Starting phenix.real_space_refine on Sat Dec 28 07:18:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8avv_15684/12_2024/8avv_15684.cif Found real_map, /net/cci-nas-00/data/ceres_data/8avv_15684/12_2024/8avv_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_15684/12_2024/8avv_15684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8avv_15684/12_2024/8avv_15684.map" model { file = "/net/cci-nas-00/data/ceres_data/8avv_15684/12_2024/8avv_15684.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8avv_15684/12_2024/8avv_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 6.75, per 1000 atoms: 0.87 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: 1.88 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.00 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: 2.31 Time building geometry restraints manager: 2.18 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: 4.880 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: 0.060 Process input model: 22.590 Find NCS groups from input model: 0.300 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: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.150 ------------------------------------------------------------------------------- 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 : 0.822 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: 0.2567 time to fit residues: 51.7697 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 : 0.792 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2127 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 9.016 10943 Z= 0.327 Chirality : 0.042 0.149 1230 Planarity : 0.005 0.034 1437 Dihedral : 8.875 83.405 1178 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.54 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: -1.07 (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 0.019 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 : 0.939 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8084 (mm-30) cc_final: 0.6906 (pm20) REVERT: A 154 ARG cc_start: 0.8438 (ptt180) cc_final: 0.7900 (tpt-90) REVERT: A 218 ARG cc_start: 0.8713 (ttm-80) cc_final: 0.7795 (mmm160) REVERT: A 243 ASN cc_start: 0.7888 (t0) cc_final: 0.7679 (t0) REVERT: B 31 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8514 (pt) REVERT: B 154 ARG cc_start: 0.8563 (mmm-85) cc_final: 0.8252 (ttm-80) REVERT: B 282 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7746 (mm-40) REVERT: B 311 LEU cc_start: 0.7848 (mt) cc_final: 0.7575 (mt) outliers start: 25 outliers final: 12 residues processed: 112 average time/residue: 0.2606 time to fit residues: 37.6794 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 : 0.862 ------------------------------------------------------------------------------- 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 50 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 B 349 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7995 Z= 0.321 Angle : 0.649 7.709 10943 Z= 0.317 Chirality : 0.044 0.182 1230 Planarity : 0.005 0.044 1437 Dihedral : 7.773 87.317 1149 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.51 % Allowed : 17.96 % Favored : 79.52 % 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: -0.90 (0.25), residues: 1000 helix: -0.33 (0.28), residues: 320 sheet: 0.77 (0.38), residues: 159 loop : -1.19 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 82 HIS 0.008 0.001 HIS A 334 PHE 0.010 0.002 PHE A 9 TYR 0.022 0.002 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 101 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7983 (mm-30) cc_final: 0.6932 (pm20) REVERT: A 154 ARG cc_start: 0.8517 (ptt180) cc_final: 0.7943 (tpt-90) REVERT: A 218 ARG cc_start: 0.8722 (ttm-80) cc_final: 0.7848 (mtp85) REVERT: A 222 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7366 (pmm150) REVERT: A 243 ASN cc_start: 0.7917 (t0) cc_final: 0.7646 (t0) REVERT: A 404 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8575 (pp30) REVERT: B 26 ARG cc_start: 0.6937 (mtp180) cc_final: 0.6710 (mmm160) REVERT: B 154 ARG cc_start: 0.8766 (mmm-85) cc_final: 0.8372 (ttm-80) REVERT: B 222 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7119 (pmm150) REVERT: B 282 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7831 (mm-40) outliers start: 20 outliers final: 12 residues processed: 99 average time/residue: 0.2587 time to fit residues: 33.4963 Evaluate side-chains 86 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 195 LEU 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 A residue 404 GLN Chi-restraints excluded: chain B residue 60 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 382 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 506 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 0.0070 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS A 317 GLN B 317 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7995 Z= 0.233 Angle : 0.574 8.166 10943 Z= 0.279 Chirality : 0.042 0.196 1230 Planarity : 0.004 0.042 1437 Dihedral : 7.356 88.279 1142 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.52 % Allowed : 18.47 % 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: -0.52 (0.25), residues: 1000 helix: 0.12 (0.29), residues: 326 sheet: 0.85 (0.37), residues: 171 loop : -1.07 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 284 HIS 0.005 0.001 HIS B 38 PHE 0.007 0.001 PHE A 9 TYR 0.014 0.002 TYR B 176 ARG 0.003 0.000 ARG B 364 *********************** 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 103 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8031 (mm-30) cc_final: 0.6875 (pm20) REVERT: A 154 ARG cc_start: 0.8498 (ptt180) cc_final: 0.7936 (tpt-90) REVERT: A 218 ARG cc_start: 0.8684 (ttm-80) cc_final: 0.7787 (mtp85) REVERT: A 222 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7136 (pmm150) REVERT: A 404 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8548 (pp30) REVERT: B 24 CYS cc_start: 0.7905 (p) cc_final: 0.7198 (m) REVERT: B 31 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8616 (pt) REVERT: B 154 ARG cc_start: 0.8739 (mmm-85) cc_final: 0.8441 (ttm-80) REVERT: B 222 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.6999 (pmm150) REVERT: B 282 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.7950 (mm-40) REVERT: B 510 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6400 (mtm110) outliers start: 28 outliers final: 10 residues processed: 98 average time/residue: 0.2631 time to fit residues: 33.4549 Evaluate side-chains 90 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 404 GLN 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 78 LEU 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 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 1 optimal weight: 2.9990 chunk 71 optimal weight: 0.0970 chunk 39 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 87 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 116 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3355 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= 0.163 Angle : 0.529 6.026 10943 Z= 0.256 Chirality : 0.041 0.193 1230 Planarity : 0.004 0.038 1437 Dihedral : 6.972 87.659 1140 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.64 % Allowed : 19.72 % Favored : 77.64 % 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: -0.06 (0.26), residues: 1000 helix: 0.55 (0.29), residues: 334 sheet: 1.13 (0.38), residues: 169 loop : -0.85 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 284 HIS 0.004 0.001 HIS A 334 PHE 0.007 0.001 PHE B 469 TYR 0.024 0.002 TYR A 176 ARG 0.006 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 99 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7983 (mm-30) cc_final: 0.6871 (pm20) REVERT: A 154 ARG cc_start: 0.8481 (ptt180) cc_final: 0.7899 (tpt-90) REVERT: A 218 ARG cc_start: 0.8604 (ttm-80) cc_final: 0.7738 (mtp85) REVERT: A 222 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.6880 (pmm150) REVERT: A 514 ARG cc_start: 0.8596 (tpp80) cc_final: 0.8313 (tpp-160) REVERT: B 24 CYS cc_start: 0.7912 (p) cc_final: 0.7260 (m) REVERT: B 26 ARG cc_start: 0.6845 (mtp180) cc_final: 0.6603 (mmm160) REVERT: B 154 ARG cc_start: 0.8700 (mmm-85) cc_final: 0.8375 (ttm-80) REVERT: B 282 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8033 (tm-30) REVERT: B 510 ARG cc_start: 0.6948 (OUTLIER) cc_final: 0.6329 (mtm110) outliers start: 21 outliers final: 13 residues processed: 94 average time/residue: 0.2874 time to fit residues: 35.7033 Evaluate side-chains 86 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 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 78 LEU 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 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 Chi-restraints excluded: chain B residue 511 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 ASN B 458 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3472 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= 0.392 Angle : 0.676 8.667 10943 Z= 0.326 Chirality : 0.045 0.196 1230 Planarity : 0.005 0.049 1437 Dihedral : 7.496 89.893 1140 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.89 % Allowed : 19.10 % 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: -0.40 (0.25), residues: 1000 helix: 0.13 (0.29), residues: 335 sheet: 1.02 (0.38), residues: 170 loop : -0.98 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 284 HIS 0.007 0.002 HIS A 334 PHE 0.010 0.002 PHE A 9 TYR 0.016 0.002 TYR B 176 ARG 0.006 0.001 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 104 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 73 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7924 (mm-30) cc_final: 0.6856 (pm20) REVERT: A 154 ARG cc_start: 0.8557 (ptt180) cc_final: 0.8041 (tpt-90) REVERT: A 218 ARG cc_start: 0.8679 (ttm-80) cc_final: 0.7748 (mtp85) REVERT: A 222 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7480 (pmm150) REVERT: B 26 ARG cc_start: 0.6894 (mtp180) cc_final: 0.6606 (mmm160) REVERT: B 154 ARG cc_start: 0.8900 (mmm-85) cc_final: 0.8572 (ttm-80) REVERT: B 222 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7501 (pmm150) REVERT: B 274 SER cc_start: 0.8716 (OUTLIER) cc_final: 0.8478 (p) REVERT: B 510 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6449 (mtm110) outliers start: 31 outliers final: 19 residues processed: 97 average time/residue: 0.2766 time to fit residues: 34.3513 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 : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 195 LEU 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 234 LEU 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 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 Chi-restraints excluded: chain B residue 511 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 44 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7995 Z= 0.266 Angle : 0.594 8.662 10943 Z= 0.286 Chirality : 0.042 0.187 1230 Planarity : 0.005 0.044 1437 Dihedral : 7.316 89.335 1140 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.14 % Allowed : 20.60 % Favored : 76.26 % 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: -0.26 (0.26), residues: 1000 helix: 0.30 (0.29), residues: 334 sheet: 1.04 (0.38), residues: 169 loop : -0.92 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 284 HIS 0.005 0.001 HIS B 290 PHE 0.007 0.001 PHE A 9 TYR 0.015 0.002 TYR B 176 ARG 0.006 0.000 ARG B 364 *********************** 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 94 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7979 (mm-30) cc_final: 0.6887 (pm20) REVERT: A 154 ARG cc_start: 0.8520 (ptt180) cc_final: 0.8022 (tpt-90) REVERT: A 222 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7387 (pmm150) REVERT: A 514 ARG cc_start: 0.8636 (tpp80) cc_final: 0.8274 (tpp-160) REVERT: B 26 ARG cc_start: 0.6901 (mtp180) cc_final: 0.6610 (mmm160) REVERT: B 154 ARG cc_start: 0.8856 (mmm-85) cc_final: 0.8509 (ttm-80) REVERT: B 222 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7173 (pmm150) REVERT: B 274 SER cc_start: 0.8662 (OUTLIER) cc_final: 0.8405 (p) REVERT: B 510 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6347 (mtm110) outliers start: 25 outliers final: 17 residues processed: 89 average time/residue: 0.2581 time to fit residues: 29.8252 Evaluate side-chains 87 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 195 LEU 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 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 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 Chi-restraints excluded: chain B residue 511 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 0.1980 chunk 89 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7995 Z= 0.212 Angle : 0.557 7.622 10943 Z= 0.269 Chirality : 0.041 0.169 1230 Planarity : 0.005 0.041 1437 Dihedral : 7.148 89.906 1140 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.52 % Allowed : 20.60 % Favored : 75.88 % 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: -0.01 (0.26), residues: 1000 helix: 0.61 (0.29), residues: 332 sheet: 1.18 (0.39), residues: 170 loop : -0.83 (0.26), residues: 498 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 0.008 0.001 PHE A 198 TYR 0.014 0.001 TYR B 176 ARG 0.009 0.000 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 97 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7950 (mm-30) cc_final: 0.6845 (pm20) REVERT: A 154 ARG cc_start: 0.8504 (ptt180) cc_final: 0.7980 (tpt-90) REVERT: A 218 ARG cc_start: 0.8570 (ttm-80) cc_final: 0.7610 (mtp85) REVERT: A 222 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7013 (pmm150) REVERT: A 514 ARG cc_start: 0.8615 (tpp80) cc_final: 0.8320 (tpp-160) REVERT: B 26 ARG cc_start: 0.6969 (mtp180) cc_final: 0.6698 (mmm160) REVERT: B 154 ARG cc_start: 0.8848 (mmm-85) cc_final: 0.8491 (ttm-80) REVERT: B 222 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.6986 (pmm150) REVERT: B 274 SER cc_start: 0.8645 (OUTLIER) cc_final: 0.8386 (p) REVERT: B 510 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6301 (mtm110) outliers start: 28 outliers final: 17 residues processed: 91 average time/residue: 0.2624 time to fit residues: 31.2764 Evaluate side-chains 88 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 271 SER 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 Chi-restraints excluded: chain B residue 511 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 58 optimal weight: 0.0980 chunk 94 optimal weight: 0.1980 chunk 57 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7995 Z= 0.153 Angle : 0.525 7.454 10943 Z= 0.252 Chirality : 0.040 0.162 1230 Planarity : 0.004 0.037 1437 Dihedral : 6.934 88.253 1140 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.26 % Allowed : 21.36 % Favored : 76.38 % 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: 0.29 (0.26), residues: 1000 helix: 0.90 (0.29), residues: 338 sheet: 1.36 (0.40), residues: 169 loop : -0.72 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 284 HIS 0.004 0.001 HIS B 38 PHE 0.004 0.001 PHE A 9 TYR 0.012 0.001 TYR B 176 ARG 0.008 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 89 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7904 (mm-30) cc_final: 0.6804 (pm20) REVERT: A 154 ARG cc_start: 0.8476 (ptt180) cc_final: 0.7980 (tpt-90) REVERT: A 181 ASP cc_start: 0.8173 (t70) cc_final: 0.7957 (t0) REVERT: A 218 ARG cc_start: 0.8555 (ttm-80) cc_final: 0.7621 (mtp85) REVERT: A 513 ASN cc_start: 0.8391 (t0) cc_final: 0.7808 (t0) REVERT: A 514 ARG cc_start: 0.8535 (tpp80) cc_final: 0.8274 (tpp-160) REVERT: B 26 ARG cc_start: 0.6936 (mtp180) cc_final: 0.6434 (mmm160) REVERT: B 154 ARG cc_start: 0.8787 (mmm-85) cc_final: 0.8434 (ttm-80) REVERT: B 222 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.6806 (pmm150) REVERT: B 274 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8354 (p) REVERT: B 282 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.7968 (tm-30) outliers start: 18 outliers final: 14 residues processed: 85 average time/residue: 0.2358 time to fit residues: 26.4745 Evaluate side-chains 86 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 195 LEU 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 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 430 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 511 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 8 optimal weight: 0.0870 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7995 Z= 0.164 Angle : 0.526 7.229 10943 Z= 0.253 Chirality : 0.040 0.184 1230 Planarity : 0.004 0.036 1437 Dihedral : 6.882 87.518 1140 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.39 % Allowed : 21.36 % Favored : 76.26 % 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: 0.39 (0.26), residues: 1000 helix: 1.03 (0.29), residues: 338 sheet: 1.19 (0.39), residues: 175 loop : -0.62 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 376 HIS 0.004 0.001 HIS B 38 PHE 0.004 0.001 PHE A 9 TYR 0.021 0.002 TYR A 176 ARG 0.007 0.000 ARG B 191 ********************** 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 90 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7898 (mm-30) cc_final: 0.6797 (pm20) REVERT: A 154 ARG cc_start: 0.8481 (ptt180) cc_final: 0.7956 (tpt-90) REVERT: A 181 ASP cc_start: 0.8183 (t70) cc_final: 0.7977 (t0) REVERT: A 218 ARG cc_start: 0.8547 (ttm-80) cc_final: 0.7609 (mtp85) REVERT: A 222 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.6839 (pmm150) REVERT: A 513 ASN cc_start: 0.8425 (t0) cc_final: 0.7909 (t0) REVERT: A 514 ARG cc_start: 0.8552 (tpp80) cc_final: 0.8305 (tpp-160) REVERT: B 26 ARG cc_start: 0.6938 (mtp180) cc_final: 0.6436 (mmm160) REVERT: B 154 ARG cc_start: 0.8799 (mmm-85) cc_final: 0.8436 (ttm-80) REVERT: B 222 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.6812 (pmm150) REVERT: B 274 SER cc_start: 0.8619 (OUTLIER) cc_final: 0.8349 (p) REVERT: B 282 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.7973 (tm-30) outliers start: 19 outliers final: 14 residues processed: 88 average time/residue: 0.2566 time to fit residues: 29.8254 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 : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 195 LEU 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 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 430 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 511 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 0.1980 chunk 79 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.146015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.118751 restraints weight = 10610.672| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.08 r_work: 0.3151 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7995 Z= 0.173 Angle : 0.539 7.797 10943 Z= 0.257 Chirality : 0.040 0.191 1230 Planarity : 0.004 0.044 1437 Dihedral : 6.860 86.919 1140 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.39 % Allowed : 21.48 % Favored : 76.13 % 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: 0.47 (0.26), residues: 1000 helix: 1.14 (0.29), residues: 338 sheet: 1.10 (0.39), residues: 180 loop : -0.56 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 0.011 0.000 ARG B 191 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2013.65 seconds wall clock time: 37 minutes 13.43 seconds (2233.43 seconds total)