Starting phenix.real_space_refine on Sat Dec 28 03:56:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8avx_15686/12_2024/8avx_15686.cif Found real_map, /net/cci-nas-00/data/ceres_data/8avx_15686/12_2024/8avx_15686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8avx_15686/12_2024/8avx_15686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8avx_15686/12_2024/8avx_15686.map" model { file = "/net/cci-nas-00/data/ceres_data/8avx_15686/12_2024/8avx_15686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8avx_15686/12_2024/8avx_15686.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 4715 2.51 5 N 1327 2.21 5 O 1363 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7427 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3668 Classifications: {'peptide': 480} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 443} Chain breaks: 3 Chain: "B" Number of atoms: 3673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3673 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 444} Chain breaks: 2 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'BLA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'BLA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.17, per 1000 atoms: 0.83 Number of scatterers: 7427 At special positions: 0 Unit cell: (81.8615, 95.6487, 121.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 1363 8.00 N 1327 7.00 C 4715 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: 1.71 Conformation dependent library (CDL) restraints added in 1.1 seconds 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1774 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 7 sheets defined 41.6% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 73 through 78 Processing helix chain 'A' and resid 81 through 89 removed outlier: 4.440A pdb=" N ALA A 87 " --> pdb=" O PRO A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.524A pdb=" N PHE A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 Processing helix chain 'A' and resid 209 through 219 removed outlier: 3.578A pdb=" N LEU A 215 " --> pdb=" O GLN A 211 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 268 removed outlier: 3.749A pdb=" N MET A 267 " --> pdb=" O TYR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 342 removed outlier: 3.644A pdb=" N ARG A 302 " --> pdb=" O PRO A 298 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 321 " --> pdb=" O GLN A 317 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 324 " --> pdb=" O GLU A 320 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A 327 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN A 329 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLU A 333 " --> pdb=" O GLN A 329 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N HIS A 334 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG A 337 " --> pdb=" O GLU A 333 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A 338 " --> pdb=" O HIS A 334 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 352 removed outlier: 3.766A pdb=" N THR A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 352 " --> pdb=" O PRO A 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 347 through 352' Processing helix chain 'A' and resid 358 through 364 removed outlier: 4.164A pdb=" N LEU A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 398 removed outlier: 3.511A pdb=" N ALA A 390 " --> pdb=" O PRO A 386 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 393 " --> pdb=" O ASP A 389 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR A 397 " --> pdb=" O ALA A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 412 removed outlier: 3.950A pdb=" N LEU A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 474 removed outlier: 3.901A pdb=" N THR A 471 " --> pdb=" O HIS A 467 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR A 472 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 492 removed outlier: 3.625A pdb=" N GLU A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 503 through 521 removed outlier: 3.738A pdb=" N SER A 507 " --> pdb=" O GLY A 503 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 509 " --> pdb=" O ARG A 505 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 510 " --> pdb=" O LEU A 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 65 through 70 Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 81 through 89 removed outlier: 4.418A pdb=" N ALA B 87 " --> pdb=" O PRO B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 149 removed outlier: 3.522A pdb=" N PHE B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 168 Processing helix chain 'B' and resid 209 through 219 removed outlier: 3.581A pdb=" N LEU B 215 " --> pdb=" O GLN B 211 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 268 removed outlier: 3.751A pdb=" N MET B 267 " --> pdb=" O TYR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 342 removed outlier: 3.675A pdb=" N ARG B 302 " --> pdb=" O PRO B 298 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL B 318 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA B 321 " --> pdb=" O GLN B 317 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 324 " --> pdb=" O GLU B 320 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE B 327 " --> pdb=" O ASP B 323 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN B 329 " --> pdb=" O ALA B 325 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU B 331 " --> pdb=" O PHE B 327 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU B 333 " --> pdb=" O GLN B 329 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N HIS B 334 " --> pdb=" O SER B 330 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG B 337 " --> pdb=" O GLU B 333 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 338 " --> pdb=" O HIS B 334 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA B 341 " --> pdb=" O ARG B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 352 removed outlier: 3.766A pdb=" N THR B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 352 " --> pdb=" O PRO B 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 347 through 352' Processing helix chain 'B' and resid 358 through 364 removed outlier: 4.171A pdb=" N LEU B 362 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N MET B 363 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 398 removed outlier: 3.512A pdb=" N ALA B 390 " --> pdb=" O PRO B 386 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 393 " --> pdb=" O ASP B 389 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR B 397 " --> pdb=" O ALA B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 removed outlier: 3.948A pdb=" N LEU B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 474 removed outlier: 3.894A pdb=" N THR B 471 " --> pdb=" O HIS B 467 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR B 472 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 492 removed outlier: 3.624A pdb=" N GLU B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 503 through 521 removed outlier: 3.716A pdb=" N SER B 507 " --> pdb=" O GLY B 503 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL B 508 " --> pdb=" O GLU B 504 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE B 509 " --> pdb=" O ARG B 505 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG B 510 " --> pdb=" O LEU B 506 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35 removed outlier: 6.774A pdb=" N VAL A 51 " --> pdb=" O ASP A 45 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP A 45 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER A 55 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU A 41 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 103 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 203 removed outlier: 3.689A pdb=" N THR A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU A 175 " --> pdb=" O ILE A 187 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU A 189 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A 173 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 288 " --> pdb=" O MET A 174 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP A 284 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A 277 " --> pdb=" O TRP A 284 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU A 286 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL A 275 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA A 288 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 273 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 375 through 380 removed outlier: 4.585A pdb=" N GLU A 436 " --> pdb=" O VAL A 430 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 424 " --> pdb=" O ARG A 442 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA5, first strand: chain 'B' and resid 34 through 35 removed outlier: 6.775A pdb=" N VAL B 51 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP B 45 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 55 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU B 41 " --> pdb=" O SER B 55 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 103 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 202 through 203 removed outlier: 3.689A pdb=" N THR B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU B 175 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU B 189 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL B 173 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA B 288 " --> pdb=" O MET B 174 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TRP B 284 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL B 277 " --> pdb=" O TRP B 284 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU B 286 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL B 275 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA B 288 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU B 273 " --> pdb=" O ALA B 288 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 375 through 380 removed outlier: 4.568A pdb=" N GLU B 436 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY B 424 " --> pdb=" O ARG B 442 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 906 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: 2.25 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1481 1.33 - 1.45: 1744 1.45 - 1.57: 4349 1.57 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 7610 Sorted by residual: bond pdb=" C2B BLA B1000 " pdb=" C3B BLA B1000 " ideal model delta sigma weight residual 1.357 1.432 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C2B BLA A1000 " pdb=" C3B BLA A1000 " ideal model delta sigma weight residual 1.357 1.429 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C1D BLA A1000 " pdb=" CHD BLA A1000 " ideal model delta sigma weight residual 1.440 1.373 0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C2C BLA A1000 " pdb=" C3C BLA A1000 " ideal model delta sigma weight residual 1.351 1.415 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C1D BLA B1000 " pdb=" CHD BLA B1000 " ideal model delta sigma weight residual 1.440 1.377 0.063 2.00e-02 2.50e+03 1.00e+01 ... (remaining 7605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 8600 1.83 - 3.65: 1643 3.65 - 5.48: 156 5.48 - 7.30: 8 7.30 - 9.13: 3 Bond angle restraints: 10410 Sorted by residual: angle pdb=" C PHE B 203 " pdb=" CA PHE B 203 " pdb=" CB PHE B 203 " ideal model delta sigma weight residual 108.87 115.23 -6.36 1.55e+00 4.16e-01 1.68e+01 angle pdb=" C PHE A 203 " pdb=" CA PHE A 203 " pdb=" CB PHE A 203 " ideal model delta sigma weight residual 108.87 115.05 -6.18 1.55e+00 4.16e-01 1.59e+01 angle pdb=" CB ARG A 375 " pdb=" CG ARG A 375 " pdb=" CD ARG A 375 " ideal model delta sigma weight residual 111.30 120.43 -9.13 2.30e+00 1.89e-01 1.58e+01 angle pdb=" C PRO B 384 " pdb=" N ALA B 385 " pdb=" CA ALA B 385 " ideal model delta sigma weight residual 120.09 124.82 -4.73 1.25e+00 6.40e-01 1.43e+01 angle pdb=" C PRO A 384 " pdb=" N ALA A 385 " pdb=" CA ALA A 385 " ideal model delta sigma weight residual 120.09 124.79 -4.70 1.25e+00 6.40e-01 1.41e+01 ... (remaining 10405 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 3915 17.27 - 34.54: 440 34.54 - 51.80: 120 51.80 - 69.07: 71 69.07 - 86.34: 6 Dihedral angle restraints: 4552 sinusoidal: 1808 harmonic: 2744 Sorted by residual: dihedral pdb=" CA HIS B 219 " pdb=" C HIS B 219 " pdb=" N LEU B 220 " pdb=" CA LEU B 220 " ideal model delta harmonic sigma weight residual -180.00 -160.72 -19.28 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA HIS A 219 " pdb=" C HIS A 219 " pdb=" N LEU A 220 " pdb=" CA LEU A 220 " ideal model delta harmonic sigma weight residual -180.00 -160.76 -19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CG ARG B 514 " pdb=" CD ARG B 514 " pdb=" NE ARG B 514 " pdb=" CZ ARG B 514 " ideal model delta sinusoidal sigma weight residual 180.00 135.38 44.62 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 4549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 627 0.050 - 0.100: 285 0.100 - 0.151: 190 0.151 - 0.201: 54 0.201 - 0.251: 17 Chirality restraints: 1173 Sorted by residual: chirality pdb=" CB VAL A 237 " pdb=" CA VAL A 237 " pdb=" CG1 VAL A 237 " pdb=" CG2 VAL A 237 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB VAL A 449 " pdb=" CA VAL A 449 " pdb=" CG1 VAL A 449 " pdb=" CG2 VAL A 449 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ASN B 243 " pdb=" N ASN B 243 " pdb=" C ASN B 243 " pdb=" CB ASN B 243 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1170 not shown) Planarity restraints: 1364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C BLA B1000 " -0.001 2.00e-02 2.50e+03 2.84e-01 2.01e+03 pdb=" C1D BLA B1000 " 0.520 2.00e-02 2.50e+03 pdb=" C2C BLA B1000 " -0.007 2.00e-02 2.50e+03 pdb=" C3C BLA B1000 " -0.040 2.00e-02 2.50e+03 pdb=" C4C BLA B1000 " -0.264 2.00e-02 2.50e+03 pdb=" CAC BLA B1000 " 0.147 2.00e-02 2.50e+03 pdb=" CHD BLA B1000 " -0.254 2.00e-02 2.50e+03 pdb=" CMC BLA B1000 " 0.055 2.00e-02 2.50e+03 pdb=" NC BLA B1000 " -0.503 2.00e-02 2.50e+03 pdb=" OC BLA B1000 " 0.347 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB BLA B1000 " -0.384 2.00e-02 2.50e+03 2.82e-01 1.98e+03 pdb=" OB BLA B1000 " 0.184 2.00e-02 2.50e+03 pdb=" C1B BLA B1000 " -0.180 2.00e-02 2.50e+03 pdb=" C2B BLA B1000 " -0.174 2.00e-02 2.50e+03 pdb=" C3B BLA B1000 " 0.071 2.00e-02 2.50e+03 pdb=" C4A BLA B1000 " 0.543 2.00e-02 2.50e+03 pdb=" C4B BLA B1000 " -0.019 2.00e-02 2.50e+03 pdb=" CAB BLA B1000 " 0.348 2.00e-02 2.50e+03 pdb=" CHB BLA B1000 " -0.032 2.00e-02 2.50e+03 pdb=" CMB BLA B1000 " -0.357 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BLA A1000 " -0.034 2.00e-02 2.50e+03 2.78e-01 1.93e+03 pdb=" C1D BLA A1000 " 0.551 2.00e-02 2.50e+03 pdb=" C2C BLA A1000 " 0.033 2.00e-02 2.50e+03 pdb=" C3C BLA A1000 " -0.075 2.00e-02 2.50e+03 pdb=" C4C BLA A1000 " -0.247 2.00e-02 2.50e+03 pdb=" CAC BLA A1000 " 0.008 2.00e-02 2.50e+03 pdb=" CHD BLA A1000 " -0.175 2.00e-02 2.50e+03 pdb=" CMC BLA A1000 " 0.210 2.00e-02 2.50e+03 pdb=" NC BLA A1000 " -0.515 2.00e-02 2.50e+03 pdb=" OC BLA A1000 " 0.243 2.00e-02 2.50e+03 ... (remaining 1361 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1574 2.83 - 3.35: 6100 3.35 - 3.87: 11931 3.87 - 4.38: 13281 4.38 - 4.90: 23340 Nonbonded interactions: 56226 Sorted by model distance: nonbonded pdb=" O ALA A 107 " pdb=" N GLY A 109 " model vdw 2.316 3.120 nonbonded pdb=" O LEU B 516 " pdb=" OG SER B 519 " model vdw 2.584 3.040 nonbonded pdb=" O LEU A 516 " pdb=" OG SER A 519 " model vdw 2.585 3.040 nonbonded pdb=" O GLY A 39 " pdb=" ND2 ASN A 57 " model vdw 2.600 3.120 nonbonded pdb=" O GLY B 39 " pdb=" ND2 ASN B 57 " model vdw 2.601 3.120 ... (remaining 56221 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 22 through 107 or resid 109 through 521 or resid 1000)) } 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 group one per residue 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: 5.780 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.300 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 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 : 0.008 0.075 7610 Z= 0.516 Angle : 1.384 9.131 10410 Z= 0.921 Chirality : 0.079 0.251 1173 Planarity : 0.015 0.284 1364 Dihedral : 17.707 86.341 2778 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.54 % Favored : 95.25 % Rotamer: Outliers : 4.23 % Allowed : 11.64 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.22), residues: 947 helix: -3.67 (0.16), residues: 369 sheet: -1.34 (0.36), residues: 180 loop : -2.13 (0.26), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 451 HIS 0.006 0.002 HIS A 349 PHE 0.011 0.002 PHE B 170 TYR 0.030 0.003 TYR B 307 ARG 0.014 0.001 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6840 (mtp180) cc_final: 0.5248 (tpt170) REVERT: A 466 ARG cc_start: 0.4224 (OUTLIER) cc_final: 0.1647 (mmp80) REVERT: B 227 THR cc_start: 0.7630 (p) cc_final: 0.7188 (p) REVERT: B 381 GLU cc_start: 0.7836 (pm20) cc_final: 0.7243 (pp20) REVERT: B 493 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.7326 (t0) outliers start: 32 outliers final: 4 residues processed: 174 average time/residue: 0.2371 time to fit residues: 53.0080 Evaluate side-chains 94 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 493 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 56 optimal weight: 0.0370 chunk 87 optimal weight: 0.6980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 110 HIS A 239 ASN ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN B 290 HIS B 334 HIS B 335 HIS B 410 GLN B 513 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7610 Z= 0.212 Angle : 0.656 8.232 10410 Z= 0.309 Chirality : 0.041 0.132 1173 Planarity : 0.004 0.031 1364 Dihedral : 7.338 80.891 1103 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 5.03 % Allowed : 15.87 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.25), residues: 947 helix: -2.05 (0.23), residues: 372 sheet: -0.83 (0.36), residues: 193 loop : -1.44 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 434 HIS 0.008 0.002 HIS B 335 PHE 0.018 0.002 PHE B 126 TYR 0.018 0.002 TYR A 479 ARG 0.004 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 99 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6733 (mtp180) cc_final: 0.5200 (tpt170) REVERT: A 363 MET cc_start: 0.5922 (tpp) cc_final: 0.5477 (tpp) REVERT: A 466 ARG cc_start: 0.4274 (OUTLIER) cc_final: 0.1624 (mmt180) REVERT: B 45 ASP cc_start: 0.5808 (t70) cc_final: 0.5164 (m-30) REVERT: B 227 THR cc_start: 0.7585 (p) cc_final: 0.7354 (p) REVERT: B 259 MET cc_start: 0.7527 (mmt) cc_final: 0.7314 (ptp) REVERT: B 313 SER cc_start: 0.7871 (m) cc_final: 0.7611 (p) REVERT: B 381 GLU cc_start: 0.8048 (pm20) cc_final: 0.7610 (pp20) REVERT: B 493 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7300 (t0) outliers start: 38 outliers final: 10 residues processed: 131 average time/residue: 0.2173 time to fit residues: 37.8174 Evaluate side-chains 94 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 493 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 HIS A 262 GLN A 266 ASN B 57 ASN B 329 GLN B 398 GLN B 513 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7610 Z= 0.360 Angle : 0.796 10.215 10410 Z= 0.382 Chirality : 0.047 0.157 1173 Planarity : 0.006 0.040 1364 Dihedral : 7.408 58.926 1098 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 5.16 % Allowed : 20.63 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.25), residues: 947 helix: -1.82 (0.24), residues: 367 sheet: -0.69 (0.37), residues: 186 loop : -1.41 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 105 HIS 0.011 0.003 HIS A 344 PHE 0.022 0.003 PHE A 198 TYR 0.024 0.003 TYR B 295 ARG 0.006 0.001 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 91 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6853 (mtp180) cc_final: 0.5276 (tpt170) REVERT: A 113 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7509 (pp) REVERT: A 238 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7208 (mm) REVERT: A 261 MET cc_start: 0.6371 (mtm) cc_final: 0.6095 (mtm) REVERT: A 307 TYR cc_start: 0.7709 (m-10) cc_final: 0.7218 (m-80) REVERT: A 466 ARG cc_start: 0.4698 (OUTLIER) cc_final: 0.1662 (mmt180) REVERT: B 45 ASP cc_start: 0.6056 (t70) cc_final: 0.5377 (m-30) REVERT: B 177 LYS cc_start: 0.8120 (tptt) cc_final: 0.7783 (tptt) REVERT: B 357 LEU cc_start: 0.5248 (mp) cc_final: 0.4888 (mp) REVERT: B 381 GLU cc_start: 0.8122 (pm20) cc_final: 0.7782 (pp20) REVERT: B 432 GLU cc_start: 0.7584 (tp30) cc_final: 0.6627 (pt0) REVERT: B 441 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6411 (tp) REVERT: B 493 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.7074 (t0) outliers start: 39 outliers final: 19 residues processed: 121 average time/residue: 0.1952 time to fit residues: 32.2477 Evaluate side-chains 96 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 493 ASP Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 87 optimal weight: 0.1980 chunk 92 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 ASN B 329 GLN B 410 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7610 Z= 0.182 Angle : 0.625 9.563 10410 Z= 0.288 Chirality : 0.041 0.136 1173 Planarity : 0.005 0.040 1364 Dihedral : 6.552 63.201 1098 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.44 % Allowed : 22.22 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.26), residues: 947 helix: -1.11 (0.26), residues: 378 sheet: -0.61 (0.36), residues: 191 loop : -1.05 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 376 HIS 0.008 0.001 HIS A 484 PHE 0.021 0.002 PHE B 327 TYR 0.011 0.002 TYR A 479 ARG 0.004 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6833 (mtp180) cc_final: 0.5345 (tpt170) REVERT: A 199 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7403 (tt) REVERT: A 363 MET cc_start: 0.6751 (tpp) cc_final: 0.6531 (tpp) REVERT: A 466 ARG cc_start: 0.4751 (OUTLIER) cc_final: 0.1728 (mmt180) REVERT: B 45 ASP cc_start: 0.5762 (t70) cc_final: 0.5248 (m-30) REVERT: B 355 PRO cc_start: 0.6107 (Cg_exo) cc_final: 0.5899 (Cg_endo) REVERT: B 381 GLU cc_start: 0.8135 (pm20) cc_final: 0.7772 (pp20) REVERT: B 432 GLU cc_start: 0.7478 (tp30) cc_final: 0.6585 (pt0) REVERT: B 493 ASP cc_start: 0.7317 (OUTLIER) cc_final: 0.7112 (t0) outliers start: 26 outliers final: 16 residues processed: 99 average time/residue: 0.1991 time to fit residues: 26.9692 Evaluate side-chains 85 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 493 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 0.0970 chunk 38 optimal weight: 1.9990 chunk 79 optimal weight: 0.0270 chunk 64 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 31 optimal weight: 6.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 484 HIS B 398 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7610 Z= 0.165 Angle : 0.610 9.897 10410 Z= 0.277 Chirality : 0.041 0.138 1173 Planarity : 0.005 0.039 1364 Dihedral : 6.187 63.049 1098 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.38 % Allowed : 24.60 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.27), residues: 947 helix: -0.67 (0.27), residues: 376 sheet: -0.44 (0.36), residues: 185 loop : -0.88 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 284 HIS 0.012 0.001 HIS A 484 PHE 0.017 0.002 PHE B 327 TYR 0.016 0.002 TYR A 263 ARG 0.009 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6934 (mtp180) cc_final: 0.5500 (tpt170) REVERT: A 199 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7284 (tt) REVERT: B 45 ASP cc_start: 0.5637 (t70) cc_final: 0.4933 (m-30) REVERT: B 105 TRP cc_start: 0.6505 (m-10) cc_final: 0.6279 (m-10) REVERT: B 381 GLU cc_start: 0.8126 (pm20) cc_final: 0.7760 (pp20) REVERT: B 432 GLU cc_start: 0.7422 (tp30) cc_final: 0.6521 (pt0) outliers start: 18 outliers final: 12 residues processed: 86 average time/residue: 0.2318 time to fit residues: 26.2849 Evaluate side-chains 79 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 238 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 ASN B 57 ASN B 398 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 7610 Z= 0.393 Angle : 0.788 9.399 10410 Z= 0.375 Chirality : 0.047 0.208 1173 Planarity : 0.006 0.046 1364 Dihedral : 7.198 71.293 1096 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 5.56 % Allowed : 23.02 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.26), residues: 947 helix: -1.11 (0.26), residues: 371 sheet: -0.45 (0.37), residues: 184 loop : -1.36 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 284 HIS 0.018 0.002 HIS A 484 PHE 0.022 0.003 PHE A 327 TYR 0.028 0.003 TYR A 307 ARG 0.010 0.001 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 72 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.7001 (mtp180) cc_final: 0.5613 (tpt170) REVERT: A 138 HIS cc_start: 0.7187 (OUTLIER) cc_final: 0.6182 (t-90) REVERT: B 45 ASP cc_start: 0.5843 (t70) cc_final: 0.5471 (m-30) REVERT: B 357 LEU cc_start: 0.5659 (mp) cc_final: 0.5350 (mp) REVERT: B 381 GLU cc_start: 0.8084 (pm20) cc_final: 0.7733 (pp20) REVERT: B 432 GLU cc_start: 0.7397 (tp30) cc_final: 0.6985 (pt0) REVERT: B 441 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6413 (tt) outliers start: 42 outliers final: 28 residues processed: 104 average time/residue: 0.2121 time to fit residues: 29.5653 Evaluate side-chains 97 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 67 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 36 optimal weight: 0.0870 chunk 55 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 ASN B 116 HIS B 398 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.5699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7610 Z= 0.187 Angle : 0.641 9.445 10410 Z= 0.298 Chirality : 0.042 0.156 1173 Planarity : 0.005 0.041 1364 Dihedral : 6.569 71.475 1096 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.84 % Allowed : 24.60 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.27), residues: 947 helix: -0.61 (0.27), residues: 380 sheet: -0.35 (0.38), residues: 183 loop : -1.12 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 284 HIS 0.009 0.001 HIS A 484 PHE 0.014 0.002 PHE B 327 TYR 0.017 0.002 TYR A 263 ARG 0.008 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.7025 (mtp180) cc_final: 0.5641 (tpt170) REVERT: A 72 GLN cc_start: 0.6227 (OUTLIER) cc_final: 0.5929 (tt0) REVERT: A 138 HIS cc_start: 0.7060 (OUTLIER) cc_final: 0.6133 (t-90) REVERT: A 199 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7442 (tt) REVERT: B 381 GLU cc_start: 0.8082 (pm20) cc_final: 0.7672 (pp20) REVERT: B 432 GLU cc_start: 0.7423 (tp30) cc_final: 0.6802 (pt0) outliers start: 29 outliers final: 21 residues processed: 94 average time/residue: 0.2209 time to fit residues: 27.9913 Evaluate side-chains 88 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 64 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 441 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 0.0050 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 398 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.5804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7610 Z= 0.169 Angle : 0.619 9.419 10410 Z= 0.286 Chirality : 0.041 0.175 1173 Planarity : 0.005 0.043 1364 Dihedral : 6.176 66.967 1096 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.63 % Allowed : 24.47 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.27), residues: 947 helix: -0.37 (0.27), residues: 374 sheet: -0.29 (0.38), residues: 186 loop : -0.92 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 284 HIS 0.008 0.001 HIS A 484 PHE 0.013 0.001 PHE B 327 TYR 0.014 0.002 TYR A 479 ARG 0.006 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 69 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.7069 (mtp180) cc_final: 0.5678 (tpt170) REVERT: A 138 HIS cc_start: 0.6882 (OUTLIER) cc_final: 0.5779 (t-90) REVERT: A 199 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7414 (tt) REVERT: A 474 GLU cc_start: 0.3683 (tp30) cc_final: 0.3300 (mp0) REVERT: B 45 ASP cc_start: 0.5432 (OUTLIER) cc_final: 0.5165 (t70) REVERT: B 381 GLU cc_start: 0.8074 (pm20) cc_final: 0.7658 (pp20) REVERT: B 432 GLU cc_start: 0.7358 (tp30) cc_final: 0.6680 (pt0) outliers start: 35 outliers final: 25 residues processed: 98 average time/residue: 0.2209 time to fit residues: 29.1448 Evaluate side-chains 93 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 479 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 8.9990 chunk 88 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 67 optimal weight: 0.1980 chunk 26 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 0.0050 chunk 91 optimal weight: 1.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 398 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.5950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7610 Z= 0.193 Angle : 0.631 9.504 10410 Z= 0.294 Chirality : 0.042 0.183 1173 Planarity : 0.005 0.045 1364 Dihedral : 6.184 60.513 1096 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.37 % Allowed : 24.87 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.27), residues: 947 helix: -0.27 (0.27), residues: 373 sheet: -0.32 (0.37), residues: 187 loop : -0.88 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 284 HIS 0.006 0.001 HIS A 484 PHE 0.013 0.002 PHE B 327 TYR 0.010 0.002 TYR B 295 ARG 0.006 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 67 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.7100 (mtp180) cc_final: 0.5699 (tpt170) REVERT: A 72 GLN cc_start: 0.6292 (OUTLIER) cc_final: 0.6023 (tt0) REVERT: A 474 GLU cc_start: 0.3846 (tp30) cc_final: 0.3455 (mp0) REVERT: B 381 GLU cc_start: 0.8085 (pm20) cc_final: 0.7653 (pp20) REVERT: B 432 GLU cc_start: 0.7380 (tp30) cc_final: 0.6874 (pt0) outliers start: 33 outliers final: 29 residues processed: 93 average time/residue: 0.2263 time to fit residues: 28.6135 Evaluate side-chains 96 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 376 TRP Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 0.0040 chunk 46 optimal weight: 0.9990 chunk 60 optimal weight: 0.0070 chunk 81 optimal weight: 3.9990 overall best weight: 0.5612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 HIS B 398 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.6058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7610 Z= 0.173 Angle : 0.620 9.666 10410 Z= 0.285 Chirality : 0.041 0.195 1173 Planarity : 0.005 0.046 1364 Dihedral : 6.163 74.802 1096 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.37 % Allowed : 24.60 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.28), residues: 947 helix: -0.08 (0.28), residues: 367 sheet: -0.27 (0.38), residues: 186 loop : -0.73 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 284 HIS 0.005 0.001 HIS A 484 PHE 0.013 0.001 PHE B 327 TYR 0.009 0.001 TYR A 307 ARG 0.005 0.000 ARG A 202 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 67 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.7153 (mtp180) cc_final: 0.5776 (tpt170) REVERT: A 72 GLN cc_start: 0.6275 (OUTLIER) cc_final: 0.6002 (tt0) REVERT: A 376 TRP cc_start: 0.6978 (p-90) cc_final: 0.5701 (p-90) REVERT: A 474 GLU cc_start: 0.3866 (tp30) cc_final: 0.3539 (mp0) REVERT: B 45 ASP cc_start: 0.5422 (OUTLIER) cc_final: 0.5194 (t70) REVERT: B 381 GLU cc_start: 0.8101 (pm20) cc_final: 0.7651 (pp20) REVERT: B 432 GLU cc_start: 0.7273 (tp30) cc_final: 0.6703 (pt0) outliers start: 33 outliers final: 30 residues processed: 92 average time/residue: 0.2078 time to fit residues: 25.4903 Evaluate side-chains 98 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 66 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.0670 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 398 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.181520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.159318 restraints weight = 13495.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.162304 restraints weight = 8315.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.162995 restraints weight = 5690.026| |-----------------------------------------------------------------------------| r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.6088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7610 Z= 0.204 Angle : 0.629 9.469 10410 Z= 0.292 Chirality : 0.042 0.189 1173 Planarity : 0.005 0.046 1364 Dihedral : 6.251 79.039 1096 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.23 % Allowed : 24.87 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.28), residues: 947 helix: -0.05 (0.28), residues: 367 sheet: -0.39 (0.36), residues: 196 loop : -0.72 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 284 HIS 0.005 0.001 HIS A 484 PHE 0.013 0.001 PHE A 203 TYR 0.010 0.002 TYR B 295 ARG 0.005 0.000 ARG A 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1924.08 seconds wall clock time: 36 minutes 8.26 seconds (2168.26 seconds total)