.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ya7_72723/05_2026/9ya7_72723.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ya7_72723/05_2026/9ya7_72723.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ya7_72723/05_2026/9ya7_72723.map" } resolution = 3.29 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= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 65 5.16 5 C 6094 2.51 5 N 1668 2.21 5 O 1908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9741 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3437 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain: "B" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3407 Classifications: {'peptide': 433} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 412} Chain: "K" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2774 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 12, 'TRANS': 341} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.65, per 1000 atoms: 0.27 Number of scatterers: 9741 At special positions: 0 Unit cell: (107.38, 82.6, 113.162, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 65 16.00 P 5 15.00 Mg 1 11.99 O 1908 8.00 N 1668 7.00 C 6094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 433.3 milliseconds 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2282 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 47.5% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 36 through 43 removed outlier: 3.804A pdb=" N LYS A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 80 removed outlier: 4.151A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 143 through 161 Processing helix chain 'A' and resid 182 through 190 Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.687A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.656A pdb=" N VAL A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.372A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.944A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.690A pdb=" N GLN A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.506A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 399 removed outlier: 4.097A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.766A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 436 removed outlier: 4.291A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY A 436 " --> pdb=" O TYR A 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 41 through 46 removed outlier: 3.955A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 69 through 78 removed outlier: 4.576A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 126 removed outlier: 3.767A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 4.046A pdb=" N GLY B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.976A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.519A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 295 through 299 removed outlier: 3.581A pdb=" N MET B 299 " --> pdb=" O SER B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.650A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 373 through 390 removed outlier: 4.278A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 removed outlier: 4.059A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU B 401 " --> pdb=" O TRP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 424 removed outlier: 3.817A pdb=" N THR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 22 Processing helix chain 'K' and resid 69 through 77 Processing helix chain 'K' and resid 77 through 87 Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 117 through 133 Processing helix chain 'K' and resid 188 through 202 removed outlier: 3.541A pdb=" N ILE K 192 " --> pdb=" O SER K 188 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA K 202 " --> pdb=" O SER K 198 " (cutoff:3.500A) Processing helix chain 'K' and resid 262 through 295 Proline residue: K 292 - end of helix Processing helix chain 'K' and resid 309 through 315 Processing helix chain 'K' and resid 315 through 320 Processing helix chain 'K' and resid 334 through 336 No H-bonds generated for 'chain 'K' and resid 334 through 336' Processing helix chain 'K' and resid 337 through 350 removed outlier: 3.650A pdb=" N GLY K 350 " --> pdb=" O ARG K 346 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 7.478A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 272 Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 7.914A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY B 132 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N SER B 138 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS B 137 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 10.761A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 13.589A pdb=" N ASP B 203 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AA6, first strand: chain 'K' and resid 54 through 57 removed outlier: 8.448A pdb=" N TYR K 54 " --> pdb=" O VAL K 6 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL K 8 " --> pdb=" O TYR K 54 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N TYR K 56 " --> pdb=" O VAL K 8 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL K 10 " --> pdb=" O TYR K 56 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N CYS K 92 " --> pdb=" O ALA K 326 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL K 328 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE K 94 " --> pdb=" O VAL K 328 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ALA K 330 " --> pdb=" O PHE K 94 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N TYR K 96 " --> pdb=" O ALA K 330 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS K 240 " --> pdb=" O GLN K 227 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 54 through 57 removed outlier: 8.448A pdb=" N TYR K 54 " --> pdb=" O VAL K 6 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL K 8 " --> pdb=" O TYR K 54 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N TYR K 56 " --> pdb=" O VAL K 8 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL K 10 " --> pdb=" O TYR K 56 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N CYS K 92 " --> pdb=" O ALA K 326 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL K 328 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE K 94 " --> pdb=" O VAL K 328 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ALA K 330 " --> pdb=" O PHE K 94 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N TYR K 96 " --> pdb=" O ALA K 330 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS K 240 " --> pdb=" O GLN K 227 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 28 through 31 Processing sheet with id=AA9, first strand: chain 'K' and resid 168 through 171 Processing sheet with id=AB1, first strand: chain 'K' and resid 205 through 206 removed outlier: 3.589A pdb=" N SER K 214 " --> pdb=" O ALA K 206 " (cutoff:3.500A) 503 hydrogen bonds defined for protein. 1452 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: 1.43 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1728 1.32 - 1.44: 2587 1.44 - 1.57: 5515 1.57 - 1.69: 12 1.69 - 1.81: 105 Bond restraints: 9947 Sorted by residual: bond pdb=" C5 GDP B 501 " pdb=" C4 GDP B 501 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.21e+00 bond pdb=" C GLN A 176 " pdb=" N VAL A 177 " ideal model delta sigma weight residual 1.330 1.320 0.010 1.26e-02 6.30e+03 6.91e-01 bond pdb=" CA ILE A 341 " pdb=" CB ILE A 341 " ideal model delta sigma weight residual 1.530 1.539 -0.008 1.05e-02 9.07e+03 6.48e-01 bond pdb=" N PRO K 305 " pdb=" CA PRO K 305 " ideal model delta sigma weight residual 1.469 1.479 -0.010 1.28e-02 6.10e+03 6.15e-01 bond pdb=" C TYR K 96 " pdb=" N GLY K 97 " ideal model delta sigma weight residual 1.319 1.329 -0.010 1.34e-02 5.57e+03 5.52e-01 ... (remaining 9942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 13111 1.24 - 2.47: 289 2.47 - 3.71: 77 3.71 - 4.94: 12 4.94 - 6.18: 6 Bond angle restraints: 13495 Sorted by residual: angle pdb=" C LYS A 112 " pdb=" N GLU A 113 " pdb=" CA GLU A 113 " ideal model delta sigma weight residual 121.54 126.95 -5.41 1.91e+00 2.74e-01 8.01e+00 angle pdb=" C ILE K 119 " pdb=" CA ILE K 119 " pdb=" CB ILE K 119 " ideal model delta sigma weight residual 114.00 111.27 2.73 1.31e+00 5.83e-01 4.34e+00 angle pdb=" C2' GTP A 501 " pdb=" C3' GTP A 501 " pdb=" C4' GTP A 501 " ideal model delta sigma weight residual 111.00 104.82 6.18 3.00e+00 1.11e-01 4.24e+00 angle pdb=" C20 TA1 B 502 " pdb=" C21 TA1 B 502 " pdb=" C24 TA1 B 502 " ideal model delta sigma weight residual 107.07 113.08 -6.01 3.00e+00 1.11e-01 4.02e+00 angle pdb=" CA GLY K 97 " pdb=" C GLY K 97 " pdb=" N GLN K 98 " ideal model delta sigma weight residual 115.34 116.95 -1.61 8.10e-01 1.52e+00 3.94e+00 ... (remaining 13490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.11: 5929 30.11 - 60.23: 97 60.23 - 90.34: 15 90.34 - 120.45: 3 120.45 - 150.57: 8 Dihedral angle restraints: 6052 sinusoidal: 2497 harmonic: 3555 Sorted by residual: dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -41.94 146.53 1 2.00e+01 2.50e-03 4.40e+01 dihedral pdb=" C4' GTP A 501 " pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " ideal model delta sinusoidal sigma weight residual 260.87 173.76 87.11 1 2.00e+01 2.50e-03 2.28e+01 dihedral pdb=" O08 TA1 B 502 " pdb=" C20 TA1 B 502 " pdb=" C21 TA1 B 502 " pdb=" O09 TA1 B 502 " ideal model delta sinusoidal sigma weight residual -128.50 22.07 -150.57 1 3.00e+01 1.11e-03 2.00e+01 ... (remaining 6049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 953 0.032 - 0.063: 357 0.063 - 0.095: 102 0.095 - 0.126: 68 0.126 - 0.158: 2 Chirality restraints: 1482 Sorted by residual: chirality pdb=" CA ILE K 244 " pdb=" N ILE K 244 " pdb=" C ILE K 244 " pdb=" CB ILE K 244 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CA ILE K 93 " pdb=" N ILE K 93 " pdb=" C ILE K 93 " pdb=" CB ILE K 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA VAL K 241 " pdb=" N VAL K 241 " pdb=" C VAL K 241 " pdb=" CB VAL K 241 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 1479 not shown) Planarity restraints: 1756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY K 291 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.44e+00 pdb=" N PRO K 292 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO K 292 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO K 292 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 88 " 0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO A 89 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 89 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 89 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 357 " -0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO B 358 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 358 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 358 " -0.018 5.00e-02 4.00e+02 ... (remaining 1753 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 111 2.61 - 3.18: 8706 3.18 - 3.76: 14965 3.76 - 4.33: 21042 4.33 - 4.90: 35207 Nonbonded interactions: 80031 Sorted by model distance: nonbonded pdb=" OE1 GLU A 71 " pdb="MG MG A 502 " model vdw 2.039 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 2.094 2.170 nonbonded pdb=" OG SER A 287 " pdb=" OE1 GLU A 290 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR B 183 " pdb=" O MET B 388 " model vdw 2.231 3.040 nonbonded pdb=" O LEU B 192 " pdb=" OG1 THR B 196 " model vdw 2.236 3.040 ... (remaining 80026 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.130 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.200 Find NCS groups from input model: 0.050 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 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 0.023 9947 Z= 0.128 Angle : 0.509 6.180 13495 Z= 0.279 Chirality : 0.041 0.158 1482 Planarity : 0.004 0.039 1756 Dihedral : 13.461 150.567 3770 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.09 % Allowed : 4.55 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.82 (0.25), residues: 1221 helix: 2.09 (0.25), residues: 480 sheet: 0.28 (0.35), residues: 242 loop : -0.86 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 282 TYR 0.008 0.001 TYR A 108 PHE 0.009 0.001 PHE A 149 TRP 0.014 0.001 TRP A 21 HIS 0.003 0.001 HIS B 396 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9947) covalent geometry : angle 0.50944 (13495) hydrogen bonds : bond 0.13535 ( 470) hydrogen bonds : angle 5.53576 ( 1452) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8756 (t0) cc_final: 0.8471 (t0) REVERT: A 108 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.6619 (p90) REVERT: A 120 ASP cc_start: 0.8692 (t0) cc_final: 0.8486 (t0) REVERT: A 212 ILE cc_start: 0.8580 (mt) cc_final: 0.8380 (mt) REVERT: A 290 GLU cc_start: 0.8476 (mp0) cc_final: 0.7987 (mp0) REVERT: A 381 THR cc_start: 0.8602 (p) cc_final: 0.7268 (t) REVERT: A 432 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.6461 (t80) REVERT: B 121 ARG cc_start: 0.8116 (mtm-85) cc_final: 0.7906 (mtm-85) REVERT: B 125 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8371 (mm-30) REVERT: B 282 ARG cc_start: 0.8334 (ttm-80) cc_final: 0.7989 (ttm-80) REVERT: B 343 GLU cc_start: 0.7856 (mp0) cc_final: 0.7243 (mp0) REVERT: B 391 ARG cc_start: 0.6289 (mtm180) cc_final: 0.5101 (mtm180) REVERT: K 19 GLU cc_start: 0.7611 (mt-10) cc_final: 0.6956 (mt-10) REVERT: K 81 MET cc_start: 0.7731 (mmp) cc_final: 0.7275 (mmm) REVERT: K 143 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7907 (mt-10) REVERT: K 152 GLU cc_start: 0.8870 (mp0) cc_final: 0.8659 (mp0) REVERT: K 180 ASP cc_start: 0.8872 (t0) cc_final: 0.8560 (t0) REVERT: K 182 SER cc_start: 0.9252 (t) cc_final: 0.8908 (p) REVERT: K 184 LEU cc_start: 0.9285 (mm) cc_final: 0.8999 (mp) outliers start: 22 outliers final: 9 residues processed: 202 average time/residue: 0.0981 time to fit residues: 27.6976 Evaluate side-chains 150 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain K residue 289 ASP Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain K residue 299 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 HIS B 245 GLN K 70 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.107210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.088755 restraints weight = 16966.412| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 3.14 r_work: 0.2982 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9947 Z= 0.153 Angle : 0.562 9.015 13495 Z= 0.281 Chirality : 0.045 0.267 1482 Planarity : 0.004 0.036 1756 Dihedral : 12.634 145.608 1494 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.46 % Allowed : 9.19 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.90 (0.25), residues: 1221 helix: 2.06 (0.24), residues: 498 sheet: 0.33 (0.35), residues: 242 loop : -0.83 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 339 TYR 0.031 0.001 TYR A 24 PHE 0.012 0.001 PHE A 149 TRP 0.013 0.001 TRP A 21 HIS 0.005 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9947) covalent geometry : angle 0.56190 (13495) hydrogen bonds : bond 0.04370 ( 470) hydrogen bonds : angle 4.45141 ( 1452) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.7851 (mp0) REVERT: A 102 ASN cc_start: 0.8770 (t0) cc_final: 0.8400 (t0) REVERT: A 108 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.6987 (p90) REVERT: A 123 ARG cc_start: 0.8238 (tpp-160) cc_final: 0.7958 (tpp-160) REVERT: A 212 ILE cc_start: 0.8686 (mt) cc_final: 0.8456 (mt) REVERT: A 357 TYR cc_start: 0.9060 (m-80) cc_final: 0.8669 (m-80) REVERT: A 381 THR cc_start: 0.8601 (p) cc_final: 0.7402 (t) REVERT: A 432 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.6530 (t80) REVERT: B 3 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: B 121 ARG cc_start: 0.8300 (mtm-85) cc_final: 0.7968 (ttm110) REVERT: B 125 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8527 (mm-30) REVERT: B 147 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8785 (ttm) REVERT: B 170 MET cc_start: 0.8921 (mmm) cc_final: 0.8468 (mmm) REVERT: B 297 LYS cc_start: 0.8981 (mmtm) cc_final: 0.8644 (mmtt) REVERT: B 391 ARG cc_start: 0.6784 (mtm180) cc_final: 0.5680 (mtm180) REVERT: B 406 MET cc_start: 0.8697 (ttp) cc_final: 0.8218 (ttp) REVERT: B 429 THR cc_start: 0.3992 (OUTLIER) cc_final: 0.3473 (m) REVERT: K 23 ASP cc_start: 0.7480 (t0) cc_final: 0.6918 (t0) REVERT: K 70 GLN cc_start: 0.8064 (mt0) cc_final: 0.7849 (mt0) REVERT: K 81 MET cc_start: 0.7909 (mmp) cc_final: 0.7361 (mmm) REVERT: K 143 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8198 (mt-10) REVERT: K 180 ASP cc_start: 0.9109 (t0) cc_final: 0.8809 (t0) REVERT: K 182 SER cc_start: 0.9234 (t) cc_final: 0.8827 (p) outliers start: 26 outliers final: 16 residues processed: 170 average time/residue: 0.0956 time to fit residues: 22.5486 Evaluate side-chains 155 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain K residue 289 ASP Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain K residue 299 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 44 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 ASN B 264 HIS K 209 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.106594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.088163 restraints weight = 17056.023| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.13 r_work: 0.2965 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9947 Z= 0.156 Angle : 0.549 10.010 13495 Z= 0.273 Chirality : 0.044 0.400 1482 Planarity : 0.004 0.037 1756 Dihedral : 10.994 144.340 1492 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.94 % Allowed : 10.62 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.90 (0.25), residues: 1221 helix: 2.03 (0.24), residues: 499 sheet: 0.43 (0.35), residues: 240 loop : -0.85 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 339 TYR 0.020 0.001 TYR A 24 PHE 0.012 0.001 PHE A 149 TRP 0.014 0.001 TRP A 21 HIS 0.004 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9947) covalent geometry : angle 0.54878 (13495) hydrogen bonds : bond 0.04102 ( 470) hydrogen bonds : angle 4.29988 ( 1452) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8716 (t0) cc_final: 0.8331 (t0) REVERT: A 108 TYR cc_start: 0.8694 (OUTLIER) cc_final: 0.7009 (p90) REVERT: A 123 ARG cc_start: 0.8245 (tpp-160) cc_final: 0.8017 (tpp-160) REVERT: A 212 ILE cc_start: 0.8651 (mt) cc_final: 0.8426 (mt) REVERT: A 276 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8703 (tp) REVERT: B 121 ARG cc_start: 0.8293 (mtm-85) cc_final: 0.8011 (ttm-80) REVERT: B 125 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8502 (mm-30) REVERT: B 147 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8812 (ttm) REVERT: B 170 MET cc_start: 0.8897 (mmm) cc_final: 0.8574 (mmm) REVERT: B 297 LYS cc_start: 0.8888 (mmtm) cc_final: 0.8610 (mmtt) REVERT: B 391 ARG cc_start: 0.6784 (mtm180) cc_final: 0.5474 (mtm180) REVERT: K 23 ASP cc_start: 0.7500 (t0) cc_final: 0.6943 (t0) REVERT: K 70 GLN cc_start: 0.8080 (mt0) cc_final: 0.7868 (mt0) REVERT: K 81 MET cc_start: 0.7896 (mmp) cc_final: 0.7308 (mmm) REVERT: K 143 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8214 (mt-10) REVERT: K 180 ASP cc_start: 0.9107 (t0) cc_final: 0.8776 (t0) REVERT: K 182 SER cc_start: 0.9237 (t) cc_final: 0.8822 (p) REVERT: K 349 ASP cc_start: 0.7710 (t0) cc_final: 0.7334 (t70) outliers start: 31 outliers final: 18 residues processed: 163 average time/residue: 0.1011 time to fit residues: 22.7925 Evaluate side-chains 152 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain K residue 289 ASP Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain K residue 299 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 41 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 36 optimal weight: 0.0980 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN B 48 ASN K 209 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.107508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.088649 restraints weight = 17112.532| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.21 r_work: 0.2981 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9947 Z= 0.120 Angle : 0.525 7.789 13495 Z= 0.263 Chirality : 0.045 0.489 1482 Planarity : 0.004 0.038 1756 Dihedral : 9.464 144.116 1492 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.94 % Allowed : 11.28 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.93 (0.25), residues: 1221 helix: 2.05 (0.24), residues: 500 sheet: 0.74 (0.36), residues: 226 loop : -0.98 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 339 TYR 0.017 0.001 TYR A 24 PHE 0.026 0.001 PHE K 225 TRP 0.013 0.001 TRP A 21 HIS 0.003 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9947) covalent geometry : angle 0.52489 (13495) hydrogen bonds : bond 0.03711 ( 470) hydrogen bonds : angle 4.21949 ( 1452) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9014 (mm) REVERT: A 36 MET cc_start: 0.8514 (ttt) cc_final: 0.8313 (ttt) REVERT: A 102 ASN cc_start: 0.8689 (t0) cc_final: 0.8278 (t0) REVERT: A 108 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.7139 (p90) REVERT: A 212 ILE cc_start: 0.8623 (mt) cc_final: 0.8399 (mt) REVERT: A 276 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8710 (tp) REVERT: A 322 ASP cc_start: 0.9001 (t0) cc_final: 0.8782 (t0) REVERT: A 357 TYR cc_start: 0.9064 (m-80) cc_final: 0.8643 (m-80) REVERT: A 392 ASP cc_start: 0.9129 (m-30) cc_final: 0.8802 (m-30) REVERT: A 423 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8486 (mm-30) REVERT: A 430 LYS cc_start: 0.9251 (tppt) cc_final: 0.8856 (mppt) REVERT: A 432 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.6682 (t80) REVERT: B 170 MET cc_start: 0.8834 (mmm) cc_final: 0.8534 (mmm) REVERT: B 282 ARG cc_start: 0.8498 (ttm-80) cc_final: 0.7706 (ttm170) REVERT: B 288 GLU cc_start: 0.8302 (tp30) cc_final: 0.7759 (tp30) REVERT: B 297 LYS cc_start: 0.8910 (mmtm) cc_final: 0.8662 (mmtm) REVERT: B 306 ARG cc_start: 0.8798 (mtt180) cc_final: 0.8487 (mtt180) REVERT: B 343 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8714 (mt-10) REVERT: B 391 ARG cc_start: 0.6789 (mtm180) cc_final: 0.5423 (mtm180) REVERT: K 23 ASP cc_start: 0.7477 (t0) cc_final: 0.6924 (t0) REVERT: K 81 MET cc_start: 0.7865 (mmp) cc_final: 0.7303 (mmm) REVERT: K 143 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8212 (mt-10) REVERT: K 166 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8740 (mm) REVERT: K 180 ASP cc_start: 0.9115 (t0) cc_final: 0.8829 (t0) REVERT: K 182 SER cc_start: 0.9227 (t) cc_final: 0.8796 (p) REVERT: K 349 ASP cc_start: 0.7744 (t0) cc_final: 0.7354 (t70) outliers start: 31 outliers final: 18 residues processed: 173 average time/residue: 0.0981 time to fit residues: 23.6919 Evaluate side-chains 155 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain K residue 137 ASN Chi-restraints excluded: chain K residue 166 LEU Chi-restraints excluded: chain K residue 289 ASP Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain K residue 299 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 64 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 81 optimal weight: 0.0870 chunk 25 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 70 GLN K 209 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.103984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.085318 restraints weight = 17301.960| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.16 r_work: 0.2922 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9947 Z= 0.221 Angle : 0.585 5.888 13495 Z= 0.297 Chirality : 0.046 0.404 1482 Planarity : 0.004 0.038 1756 Dihedral : 9.069 142.982 1489 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.03 % Allowed : 12.04 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.83 (0.25), residues: 1221 helix: 2.02 (0.24), residues: 494 sheet: 0.59 (0.36), residues: 225 loop : -1.00 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 339 TYR 0.044 0.002 TYR A 24 PHE 0.025 0.001 PHE K 225 TRP 0.014 0.001 TRP A 21 HIS 0.004 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 9947) covalent geometry : angle 0.58474 (13495) hydrogen bonds : bond 0.04377 ( 470) hydrogen bonds : angle 4.38921 ( 1452) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8951 (mm) REVERT: A 108 TYR cc_start: 0.8853 (OUTLIER) cc_final: 0.7395 (p90) REVERT: A 123 ARG cc_start: 0.8380 (tpp-160) cc_final: 0.7787 (tpp-160) REVERT: A 127 ASP cc_start: 0.8413 (m-30) cc_final: 0.7800 (m-30) REVERT: A 212 ILE cc_start: 0.8664 (mt) cc_final: 0.8436 (mt) REVERT: A 276 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8712 (tp) REVERT: A 322 ASP cc_start: 0.9053 (t0) cc_final: 0.8782 (t0) REVERT: A 392 ASP cc_start: 0.9192 (m-30) cc_final: 0.8814 (m-30) REVERT: B 170 MET cc_start: 0.8966 (mmm) cc_final: 0.8730 (mmm) REVERT: B 257 MET cc_start: 0.8784 (mmm) cc_final: 0.8525 (mmm) REVERT: B 282 ARG cc_start: 0.8506 (ttm-80) cc_final: 0.7939 (ttm170) REVERT: B 288 GLU cc_start: 0.8346 (tp30) cc_final: 0.7813 (tp30) REVERT: B 297 LYS cc_start: 0.8904 (mmtm) cc_final: 0.8674 (mmtm) REVERT: B 306 ARG cc_start: 0.8776 (mtt180) cc_final: 0.8420 (mtt180) REVERT: B 343 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8660 (mt-10) REVERT: B 391 ARG cc_start: 0.6691 (mtm180) cc_final: 0.5557 (mtm180) REVERT: K 23 ASP cc_start: 0.7477 (t0) cc_final: 0.6926 (t0) REVERT: K 70 GLN cc_start: 0.8168 (mt0) cc_final: 0.7919 (mt0) REVERT: K 81 MET cc_start: 0.7865 (mmp) cc_final: 0.7313 (mmm) REVERT: K 108 MET cc_start: 0.8769 (tpp) cc_final: 0.8444 (mpp) REVERT: K 166 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8800 (mm) REVERT: K 180 ASP cc_start: 0.9132 (t0) cc_final: 0.8853 (t0) REVERT: K 182 SER cc_start: 0.9249 (t) cc_final: 0.8839 (p) outliers start: 32 outliers final: 21 residues processed: 158 average time/residue: 0.0992 time to fit residues: 21.8871 Evaluate side-chains 150 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 166 LEU Chi-restraints excluded: chain K residue 196 MET Chi-restraints excluded: chain K residue 289 ASP Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain K residue 299 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 50 optimal weight: 0.7980 chunk 120 optimal weight: 0.3980 chunk 2 optimal weight: 0.9990 chunk 43 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS B 48 ASN K 209 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.107575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.088586 restraints weight = 17202.494| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.24 r_work: 0.2980 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9947 Z= 0.121 Angle : 0.531 8.482 13495 Z= 0.270 Chirality : 0.044 0.323 1482 Planarity : 0.004 0.039 1756 Dihedral : 8.855 143.387 1489 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.65 % Allowed : 13.18 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.91 (0.25), residues: 1221 helix: 2.12 (0.24), residues: 493 sheet: 0.71 (0.37), residues: 219 loop : -1.01 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 339 TYR 0.038 0.001 TYR A 24 PHE 0.023 0.001 PHE K 225 TRP 0.013 0.001 TRP A 21 HIS 0.003 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9947) covalent geometry : angle 0.53148 (13495) hydrogen bonds : bond 0.03774 ( 470) hydrogen bonds : angle 4.24686 ( 1452) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.9010 (mm) REVERT: A 102 ASN cc_start: 0.8666 (t0) cc_final: 0.8251 (t0) REVERT: A 108 TYR cc_start: 0.8798 (OUTLIER) cc_final: 0.7290 (p90) REVERT: A 123 ARG cc_start: 0.8334 (tpp-160) cc_final: 0.8038 (tpp-160) REVERT: A 212 ILE cc_start: 0.8627 (mt) cc_final: 0.8399 (mt) REVERT: A 220 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8516 (mm-30) REVERT: A 276 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8707 (tp) REVERT: A 295 CYS cc_start: 0.8639 (m) cc_final: 0.8342 (m) REVERT: A 322 ASP cc_start: 0.9000 (t0) cc_final: 0.8760 (t0) REVERT: A 357 TYR cc_start: 0.9087 (m-80) cc_final: 0.8675 (m-80) REVERT: A 432 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.6747 (t80) REVERT: B 170 MET cc_start: 0.8830 (mmm) cc_final: 0.8618 (mmm) REVERT: B 282 ARG cc_start: 0.8514 (ttm-80) cc_final: 0.7942 (ttm170) REVERT: B 288 GLU cc_start: 0.8281 (tp30) cc_final: 0.7763 (tp30) REVERT: B 297 LYS cc_start: 0.8895 (mmtm) cc_final: 0.8668 (mmtm) REVERT: B 306 ARG cc_start: 0.8801 (mtt180) cc_final: 0.8503 (mtt180) REVERT: B 343 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8669 (mt-10) REVERT: B 391 ARG cc_start: 0.6735 (mtm180) cc_final: 0.5503 (mtm180) REVERT: K 81 MET cc_start: 0.7863 (mmp) cc_final: 0.7282 (mmm) REVERT: K 108 MET cc_start: 0.8769 (tpp) cc_final: 0.8460 (mpp) REVERT: K 166 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8757 (mm) REVERT: K 180 ASP cc_start: 0.9155 (t0) cc_final: 0.8847 (t0) REVERT: K 182 SER cc_start: 0.9237 (t) cc_final: 0.8804 (p) REVERT: K 261 LYS cc_start: 0.8775 (mmtm) cc_final: 0.8573 (mmtm) outliers start: 28 outliers final: 19 residues processed: 163 average time/residue: 0.0971 time to fit residues: 21.9041 Evaluate side-chains 154 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 166 LEU Chi-restraints excluded: chain K residue 196 MET Chi-restraints excluded: chain K residue 289 ASP Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain K residue 299 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 75 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 ASN K 70 GLN K 209 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.104973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.086213 restraints weight = 16952.405| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.15 r_work: 0.2965 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9947 Z= 0.166 Angle : 0.557 9.109 13495 Z= 0.281 Chirality : 0.044 0.295 1482 Planarity : 0.004 0.040 1756 Dihedral : 8.792 143.230 1489 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.84 % Allowed : 13.18 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.86 (0.25), residues: 1221 helix: 2.09 (0.24), residues: 496 sheet: 0.68 (0.36), residues: 219 loop : -1.06 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 339 TYR 0.033 0.001 TYR A 24 PHE 0.027 0.001 PHE K 225 TRP 0.013 0.001 TRP A 21 HIS 0.003 0.001 HIS B 396 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 9947) covalent geometry : angle 0.55650 (13495) hydrogen bonds : bond 0.03972 ( 470) hydrogen bonds : angle 4.30201 ( 1452) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8983 (mm) REVERT: A 102 ASN cc_start: 0.8725 (t0) cc_final: 0.8303 (t0) REVERT: A 108 TYR cc_start: 0.8835 (OUTLIER) cc_final: 0.7377 (p90) REVERT: A 123 ARG cc_start: 0.8383 (tpp-160) cc_final: 0.8072 (tpp-160) REVERT: A 212 ILE cc_start: 0.8667 (mt) cc_final: 0.8437 (mt) REVERT: A 220 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8516 (mm-30) REVERT: A 276 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8703 (tp) REVERT: A 295 CYS cc_start: 0.8660 (m) cc_final: 0.8370 (m) REVERT: A 322 ASP cc_start: 0.9010 (t0) cc_final: 0.8760 (t0) REVERT: A 357 TYR cc_start: 0.9102 (m-80) cc_final: 0.8675 (m-80) REVERT: A 423 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8491 (mm-30) REVERT: A 432 TYR cc_start: 0.8292 (OUTLIER) cc_final: 0.6713 (t80) REVERT: B 68 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9137 (mt) REVERT: B 282 ARG cc_start: 0.8492 (ttm-80) cc_final: 0.7938 (ttm170) REVERT: B 288 GLU cc_start: 0.8295 (tp30) cc_final: 0.7799 (tp30) REVERT: B 297 LYS cc_start: 0.8922 (mmtm) cc_final: 0.8718 (mmtm) REVERT: B 306 ARG cc_start: 0.8755 (mtt180) cc_final: 0.8451 (mtt180) REVERT: B 343 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8657 (mt-10) REVERT: B 391 ARG cc_start: 0.6704 (mtm180) cc_final: 0.5567 (mtm180) REVERT: K 23 ASP cc_start: 0.7429 (t0) cc_final: 0.6880 (t0) REVERT: K 81 MET cc_start: 0.7865 (mmp) cc_final: 0.7328 (mmm) REVERT: K 166 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8806 (mm) REVERT: K 180 ASP cc_start: 0.9123 (t0) cc_final: 0.8824 (t0) REVERT: K 182 SER cc_start: 0.9262 (t) cc_final: 0.8835 (p) outliers start: 30 outliers final: 18 residues processed: 160 average time/residue: 0.1005 time to fit residues: 22.3718 Evaluate side-chains 153 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 166 LEU Chi-restraints excluded: chain K residue 196 MET Chi-restraints excluded: chain K residue 289 ASP Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain K residue 299 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 116 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 209 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.105721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.086921 restraints weight = 17071.724| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.16 r_work: 0.2970 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9947 Z= 0.144 Angle : 0.562 15.620 13495 Z= 0.280 Chirality : 0.044 0.266 1482 Planarity : 0.004 0.039 1756 Dihedral : 8.746 144.004 1489 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.75 % Allowed : 13.55 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.86 (0.25), residues: 1221 helix: 2.09 (0.24), residues: 496 sheet: 0.50 (0.36), residues: 227 loop : -0.98 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 339 TYR 0.030 0.001 TYR A 24 PHE 0.025 0.001 PHE K 225 TRP 0.013 0.001 TRP A 21 HIS 0.003 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9947) covalent geometry : angle 0.56230 (13495) hydrogen bonds : bond 0.03862 ( 470) hydrogen bonds : angle 4.28916 ( 1452) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8985 (mm) REVERT: A 102 ASN cc_start: 0.8714 (t0) cc_final: 0.8290 (t0) REVERT: A 108 TYR cc_start: 0.8812 (OUTLIER) cc_final: 0.7368 (p90) REVERT: A 123 ARG cc_start: 0.8368 (tpp-160) cc_final: 0.8097 (tpp-160) REVERT: A 212 ILE cc_start: 0.8687 (mt) cc_final: 0.8462 (mt) REVERT: A 276 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8690 (tp) REVERT: A 290 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8267 (mp0) REVERT: A 295 CYS cc_start: 0.8640 (m) cc_final: 0.8355 (m) REVERT: A 322 ASP cc_start: 0.9001 (t0) cc_final: 0.8752 (t0) REVERT: A 357 TYR cc_start: 0.9099 (m-80) cc_final: 0.8674 (m-80) REVERT: A 423 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8488 (mm-30) REVERT: A 432 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.6803 (t80) REVERT: B 282 ARG cc_start: 0.8493 (ttm-80) cc_final: 0.7688 (ttm170) REVERT: B 288 GLU cc_start: 0.8272 (tp30) cc_final: 0.7766 (tp30) REVERT: B 297 LYS cc_start: 0.8944 (mmtm) cc_final: 0.8744 (mmtm) REVERT: B 306 ARG cc_start: 0.8758 (mtt180) cc_final: 0.8462 (mtt180) REVERT: B 327 ASP cc_start: 0.8513 (t70) cc_final: 0.8110 (t0) REVERT: B 343 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8595 (mt-10) REVERT: B 391 ARG cc_start: 0.6681 (mtm180) cc_final: 0.5518 (mtm180) REVERT: K 23 ASP cc_start: 0.7424 (t0) cc_final: 0.6949 (t70) REVERT: K 81 MET cc_start: 0.7862 (mmp) cc_final: 0.7336 (mmm) REVERT: K 166 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8794 (mm) REVERT: K 180 ASP cc_start: 0.9119 (t0) cc_final: 0.8821 (t0) REVERT: K 182 SER cc_start: 0.9247 (t) cc_final: 0.8811 (p) outliers start: 29 outliers final: 16 residues processed: 162 average time/residue: 0.0984 time to fit residues: 22.2334 Evaluate side-chains 157 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 166 LEU Chi-restraints excluded: chain K residue 196 MET Chi-restraints excluded: chain K residue 289 ASP Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain K residue 299 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 107 optimal weight: 4.9990 chunk 70 optimal weight: 0.0270 chunk 112 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.106358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.087546 restraints weight = 16860.653| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.16 r_work: 0.2982 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9947 Z= 0.129 Angle : 0.566 13.540 13495 Z= 0.279 Chirality : 0.043 0.240 1482 Planarity : 0.004 0.046 1756 Dihedral : 8.680 145.050 1489 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.18 % Allowed : 14.22 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.91 (0.25), residues: 1221 helix: 2.17 (0.24), residues: 489 sheet: 0.53 (0.36), residues: 227 loop : -0.96 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 215 TYR 0.031 0.001 TYR A 24 PHE 0.028 0.001 PHE K 225 TRP 0.013 0.001 TRP A 21 HIS 0.003 0.001 HIS B 396 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9947) covalent geometry : angle 0.56575 (13495) hydrogen bonds : bond 0.03738 ( 470) hydrogen bonds : angle 4.24475 ( 1452) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9017 (mm) REVERT: A 102 ASN cc_start: 0.8681 (t0) cc_final: 0.8261 (t0) REVERT: A 108 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.7317 (p90) REVERT: A 123 ARG cc_start: 0.8347 (tpp-160) cc_final: 0.8098 (tpp-160) REVERT: A 141 PHE cc_start: 0.9220 (m-10) cc_final: 0.8624 (m-10) REVERT: A 212 ILE cc_start: 0.8652 (mt) cc_final: 0.8422 (mt) REVERT: A 276 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8668 (tp) REVERT: A 290 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8266 (mp0) REVERT: A 295 CYS cc_start: 0.8625 (m) cc_final: 0.8359 (m) REVERT: A 322 ASP cc_start: 0.9007 (t0) cc_final: 0.8756 (t0) REVERT: A 357 TYR cc_start: 0.9075 (m-80) cc_final: 0.8653 (m-80) REVERT: A 423 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8497 (mm-30) REVERT: A 432 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.6870 (t80) REVERT: B 282 ARG cc_start: 0.8488 (ttm-80) cc_final: 0.7907 (ttm170) REVERT: B 288 GLU cc_start: 0.8276 (tp30) cc_final: 0.7780 (tp30) REVERT: B 297 LYS cc_start: 0.8929 (mmtm) cc_final: 0.8724 (mmtm) REVERT: B 306 ARG cc_start: 0.8787 (mtt180) cc_final: 0.8488 (mtt180) REVERT: B 327 ASP cc_start: 0.8463 (t70) cc_final: 0.8160 (t0) REVERT: B 343 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8568 (mt-10) REVERT: B 391 ARG cc_start: 0.6677 (mtm180) cc_final: 0.5492 (mtm180) REVERT: K 23 ASP cc_start: 0.7390 (t0) cc_final: 0.6905 (t70) REVERT: K 81 MET cc_start: 0.7874 (mmp) cc_final: 0.7351 (mmm) REVERT: K 166 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8759 (mm) REVERT: K 180 ASP cc_start: 0.9124 (t0) cc_final: 0.8816 (t0) REVERT: K 182 SER cc_start: 0.9245 (t) cc_final: 0.8798 (p) outliers start: 23 outliers final: 15 residues processed: 159 average time/residue: 0.1016 time to fit residues: 22.3357 Evaluate side-chains 158 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 166 LEU Chi-restraints excluded: chain K residue 196 MET Chi-restraints excluded: chain K residue 289 ASP Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain K residue 299 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 41 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 79 optimal weight: 0.0670 chunk 58 optimal weight: 0.9980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 59 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.107912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.089054 restraints weight = 16973.065| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 3.16 r_work: 0.3013 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9947 Z= 0.116 Angle : 0.557 12.762 13495 Z= 0.277 Chirality : 0.043 0.217 1482 Planarity : 0.004 0.042 1756 Dihedral : 8.608 145.773 1489 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.09 % Allowed : 14.50 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.96 (0.24), residues: 1221 helix: 2.22 (0.24), residues: 489 sheet: 0.60 (0.36), residues: 221 loop : -0.95 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 339 TYR 0.030 0.001 TYR A 24 PHE 0.028 0.001 PHE K 225 TRP 0.015 0.001 TRP A 21 HIS 0.003 0.001 HIS B 396 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9947) covalent geometry : angle 0.55748 (13495) hydrogen bonds : bond 0.03562 ( 470) hydrogen bonds : angle 4.18983 ( 1452) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9044 (mm) REVERT: A 102 ASN cc_start: 0.8660 (t0) cc_final: 0.8247 (t0) REVERT: A 108 TYR cc_start: 0.8657 (OUTLIER) cc_final: 0.7273 (p90) REVERT: A 212 ILE cc_start: 0.8644 (mt) cc_final: 0.8406 (mt) REVERT: A 276 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8670 (tp) REVERT: A 290 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8302 (mp0) REVERT: A 295 CYS cc_start: 0.8576 (m) cc_final: 0.8309 (m) REVERT: A 322 ASP cc_start: 0.8921 (t0) cc_final: 0.8689 (t0) REVERT: A 357 TYR cc_start: 0.9059 (m-80) cc_final: 0.8632 (m-80) REVERT: A 378 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.9043 (mt) REVERT: A 423 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8521 (mm-30) REVERT: A 432 TYR cc_start: 0.8257 (OUTLIER) cc_final: 0.6858 (t80) REVERT: B 68 LEU cc_start: 0.9543 (mt) cc_final: 0.9343 (mp) REVERT: B 282 ARG cc_start: 0.8496 (ttm-80) cc_final: 0.7904 (ttm170) REVERT: B 288 GLU cc_start: 0.8227 (tp30) cc_final: 0.7739 (tp30) REVERT: B 306 ARG cc_start: 0.8782 (mtt180) cc_final: 0.8478 (mtt180) REVERT: B 327 ASP cc_start: 0.8411 (t70) cc_final: 0.8061 (t0) REVERT: B 391 ARG cc_start: 0.6726 (mtm180) cc_final: 0.5472 (mtm180) REVERT: B 417 ASP cc_start: 0.8248 (m-30) cc_final: 0.7940 (m-30) REVERT: K 23 ASP cc_start: 0.7349 (t0) cc_final: 0.6855 (t70) REVERT: K 38 VAL cc_start: 0.8953 (t) cc_final: 0.8720 (m) REVERT: K 81 MET cc_start: 0.7923 (mmp) cc_final: 0.7401 (mmm) REVERT: K 166 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8750 (mm) REVERT: K 180 ASP cc_start: 0.9146 (t0) cc_final: 0.8840 (t0) REVERT: K 182 SER cc_start: 0.9201 (t) cc_final: 0.8765 (p) outliers start: 22 outliers final: 13 residues processed: 159 average time/residue: 0.0981 time to fit residues: 21.5199 Evaluate side-chains 159 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 166 LEU Chi-restraints excluded: chain K residue 196 MET Chi-restraints excluded: chain K residue 289 ASP Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain K residue 299 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 96 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 0.0470 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 0.2980 chunk 8 optimal weight: 0.0010 chunk 6 optimal weight: 1.9990 overall best weight: 0.4688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN K 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.108659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.089842 restraints weight = 16919.727| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.17 r_work: 0.3026 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9947 Z= 0.110 Angle : 0.555 11.787 13495 Z= 0.276 Chirality : 0.043 0.207 1482 Planarity : 0.004 0.040 1756 Dihedral : 8.550 146.094 1489 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.71 % Allowed : 15.73 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.97 (0.25), residues: 1221 helix: 2.20 (0.24), residues: 490 sheet: 0.58 (0.36), residues: 220 loop : -0.90 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 339 TYR 0.029 0.001 TYR A 24 PHE 0.029 0.001 PHE K 225 TRP 0.014 0.001 TRP A 21 HIS 0.004 0.001 HIS B 396 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 9947) covalent geometry : angle 0.55537 (13495) hydrogen bonds : bond 0.03460 ( 470) hydrogen bonds : angle 4.16096 ( 1452) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1923.35 seconds wall clock time: 33 minutes 55.03 seconds (2035.03 seconds total)