Starting phenix.real_space_refine on Wed Mar 12 15:27:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8avv_15684/03_2025/8avv_15684.cif Found real_map, /net/cci-nas-00/data/ceres_data/8avv_15684/03_2025/8avv_15684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8avv_15684/03_2025/8avv_15684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8avv_15684/03_2025/8avv_15684.map" model { file = "/net/cci-nas-00/data/ceres_data/8avv_15684/03_2025/8avv_15684.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8avv_15684/03_2025/8avv_15684.cif" } resolution = 3.4 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= 0.022 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 4958 2.51 5 N 1378 2.21 5 O 1436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7794 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3849 Classifications: {'peptide': 504} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 463} Chain breaks: 2 Chain: "B" Number of atoms: 3859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3859 Classifications: {'peptide': 506} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 465} Chain breaks: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.34, per 1000 atoms: 0.81 Number of scatterers: 7794 At special positions: 0 Unit cell: (93.0636, 98.2338, 115.468, 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 1436 8.00 N 1378 7.00 C 4958 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: 1.82 Conformation dependent library (CDL) restraints added in 896.9 milliseconds 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1856 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 36.8% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 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: 3.645A pdb=" N ALA A 87 " --> pdb=" O PRO A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 148 removed outlier: 3.592A pdb=" N GLU A 148 " --> pdb=" O MET A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 169 removed outlier: 3.518A pdb=" N THR A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 257 through 267 removed outlier: 3.520A pdb=" N GLN A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 328 removed outlier: 3.619A pdb=" N THR A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 314 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLN A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 342 removed outlier: 3.753A pdb=" N VAL A 338 " --> pdb=" O HIS A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 352 removed outlier: 3.572A pdb=" N THR A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 396 removed outlier: 3.769A pdb=" N ASP A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 412 removed outlier: 4.159A pdb=" N LEU A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 416 Processing helix chain 'A' and resid 455 through 460 removed outlier: 3.867A pdb=" N ALA A 459 " --> pdb=" O PRO A 456 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS A 460 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 501 removed outlier: 3.610A pdb=" N ILE A 488 " --> pdb=" O HIS A 484 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 496 " --> pdb=" O GLN A 492 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 497 " --> pdb=" O ASP A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 519 removed outlier: 3.664A pdb=" N ARG A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP A 511 " --> pdb=" O SER A 507 " (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: 3.643A pdb=" N ALA B 87 " --> pdb=" O PRO B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 148 removed outlier: 3.583A pdb=" N GLU B 148 " --> pdb=" O MET B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 169 removed outlier: 3.525A pdb=" N THR B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 257 through 267 removed outlier: 3.518A pdb=" N GLN B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 328 removed outlier: 3.617A pdb=" N THR B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 314 " --> pdb=" O ARG B 310 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLN B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 318 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 342 removed outlier: 3.746A pdb=" N VAL B 338 " --> pdb=" O HIS B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 352 removed outlier: 3.578A pdb=" N THR B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 396 removed outlier: 3.773A pdb=" N ASP B 389 " --> pdb=" O ALA B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 removed outlier: 4.159A pdb=" N LEU B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 416 Processing helix chain 'B' and resid 455 through 460 removed outlier: 3.868A pdb=" N ALA B 459 " --> pdb=" O PRO B 456 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS B 460 " --> pdb=" O ASP B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 501 removed outlier: 3.615A pdb=" N ILE B 488 " --> pdb=" O HIS B 484 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP B 493 " --> pdb=" O GLU B 489 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 494 " --> pdb=" O GLU B 490 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP B 496 " --> pdb=" O GLN B 492 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B 497 " --> pdb=" O ASP B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 519 removed outlier: 3.683A pdb=" N ARG B 505 " --> pdb=" O ALA B 501 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP B 511 " --> pdb=" O SER B 507 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35 removed outlier: 6.493A pdb=" N THR A 43 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N MET A 54 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU A 41 " --> pdb=" O MET A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.962A pdb=" N LEU A 175 " --> pdb=" O ILE A 187 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLU A 189 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL A 173 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TRP A 284 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LEU A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL A 279 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 285 " --> pdb=" O VAL A 277 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 238 through 239 removed outlier: 3.548A pdb=" N ALA A 244 " --> pdb=" O ASN A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 375 through 380 removed outlier: 3.528A pdb=" N PHE A 372 " --> pdb=" O ARG A 375 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 445 through 452 removed outlier: 4.616A pdb=" N TYR A 479 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N LEU A 447 " --> pdb=" O ARG A 477 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ARG A 477 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL A 449 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLU A 475 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TRP A 451 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LEU A 473 " --> pdb=" O TRP A 451 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 34 through 35 removed outlier: 6.498A pdb=" N THR B 43 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N MET B 54 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 41 " --> pdb=" O MET B 54 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.974A pdb=" N LEU B 175 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLU B 189 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL B 173 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TRP B 284 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU B 283 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL B 279 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY B 285 " --> pdb=" O VAL B 277 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 238 through 239 removed outlier: 3.538A pdb=" N ALA B 244 " --> pdb=" O ASN B 239 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 375 through 380 removed outlier: 3.529A pdb=" N PHE B 372 " --> pdb=" O ARG B 375 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 445 through 452 removed outlier: 4.557A pdb=" N TYR B 479 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N LEU B 447 " --> pdb=" O ARG B 477 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ARG B 477 " --> pdb=" O LEU B 447 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL B 449 " --> pdb=" O GLU B 475 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLU B 475 " --> pdb=" O VAL B 449 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N TRP B 451 " --> pdb=" O LEU B 473 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU B 473 " --> pdb=" O TRP B 451 " (cutoff:3.500A) 336 hydrogen bonds defined for protein. 918 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: 2.21 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1984 1.34 - 1.46: 2367 1.46 - 1.58: 3608 1.58 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 7995 Sorted by residual: bond pdb=" C2D LBV A1000 " pdb=" C3D LBV A1000 " ideal model delta sigma weight residual 1.358 1.435 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C2D LBV B1000 " pdb=" C3D LBV B1000 " ideal model delta sigma weight residual 1.358 1.432 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C3A LBV B1000 " pdb=" C4A LBV B1000 " ideal model delta sigma weight residual 1.463 1.392 0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C4C LBV B1000 " pdb=" CHD LBV B1000 " ideal model delta sigma weight residual 1.428 1.360 0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C4C LBV A1000 " pdb=" CHD LBV A1000 " ideal model delta sigma weight residual 1.428 1.363 0.065 2.00e-02 2.50e+03 1.05e+01 ... (remaining 7990 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 8756 1.69 - 3.37: 1910 3.37 - 5.06: 255 5.06 - 6.75: 18 6.75 - 8.43: 4 Bond angle restraints: 10943 Sorted by residual: angle pdb=" N LEU B 346 " pdb=" CA LEU B 346 " pdb=" C LEU B 346 " ideal model delta sigma weight residual 114.31 108.90 5.41 1.29e+00 6.01e-01 1.76e+01 angle pdb=" N LEU A 346 " pdb=" CA LEU A 346 " pdb=" C LEU A 346 " ideal model delta sigma weight residual 114.31 109.14 5.17 1.29e+00 6.01e-01 1.61e+01 angle pdb=" C LEU A 297 " pdb=" N PRO A 298 " pdb=" CA PRO A 298 " ideal model delta sigma weight residual 119.66 122.50 -2.84 7.20e-01 1.93e+00 1.56e+01 angle pdb=" C GLN B 398 " pdb=" CA GLN B 398 " pdb=" CB GLN B 398 " ideal model delta sigma weight residual 109.26 114.91 -5.65 1.47e+00 4.63e-01 1.48e+01 angle pdb=" C GLN A 398 " pdb=" CA GLN A 398 " pdb=" CB GLN A 398 " ideal model delta sigma weight residual 109.26 114.88 -5.62 1.47e+00 4.63e-01 1.46e+01 ... (remaining 10938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.78: 4031 15.78 - 31.55: 464 31.55 - 47.32: 181 47.32 - 63.10: 54 63.10 - 78.87: 41 Dihedral angle restraints: 4771 sinusoidal: 1892 harmonic: 2879 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 -157.73 -22.27 0 5.00e+00 4.00e-02 1.98e+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 -157.74 -22.26 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA MET B 54 " pdb=" C MET B 54 " pdb=" N SER B 55 " pdb=" CA SER B 55 " ideal model delta harmonic sigma weight residual 180.00 159.38 20.62 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 4768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 665 0.055 - 0.110: 337 0.110 - 0.165: 165 0.165 - 0.221: 55 0.221 - 0.276: 8 Chirality restraints: 1230 Sorted by residual: chirality pdb=" CA ARG B 337 " pdb=" N ARG B 337 " pdb=" C ARG B 337 " pdb=" CB ARG B 337 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA ASN A 243 " pdb=" N ASN A 243 " pdb=" C ASN A 243 " pdb=" CB ASN A 243 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+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 2.26 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1227 not shown) Planarity restraints: 1437 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D LBV B1000 " 0.021 2.00e-02 2.50e+03 2.03e-01 9.27e+02 pdb=" C2D LBV B1000 " -0.088 2.00e-02 2.50e+03 pdb=" C3D LBV B1000 " 0.053 2.00e-02 2.50e+03 pdb=" C4D LBV B1000 " -0.071 2.00e-02 2.50e+03 pdb=" CAD LBV B1000 " 0.269 2.00e-02 2.50e+03 pdb=" CHD LBV B1000 " 0.362 2.00e-02 2.50e+03 pdb=" CMD LBV B1000 " -0.265 2.00e-02 2.50e+03 pdb=" N_D LBV B1000 " -0.285 2.00e-02 2.50e+03 pdb=" O_D LBV B1000 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D LBV A1000 " 0.024 2.00e-02 2.50e+03 1.68e-01 6.32e+02 pdb=" C2D LBV A1000 " 0.055 2.00e-02 2.50e+03 pdb=" C3D LBV A1000 " -0.003 2.00e-02 2.50e+03 pdb=" C4D LBV A1000 " 0.040 2.00e-02 2.50e+03 pdb=" CAD LBV A1000 " -0.101 2.00e-02 2.50e+03 pdb=" CHD LBV A1000 " -0.290 2.00e-02 2.50e+03 pdb=" CMD LBV A1000 " 0.089 2.00e-02 2.50e+03 pdb=" N_D LBV A1000 " 0.346 2.00e-02 2.50e+03 pdb=" O_D LBV A1000 " -0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C LBV A1000 " 0.033 2.00e-02 2.50e+03 1.36e-01 4.17e+02 pdb=" C2C LBV A1000 " -0.009 2.00e-02 2.50e+03 pdb=" C3C LBV A1000 " 0.019 2.00e-02 2.50e+03 pdb=" C4C LBV A1000 " 0.011 2.00e-02 2.50e+03 pdb=" CAC LBV A1000 " -0.048 2.00e-02 2.50e+03 pdb=" CHC LBV A1000 " -0.148 2.00e-02 2.50e+03 pdb=" CHD LBV A1000 " -0.217 2.00e-02 2.50e+03 pdb=" CMC LBV A1000 " 0.058 2.00e-02 2.50e+03 pdb=" N_C LBV A1000 " 0.301 2.00e-02 2.50e+03 ... (remaining 1434 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.04: 3437 3.04 - 3.51: 7725 3.51 - 3.97: 11916 3.97 - 4.44: 13620 4.44 - 4.90: 22326 Nonbonded interactions: 59024 Sorted by model distance: nonbonded pdb=" O ARG A 514 " pdb=" OG1 THR A 517 " model vdw 2.580 3.040 nonbonded pdb=" O ARG B 514 " pdb=" OG1 THR B 517 " model vdw 2.581 3.040 nonbonded pdb=" N ALA B 401 " pdb=" N LEU B 402 " model vdw 2.618 2.560 nonbonded pdb=" N HIS B 344 " pdb=" N SER B 345 " model vdw 2.619 2.560 nonbonded pdb=" OD2 ASP B 45 " pdb=" N SER B 48 " model vdw 2.620 3.120 ... (remaining 59019 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 7 through 106 or resid 109 through 519 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 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: 7.040 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.190 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 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 0.077 7995 Z= 0.507 Angle : 1.381 8.435 10943 Z= 0.921 Chirality : 0.081 0.276 1230 Planarity : 0.009 0.203 1437 Dihedral : 18.227 78.875 2915 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.70 % Favored : 95.10 % Rotamer: Outliers : 5.03 % Allowed : 12.94 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -3.08 (0.22), residues: 1000 helix: -3.09 (0.22), residues: 316 sheet: 0.12 (0.37), residues: 174 loop : -2.11 (0.22), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 412 HIS 0.008 0.002 HIS B 484 PHE 0.016 0.003 PHE A 170 TYR 0.016 0.002 TYR A 263 ARG 0.004 0.001 ARG B 154 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7002 (pm20) REVERT: A 148 GLU cc_start: 0.8703 (mt-10) cc_final: 0.7809 (mp0) REVERT: A 154 ARG cc_start: 0.8383 (ptt180) cc_final: 0.7959 (tpt-90) REVERT: A 218 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7740 (tpt-90) REVERT: A 259 MET cc_start: 0.8754 (tpp) cc_final: 0.8541 (mmm) REVERT: A 261 MET cc_start: 0.7975 (mmm) cc_final: 0.7718 (mtt) REVERT: A 340 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7668 (tt) REVERT: A 408 LEU cc_start: 0.7990 (tp) cc_final: 0.7724 (tt) REVERT: A 493 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.8079 (m-30) REVERT: B 31 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8425 (pt) REVERT: B 261 MET cc_start: 0.8331 (mmm) cc_final: 0.8114 (mtp) REVERT: B 282 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7584 (mm-40) REVERT: B 317 GLN cc_start: 0.8582 (mt0) cc_final: 0.8308 (tt0) REVERT: B 363 MET cc_start: 0.8898 (mmt) cc_final: 0.8504 (mmt) REVERT: B 411 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8298 (tp) outliers start: 40 outliers final: 16 residues processed: 158 average time/residue: 0.2574 time to fit residues: 51.9725 Evaluate side-chains 100 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 218 ARG Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 58 optimal weight: 0.0070 chunk 90 optimal weight: 0.8980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 290 HIS A 349 HIS B 72 GLN B 266 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.148809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.123207 restraints weight = 10494.466| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.76 r_work: 0.3135 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7995 Z= 0.210 Angle : 0.658 9.041 10943 Z= 0.327 Chirality : 0.042 0.149 1230 Planarity : 0.005 0.034 1437 Dihedral : 8.876 83.400 1178 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.14 % Allowed : 16.08 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.41 (0.24), residues: 1000 helix: -1.08 (0.27), residues: 320 sheet: 0.40 (0.34), residues: 185 loop : -1.32 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 82 HIS 0.005 0.001 HIS A 334 PHE 0.009 0.001 PHE B 170 TYR 0.019 0.002 TYR A 307 ARG 0.005 0.001 ARG B 332 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6715 (pm20) REVERT: A 218 ARG cc_start: 0.8541 (ttm-80) cc_final: 0.7807 (mmm160) REVERT: A 243 ASN cc_start: 0.7981 (t0) cc_final: 0.7777 (t0) REVERT: B 31 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8713 (pt) REVERT: B 154 ARG cc_start: 0.8302 (mmm-85) cc_final: 0.8018 (ttm-80) REVERT: B 282 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7368 (mm-40) REVERT: B 311 LEU cc_start: 0.8076 (mt) cc_final: 0.7806 (mt) outliers start: 25 outliers final: 12 residues processed: 112 average time/residue: 0.2671 time to fit residues: 38.5898 Evaluate side-chains 84 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 506 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 0.1980 chunk 76 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 19 optimal weight: 0.0980 chunk 8 optimal weight: 0.0670 chunk 30 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 70 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 0.2718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 ASN B 291 HIS B 329 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.150921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.124706 restraints weight = 10517.700| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.02 r_work: 0.3181 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7995 Z= 0.134 Angle : 0.530 6.971 10943 Z= 0.258 Chirality : 0.040 0.167 1230 Planarity : 0.004 0.030 1437 Dihedral : 7.093 81.803 1149 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.88 % Allowed : 17.46 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.25), residues: 1000 helix: 0.26 (0.29), residues: 319 sheet: 0.82 (0.37), residues: 158 loop : -1.05 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 82 HIS 0.003 0.001 HIS A 334 PHE 0.005 0.001 PHE B 327 TYR 0.023 0.001 TYR A 176 ARG 0.005 0.000 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6745 (pm20) REVERT: A 218 ARG cc_start: 0.8583 (ttm-80) cc_final: 0.7885 (mtp85) REVERT: A 222 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7270 (pmm150) REVERT: A 243 ASN cc_start: 0.8071 (t0) cc_final: 0.7739 (t0) REVERT: A 514 ARG cc_start: 0.8549 (tpp80) cc_final: 0.8272 (tpp-160) REVERT: B 24 CYS cc_start: 0.7696 (p) cc_final: 0.7293 (m) REVERT: B 154 ARG cc_start: 0.8308 (mmm-85) cc_final: 0.7988 (ttm-80) REVERT: B 222 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7028 (pmm150) REVERT: B 282 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7744 (tm-30) REVERT: B 311 LEU cc_start: 0.8051 (mt) cc_final: 0.7799 (mt) REVERT: B 411 LEU cc_start: 0.8545 (mp) cc_final: 0.8297 (tp) outliers start: 15 outliers final: 9 residues processed: 89 average time/residue: 0.2817 time to fit residues: 32.3921 Evaluate side-chains 81 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 37 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 94 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.145258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.116834 restraints weight = 10633.067| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.99 r_work: 0.3193 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7995 Z= 0.294 Angle : 0.612 8.822 10943 Z= 0.297 Chirality : 0.044 0.197 1230 Planarity : 0.005 0.042 1437 Dihedral : 7.226 85.304 1144 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.14 % Allowed : 17.84 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.25), residues: 1000 helix: 0.28 (0.29), residues: 327 sheet: 0.96 (0.39), residues: 158 loop : -1.02 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 82 HIS 0.007 0.001 HIS A 334 PHE 0.008 0.001 PHE B 469 TYR 0.017 0.002 TYR B 176 ARG 0.006 0.000 ARG B 332 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6781 (pm20) REVERT: A 218 ARG cc_start: 0.8600 (ttm-80) cc_final: 0.7784 (mtp85) REVERT: A 222 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7321 (pmm150) REVERT: B 154 ARG cc_start: 0.8494 (mmm-85) cc_final: 0.8093 (ttm-80) REVERT: B 222 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7385 (pmm150) REVERT: B 282 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7759 (tm-30) REVERT: B 311 LEU cc_start: 0.8097 (mt) cc_final: 0.7853 (mt) REVERT: B 510 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6479 (mtm110) outliers start: 25 outliers final: 14 residues processed: 100 average time/residue: 0.2702 time to fit residues: 34.5133 Evaluate side-chains 88 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 510 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.0570 chunk 48 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 291 HIS A 317 GLN B 72 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.145794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.116328 restraints weight = 10654.999| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.12 r_work: 0.3184 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7995 Z= 0.165 Angle : 0.522 5.662 10943 Z= 0.255 Chirality : 0.041 0.188 1230 Planarity : 0.004 0.038 1437 Dihedral : 6.719 85.886 1140 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.64 % Allowed : 18.84 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.03 (0.26), residues: 1000 helix: 0.68 (0.29), residues: 329 sheet: 1.14 (0.38), residues: 169 loop : -0.81 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 451 HIS 0.004 0.001 HIS B 38 PHE 0.006 0.001 PHE B 327 TYR 0.013 0.001 TYR B 176 ARG 0.005 0.000 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6750 (pm20) REVERT: A 85 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8046 (mt) REVERT: A 218 ARG cc_start: 0.8601 (ttm-80) cc_final: 0.7732 (mtp85) REVERT: A 222 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7254 (pmm150) REVERT: A 514 ARG cc_start: 0.8549 (tpp80) cc_final: 0.8169 (tpp-160) REVERT: B 24 CYS cc_start: 0.7642 (p) cc_final: 0.7220 (m) REVERT: B 154 ARG cc_start: 0.8376 (mmm-85) cc_final: 0.8051 (ttm-80) REVERT: B 282 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7623 (tm-30) REVERT: B 311 LEU cc_start: 0.7985 (mt) cc_final: 0.7726 (mt) outliers start: 21 outliers final: 8 residues processed: 91 average time/residue: 0.2472 time to fit residues: 29.6417 Evaluate side-chains 82 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 506 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 90 optimal weight: 0.0970 chunk 40 optimal weight: 5.9990 chunk 7 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.146688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.118768 restraints weight = 10526.668| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.95 r_work: 0.3143 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 7995 Z= 0.164 Angle : 0.522 9.485 10943 Z= 0.252 Chirality : 0.040 0.188 1230 Planarity : 0.004 0.035 1437 Dihedral : 6.606 86.061 1140 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.89 % Allowed : 19.10 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.26), residues: 1000 helix: 1.06 (0.29), residues: 331 sheet: 1.28 (0.39), residues: 170 loop : -0.73 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 284 HIS 0.004 0.001 HIS B 38 PHE 0.006 0.001 PHE A 198 TYR 0.013 0.001 TYR B 176 ARG 0.007 0.000 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 1.140 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6733 (pm20) REVERT: A 85 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8050 (mt) REVERT: A 218 ARG cc_start: 0.8529 (ttm-80) cc_final: 0.7672 (mtp85) REVERT: A 222 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7144 (pmm150) REVERT: A 514 ARG cc_start: 0.8504 (tpp80) cc_final: 0.8110 (tpp-160) REVERT: B 154 ARG cc_start: 0.8368 (mmm-85) cc_final: 0.8050 (ttm-80) REVERT: B 222 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7059 (pmm150) REVERT: B 282 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7586 (tm-30) REVERT: B 311 LEU cc_start: 0.7990 (mt) cc_final: 0.7737 (mt) REVERT: B 510 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6482 (mtm110) outliers start: 23 outliers final: 14 residues processed: 97 average time/residue: 0.2633 time to fit residues: 33.1874 Evaluate side-chains 88 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 510 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 89 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 8 optimal weight: 0.3980 chunk 46 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.144424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.117308 restraints weight = 10578.770| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.99 r_work: 0.3126 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7995 Z= 0.280 Angle : 0.598 8.822 10943 Z= 0.290 Chirality : 0.043 0.188 1230 Planarity : 0.005 0.043 1437 Dihedral : 6.978 88.828 1140 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.39 % Allowed : 19.97 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.07 (0.26), residues: 1000 helix: 0.70 (0.29), residues: 332 sheet: 0.94 (0.38), residues: 180 loop : -0.72 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 284 HIS 0.006 0.001 HIS A 334 PHE 0.010 0.001 PHE B 469 TYR 0.018 0.002 TYR A 176 ARG 0.004 0.000 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6736 (pm20) REVERT: A 85 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8078 (mt) REVERT: A 218 ARG cc_start: 0.8571 (ttm-80) cc_final: 0.7655 (mtp85) REVERT: A 222 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7274 (pmm150) REVERT: A 514 ARG cc_start: 0.8586 (tpp80) cc_final: 0.8101 (tpp-160) REVERT: B 26 ARG cc_start: 0.7156 (mtp180) cc_final: 0.6831 (mmm160) REVERT: B 154 ARG cc_start: 0.8471 (mmm-85) cc_final: 0.8160 (ttm-80) REVERT: B 222 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7444 (pmm150) REVERT: B 311 LEU cc_start: 0.8051 (mt) cc_final: 0.7798 (mt) REVERT: B 510 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6381 (mtm110) outliers start: 27 outliers final: 18 residues processed: 93 average time/residue: 0.2541 time to fit residues: 30.7794 Evaluate side-chains 88 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 510 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 2 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS B 266 ASN B 458 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.142414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.114214 restraints weight = 10737.696| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.96 r_work: 0.3113 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 7995 Z= 0.374 Angle : 0.661 8.972 10943 Z= 0.320 Chirality : 0.045 0.188 1230 Planarity : 0.005 0.049 1437 Dihedral : 7.495 89.770 1140 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.52 % Allowed : 19.72 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.31 (0.26), residues: 1000 helix: 0.25 (0.29), residues: 333 sheet: 0.85 (0.39), residues: 175 loop : -0.88 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 284 HIS 0.007 0.001 HIS A 334 PHE 0.011 0.002 PHE A 145 TYR 0.017 0.002 TYR B 176 ARG 0.011 0.001 ARG A 510 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7406 (mm-30) cc_final: 0.6701 (pm20) REVERT: A 85 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8079 (mt) REVERT: A 218 ARG cc_start: 0.8630 (ttm-80) cc_final: 0.7479 (tpt-90) REVERT: A 222 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7982 (pmm150) REVERT: A 243 ASN cc_start: 0.7823 (t0) cc_final: 0.7621 (t0) REVERT: B 26 ARG cc_start: 0.7023 (mtp180) cc_final: 0.6550 (mmm160) REVERT: B 154 ARG cc_start: 0.8503 (mmm-85) cc_final: 0.8170 (ttm-80) REVERT: B 222 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7587 (pmm150) REVERT: B 311 LEU cc_start: 0.8029 (mt) cc_final: 0.7798 (mt) REVERT: B 510 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6464 (mtm110) outliers start: 28 outliers final: 19 residues processed: 98 average time/residue: 0.2476 time to fit residues: 31.7390 Evaluate side-chains 93 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 510 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 72 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 29 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 95 optimal weight: 0.0270 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.145332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.118221 restraints weight = 10828.329| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.99 r_work: 0.3149 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7995 Z= 0.169 Angle : 0.544 8.792 10943 Z= 0.263 Chirality : 0.041 0.173 1230 Planarity : 0.005 0.042 1437 Dihedral : 7.160 89.420 1140 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.89 % Allowed : 20.35 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.12 (0.26), residues: 1000 helix: 0.73 (0.29), residues: 332 sheet: 1.02 (0.39), residues: 174 loop : -0.69 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 284 HIS 0.004 0.001 HIS B 38 PHE 0.005 0.001 PHE A 9 TYR 0.013 0.001 TYR B 176 ARG 0.006 0.000 ARG A 510 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7320 (mm-30) cc_final: 0.6702 (pm20) REVERT: A 85 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8029 (mt) REVERT: A 218 ARG cc_start: 0.8529 (ttm-80) cc_final: 0.7394 (tpt-90) REVERT: A 222 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7165 (pmm150) REVERT: A 243 ASN cc_start: 0.7900 (t0) cc_final: 0.7668 (t0) REVERT: A 514 ARG cc_start: 0.8597 (tpp80) cc_final: 0.8219 (tpp-160) REVERT: B 26 ARG cc_start: 0.7068 (mtp180) cc_final: 0.6615 (mmm160) REVERT: B 154 ARG cc_start: 0.8325 (mmm-85) cc_final: 0.7976 (ttm-80) REVERT: B 222 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7045 (pmm150) REVERT: B 311 LEU cc_start: 0.7970 (mt) cc_final: 0.7723 (mt) REVERT: B 510 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6447 (mtm110) outliers start: 23 outliers final: 18 residues processed: 91 average time/residue: 0.3218 time to fit residues: 37.9845 Evaluate side-chains 92 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 510 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.144449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.116294 restraints weight = 10684.399| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.95 r_work: 0.3154 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7995 Z= 0.223 Angle : 0.566 9.200 10943 Z= 0.272 Chirality : 0.042 0.177 1230 Planarity : 0.005 0.043 1437 Dihedral : 7.185 89.770 1140 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.51 % Allowed : 20.48 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.13 (0.26), residues: 1000 helix: 0.79 (0.29), residues: 332 sheet: 0.95 (0.39), residues: 180 loop : -0.71 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 284 HIS 0.005 0.001 HIS B 38 PHE 0.007 0.001 PHE A 9 TYR 0.020 0.002 TYR A 176 ARG 0.007 0.000 ARG A 510 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7330 (mm-30) cc_final: 0.6700 (pm20) REVERT: A 85 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8036 (mt) REVERT: A 218 ARG cc_start: 0.8545 (ttm-80) cc_final: 0.7391 (tpt-90) REVERT: A 222 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7252 (pmm150) REVERT: A 514 ARG cc_start: 0.8592 (tpp80) cc_final: 0.8249 (tpp-160) REVERT: B 26 ARG cc_start: 0.7042 (mtp180) cc_final: 0.6271 (mmm160) REVERT: B 154 ARG cc_start: 0.8403 (mmm-85) cc_final: 0.8051 (ttm-80) REVERT: B 222 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7238 (pmm150) REVERT: B 311 LEU cc_start: 0.7987 (mt) cc_final: 0.7737 (mt) REVERT: B 510 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6441 (mtm110) outliers start: 20 outliers final: 16 residues processed: 86 average time/residue: 0.2536 time to fit residues: 28.6628 Evaluate side-chains 89 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 510 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 73 optimal weight: 0.0270 chunk 23 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.9042 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.145038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.117090 restraints weight = 10698.563| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.94 r_work: 0.3147 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7995 Z= 0.218 Angle : 0.562 9.253 10943 Z= 0.270 Chirality : 0.041 0.170 1230 Planarity : 0.005 0.041 1437 Dihedral : 7.155 89.471 1140 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.51 % Allowed : 20.35 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.18 (0.26), residues: 1000 helix: 0.82 (0.29), residues: 332 sheet: 0.96 (0.39), residues: 180 loop : -0.66 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 284 HIS 0.005 0.001 HIS B 38 PHE 0.006 0.001 PHE A 9 TYR 0.014 0.001 TYR B 176 ARG 0.008 0.000 ARG B 191 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4464.25 seconds wall clock time: 78 minutes 12.89 seconds (4692.89 seconds total)