Starting phenix.real_space_refine on Sat Mar 7 07:45:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xev_33160/03_2026/7xev_33160_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xev_33160/03_2026/7xev_33160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xev_33160/03_2026/7xev_33160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xev_33160/03_2026/7xev_33160.map" model { file = "/net/cci-nas-00/data/ceres_data/7xev_33160/03_2026/7xev_33160_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xev_33160/03_2026/7xev_33160_trim.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 108 5.16 5 B 4 2.79 5 C 13120 2.51 5 N 3376 2.21 5 O 3440 1.98 5 H 20284 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40332 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 10066 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "B" Number of atoms: 10066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 10066 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "C" Number of atoms: 10066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 10066 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "D" Number of atoms: 10066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 10066 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'FZ4': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'FZ4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'FZ4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'FZ4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.38, per 1000 atoms: 0.18 Number of scatterers: 40332 At special positions: 0 Unit cell: (153.114, 153.114, 118.638, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 108 16.00 O 3440 8.00 N 3376 7.00 C 13120 6.00 B 4 5.00 H 20284 1.00 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: 4.15 Conformation dependent library (CDL) restraints added in 1.2 seconds 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 4 sheets defined 63.2% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.814A pdb=" N GLY A 82 " --> pdb=" O VAL A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.920A pdb=" N THR A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 97 Processing helix chain 'A' and resid 114 through 122 Processing helix chain 'A' and resid 130 through 141 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.958A pdb=" N ARG A 158 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 169 removed outlier: 3.606A pdb=" N ILE A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 181 Processing helix chain 'A' and resid 207 through 215 Processing helix chain 'A' and resid 219 through 227 Processing helix chain 'A' and resid 243 through 251 Processing helix chain 'A' and resid 255 through 277 Processing helix chain 'A' and resid 292 through 300 Processing helix chain 'A' and resid 303 through 311 Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 363 through 368 removed outlier: 3.872A pdb=" N VAL A 368 " --> pdb=" O HIS A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 408 Proline residue: A 386 - end of helix Processing helix chain 'A' and resid 424 through 454 Processing helix chain 'A' and resid 461 through 466 removed outlier: 4.623A pdb=" N SER A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 487 Processing helix chain 'A' and resid 491 through 507 removed outlier: 3.670A pdb=" N LEU A 495 " --> pdb=" O TRP A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 512 Processing helix chain 'A' and resid 514 through 531 removed outlier: 3.878A pdb=" N ILE A 519 " --> pdb=" O GLN A 515 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR A 520 " --> pdb=" O HIS A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 553 Processing helix chain 'A' and resid 587 through 601 Processing helix chain 'A' and resid 613 through 630 removed outlier: 3.785A pdb=" N VAL A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 647 removed outlier: 3.878A pdb=" N ASN A 634 " --> pdb=" O VAL A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 668 removed outlier: 3.686A pdb=" N TRP A 652 " --> pdb=" O ALA A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 713 Processing helix chain 'B' and resid 71 through 81 Processing helix chain 'B' and resid 83 through 88 removed outlier: 3.786A pdb=" N GLU B 86 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR B 88 " --> pdb=" O GLU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 114 through 122 Processing helix chain 'B' and resid 130 through 141 Processing helix chain 'B' and resid 154 through 158 removed outlier: 3.908A pdb=" N ARG B 158 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 169 removed outlier: 3.745A pdb=" N LYS B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 181 Processing helix chain 'B' and resid 207 through 215 Processing helix chain 'B' and resid 219 through 226 Processing helix chain 'B' and resid 243 through 251 Processing helix chain 'B' and resid 255 through 277 Processing helix chain 'B' and resid 292 through 300 Processing helix chain 'B' and resid 303 through 311 Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 363 through 368 removed outlier: 3.861A pdb=" N VAL B 368 " --> pdb=" O HIS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 408 Proline residue: B 386 - end of helix Processing helix chain 'B' and resid 424 through 454 Processing helix chain 'B' and resid 461 through 466 removed outlier: 4.632A pdb=" N SER B 465 " --> pdb=" O SER B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 487 Processing helix chain 'B' and resid 491 through 507 removed outlier: 3.666A pdb=" N LEU B 495 " --> pdb=" O TRP B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 512 Processing helix chain 'B' and resid 514 through 531 removed outlier: 3.879A pdb=" N ILE B 519 " --> pdb=" O GLN B 515 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR B 520 " --> pdb=" O HIS B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 553 Processing helix chain 'B' and resid 587 through 601 Processing helix chain 'B' and resid 613 through 630 removed outlier: 3.782A pdb=" N VAL B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 647 removed outlier: 3.878A pdb=" N ASN B 634 " --> pdb=" O VAL B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 668 removed outlier: 3.691A pdb=" N TRP B 652 " --> pdb=" O ALA B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 713 Processing helix chain 'C' and resid 71 through 81 Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.875A pdb=" N THR C 88 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 98 Processing helix chain 'C' and resid 114 through 122 removed outlier: 3.720A pdb=" N ASN C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 141 Processing helix chain 'C' and resid 154 through 158 removed outlier: 3.903A pdb=" N ARG C 158 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 169 removed outlier: 3.605A pdb=" N ILE C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS C 169 " --> pdb=" O ILE C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 181 Processing helix chain 'C' and resid 207 through 215 Processing helix chain 'C' and resid 219 through 227 Processing helix chain 'C' and resid 243 through 251 Processing helix chain 'C' and resid 255 through 277 Processing helix chain 'C' and resid 292 through 300 Processing helix chain 'C' and resid 303 through 311 Processing helix chain 'C' and resid 350 through 358 Processing helix chain 'C' and resid 363 through 368 removed outlier: 3.865A pdb=" N VAL C 368 " --> pdb=" O HIS C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 408 Proline residue: C 386 - end of helix Processing helix chain 'C' and resid 424 through 454 Processing helix chain 'C' and resid 461 through 466 removed outlier: 4.629A pdb=" N SER C 465 " --> pdb=" O SER C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 487 Processing helix chain 'C' and resid 491 through 507 removed outlier: 3.691A pdb=" N LEU C 495 " --> pdb=" O TRP C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 512 Processing helix chain 'C' and resid 514 through 531 removed outlier: 3.877A pdb=" N ILE C 519 " --> pdb=" O GLN C 515 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR C 520 " --> pdb=" O HIS C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 553 Processing helix chain 'C' and resid 587 through 601 Processing helix chain 'C' and resid 613 through 630 removed outlier: 3.775A pdb=" N VAL C 630 " --> pdb=" O LEU C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 647 removed outlier: 3.864A pdb=" N ASN C 634 " --> pdb=" O VAL C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 668 removed outlier: 3.688A pdb=" N TRP C 652 " --> pdb=" O ALA C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 713 Processing helix chain 'D' and resid 71 through 81 Processing helix chain 'D' and resid 83 through 88 removed outlier: 3.803A pdb=" N GLU D 86 " --> pdb=" O VAL D 83 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR D 88 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 97 Processing helix chain 'D' and resid 114 through 122 Processing helix chain 'D' and resid 130 through 141 Processing helix chain 'D' and resid 154 through 158 removed outlier: 3.921A pdb=" N ARG D 158 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 169 removed outlier: 3.769A pdb=" N LYS D 169 " --> pdb=" O ILE D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 181 Processing helix chain 'D' and resid 207 through 215 Processing helix chain 'D' and resid 219 through 226 Processing helix chain 'D' and resid 243 through 251 Processing helix chain 'D' and resid 255 through 277 Processing helix chain 'D' and resid 292 through 300 Processing helix chain 'D' and resid 303 through 311 Processing helix chain 'D' and resid 350 through 358 Processing helix chain 'D' and resid 363 through 368 removed outlier: 3.886A pdb=" N VAL D 368 " --> pdb=" O HIS D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 408 Proline residue: D 386 - end of helix Processing helix chain 'D' and resid 424 through 454 Processing helix chain 'D' and resid 461 through 466 removed outlier: 4.629A pdb=" N SER D 465 " --> pdb=" O SER D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 487 Processing helix chain 'D' and resid 491 through 507 removed outlier: 3.691A pdb=" N LEU D 495 " --> pdb=" O TRP D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 512 Processing helix chain 'D' and resid 514 through 531 removed outlier: 3.878A pdb=" N ILE D 519 " --> pdb=" O GLN D 515 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR D 520 " --> pdb=" O HIS D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 553 Processing helix chain 'D' and resid 587 through 601 Processing helix chain 'D' and resid 613 through 630 removed outlier: 3.792A pdb=" N VAL D 630 " --> pdb=" O LEU D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 647 Processing helix chain 'D' and resid 648 through 668 removed outlier: 3.688A pdb=" N TRP D 652 " --> pdb=" O ALA D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 713 Processing sheet with id=AA1, first strand: chain 'A' and resid 333 through 339 Processing sheet with id=AA2, first strand: chain 'B' and resid 333 through 339 removed outlier: 3.659A pdb=" N TYR B 338 " --> pdb=" O PHE B 700 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 333 through 339 removed outlier: 3.656A pdb=" N TYR C 338 " --> pdb=" O PHE C 700 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 333 through 339 removed outlier: 3.656A pdb=" N TYR D 338 " --> pdb=" O PHE D 700 " (cutoff:3.500A) 1068 hydrogen bonds defined for protein. 3114 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: 9.76 Time building geometry restraints manager: 5.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 20228 1.03 - 1.23: 56 1.23 - 1.42: 8780 1.42 - 1.62: 11616 1.62 - 1.81: 160 Bond restraints: 40840 Sorted by residual: bond pdb=" CB PRO D 372 " pdb=" CG PRO D 372 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.99e+00 bond pdb=" C02 FZ4 C1001 " pdb=" C03 FZ4 C1001 " ideal model delta sigma weight residual 1.400 1.371 0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" C02 FZ4 D1001 " pdb=" C03 FZ4 D1001 " ideal model delta sigma weight residual 1.400 1.371 0.029 2.00e-02 2.50e+03 2.11e+00 bond pdb=" C02 FZ4 B1001 " pdb=" C03 FZ4 B1001 " ideal model delta sigma weight residual 1.400 1.371 0.029 2.00e-02 2.50e+03 2.09e+00 bond pdb=" C02 FZ4 A1001 " pdb=" C03 FZ4 A1001 " ideal model delta sigma weight residual 1.400 1.371 0.029 2.00e-02 2.50e+03 2.09e+00 ... (remaining 40835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 73387 2.11 - 4.23: 342 4.23 - 6.34: 25 6.34 - 8.46: 0 8.46 - 10.57: 2 Bond angle restraints: 73756 Sorted by residual: angle pdb=" N LEU A 373 " pdb=" CA LEU A 373 " pdb=" C LEU A 373 " ideal model delta sigma weight residual 114.12 104.73 9.39 1.39e+00 5.18e-01 4.57e+01 angle pdb=" N LEU B 373 " pdb=" CA LEU B 373 " pdb=" C LEU B 373 " ideal model delta sigma weight residual 114.75 108.91 5.84 1.26e+00 6.30e-01 2.15e+01 angle pdb=" N LEU C 373 " pdb=" CA LEU C 373 " pdb=" C LEU C 373 " ideal model delta sigma weight residual 114.75 109.01 5.74 1.26e+00 6.30e-01 2.07e+01 angle pdb=" N ASN D 374 " pdb=" CA ASN D 374 " pdb=" C ASN D 374 " ideal model delta sigma weight residual 112.72 107.78 4.94 1.28e+00 6.10e-01 1.49e+01 angle pdb=" CA PRO D 372 " pdb=" N PRO D 372 " pdb=" CD PRO D 372 " ideal model delta sigma weight residual 112.00 106.89 5.11 1.40e+00 5.10e-01 1.33e+01 ... (remaining 73751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.39: 17471 20.39 - 40.78: 1203 40.78 - 61.17: 338 61.17 - 81.56: 23 81.56 - 101.95: 5 Dihedral angle restraints: 19040 sinusoidal: 10212 harmonic: 8828 Sorted by residual: dihedral pdb=" CA PRO A 372 " pdb=" C PRO A 372 " pdb=" N LEU A 373 " pdb=" CA LEU A 373 " ideal model delta harmonic sigma weight residual 180.00 141.39 38.61 0 5.00e+00 4.00e-02 5.96e+01 dihedral pdb=" CA GLU B 371 " pdb=" C GLU B 371 " pdb=" N PRO B 372 " pdb=" CA PRO B 372 " ideal model delta harmonic sigma weight residual -180.00 -150.74 -29.26 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA GLU C 371 " pdb=" C GLU C 371 " pdb=" N PRO C 372 " pdb=" CA PRO C 372 " ideal model delta harmonic sigma weight residual -180.00 -150.78 -29.22 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 19037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2647 0.048 - 0.096: 434 0.096 - 0.145: 55 0.145 - 0.193: 1 0.193 - 0.241: 3 Chirality restraints: 3140 Sorted by residual: chirality pdb=" CA PRO A 372 " pdb=" N PRO A 372 " pdb=" C PRO A 372 " pdb=" CB PRO A 372 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA PRO D 372 " pdb=" N PRO D 372 " pdb=" C PRO D 372 " pdb=" CB PRO D 372 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA PRO B 372 " pdb=" N PRO B 372 " pdb=" C PRO B 372 " pdb=" CB PRO B 372 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.54e-01 ... (remaining 3137 not shown) Planarity restraints: 5808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" B01 FZ4 B1001 " -0.443 2.00e-02 2.50e+03 2.82e-01 1.40e+03 pdb=" C02 FZ4 B1001 " 0.247 2.00e-02 2.50e+03 pdb=" C03 FZ4 B1001 " 0.365 2.00e-02 2.50e+03 pdb=" C04 FZ4 B1001 " -0.091 2.00e-02 2.50e+03 pdb=" C05 FZ4 B1001 " -0.306 2.00e-02 2.50e+03 pdb=" C06 FZ4 B1001 " -0.027 2.00e-02 2.50e+03 pdb=" C07 FZ4 B1001 " 0.256 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" B01 FZ4 C1001 " -0.442 2.00e-02 2.50e+03 2.82e-01 1.39e+03 pdb=" C02 FZ4 C1001 " 0.247 2.00e-02 2.50e+03 pdb=" C03 FZ4 C1001 " 0.364 2.00e-02 2.50e+03 pdb=" C04 FZ4 C1001 " -0.092 2.00e-02 2.50e+03 pdb=" C05 FZ4 C1001 " -0.304 2.00e-02 2.50e+03 pdb=" C06 FZ4 C1001 " -0.028 2.00e-02 2.50e+03 pdb=" C07 FZ4 C1001 " 0.256 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" B01 FZ4 A1001 " 0.434 2.00e-02 2.50e+03 2.77e-01 1.34e+03 pdb=" C02 FZ4 A1001 " -0.244 2.00e-02 2.50e+03 pdb=" C03 FZ4 A1001 " -0.359 2.00e-02 2.50e+03 pdb=" C04 FZ4 A1001 " 0.096 2.00e-02 2.50e+03 pdb=" C05 FZ4 A1001 " 0.293 2.00e-02 2.50e+03 pdb=" C06 FZ4 A1001 " 0.031 2.00e-02 2.50e+03 pdb=" C07 FZ4 A1001 " -0.250 2.00e-02 2.50e+03 ... (remaining 5805 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 2498 2.20 - 2.80: 82764 2.80 - 3.40: 110756 3.40 - 4.00: 138744 4.00 - 4.60: 219758 Nonbonded interactions: 554520 Sorted by model distance: nonbonded pdb=" OE1 GLN C 145 " pdb=" H GLN C 145 " model vdw 1.595 2.450 nonbonded pdb=" OE1 GLN B 145 " pdb=" H GLN B 145 " model vdw 1.618 2.450 nonbonded pdb=" OE1 GLN A 145 " pdb=" H GLN A 145 " model vdw 1.624 2.450 nonbonded pdb=" OH TYR B 539 " pdb=" HG1 THR B 599 " model vdw 1.624 2.450 nonbonded pdb=" OE1 GLN D 145 " pdb=" H GLN D 145 " model vdw 1.627 2.450 ... (remaining 554515 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.890 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: 0.210 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 38.600 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 20556 Z= 0.121 Angle : 0.536 10.574 27884 Z= 0.289 Chirality : 0.036 0.241 3140 Planarity : 0.014 0.282 3440 Dihedral : 14.964 101.945 7424 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.93 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.19), residues: 2432 helix: 2.01 (0.15), residues: 1448 sheet: -3.57 (0.48), residues: 84 loop : -1.84 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 188 TYR 0.020 0.001 TYR A 539 PHE 0.010 0.001 PHE C 76 TRP 0.013 0.001 TRP C 173 HIS 0.004 0.001 HIS D 516 Details of bonding type rmsd covalent geometry : bond 0.00254 (20556) covalent geometry : angle 0.53580 (27884) hydrogen bonds : bond 0.12161 ( 1068) hydrogen bonds : angle 4.96703 ( 3114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 539 TYR cc_start: 0.7757 (t80) cc_final: 0.7404 (t80) REVERT: D 539 TYR cc_start: 0.7466 (t80) cc_final: 0.7153 (t80) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.3322 time to fit residues: 137.7733 Evaluate side-chains 213 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN ** B 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 ASN ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.155044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.118968 restraints weight = 104866.305| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 3.06 r_work: 0.3650 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20556 Z= 0.202 Angle : 0.565 6.002 27884 Z= 0.302 Chirality : 0.036 0.251 3140 Planarity : 0.005 0.124 3440 Dihedral : 6.191 69.614 2720 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.22 % Favored : 94.61 % Rotamer: Outliers : 0.55 % Allowed : 5.38 % Favored : 94.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.95 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.18), residues: 2432 helix: 1.73 (0.14), residues: 1472 sheet: -3.64 (0.45), residues: 84 loop : -1.95 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 170 TYR 0.023 0.002 TYR B 338 PHE 0.016 0.001 PHE B 462 TRP 0.006 0.001 TRP B 452 HIS 0.004 0.001 HIS D 408 Details of bonding type rmsd covalent geometry : bond 0.00445 (20556) covalent geometry : angle 0.56493 (27884) hydrogen bonds : bond 0.05236 ( 1068) hydrogen bonds : angle 4.65106 ( 3114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 214 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 PHE cc_start: 0.6165 (m-80) cc_final: 0.5842 (m-80) REVERT: D 539 TYR cc_start: 0.8165 (t80) cc_final: 0.7819 (t80) outliers start: 12 outliers final: 11 residues processed: 226 average time/residue: 0.3271 time to fit residues: 116.7642 Evaluate side-chains 216 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 205 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 511 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 192 optimal weight: 3.9990 chunk 4 optimal weight: 20.0000 chunk 124 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 206 optimal weight: 5.9990 chunk 165 optimal weight: 0.5980 chunk 231 optimal weight: 6.9990 chunk 202 optimal weight: 0.9980 chunk 162 optimal weight: 0.8980 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN ** B 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.156055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.119854 restraints weight = 104053.611| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 3.08 r_work: 0.3658 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20556 Z= 0.138 Angle : 0.512 10.539 27884 Z= 0.270 Chirality : 0.035 0.242 3140 Planarity : 0.005 0.135 3440 Dihedral : 6.085 81.275 2720 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.93 % Favored : 94.90 % Rotamer: Outliers : 0.97 % Allowed : 8.13 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.95 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.18), residues: 2432 helix: 1.84 (0.14), residues: 1476 sheet: -3.56 (0.45), residues: 84 loop : -1.89 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 170 TYR 0.017 0.001 TYR D 466 PHE 0.011 0.001 PHE C 462 TRP 0.007 0.001 TRP A 173 HIS 0.004 0.001 HIS B 516 Details of bonding type rmsd covalent geometry : bond 0.00307 (20556) covalent geometry : angle 0.51222 (27884) hydrogen bonds : bond 0.04593 ( 1068) hydrogen bonds : angle 4.41458 ( 3114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 215 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 PHE cc_start: 0.6193 (m-80) cc_final: 0.5830 (m-80) REVERT: C 539 TYR cc_start: 0.8208 (t80) cc_final: 0.7970 (t80) REVERT: D 539 TYR cc_start: 0.8097 (t80) cc_final: 0.7723 (t80) outliers start: 21 outliers final: 17 residues processed: 232 average time/residue: 0.3120 time to fit residues: 114.8365 Evaluate side-chains 221 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 462 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 462 PHE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 511 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 222 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 231 optimal weight: 0.6980 chunk 156 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.154316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.117827 restraints weight = 104227.574| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 3.08 r_work: 0.3629 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20556 Z= 0.173 Angle : 0.520 6.566 27884 Z= 0.276 Chirality : 0.035 0.231 3140 Planarity : 0.005 0.122 3440 Dihedral : 6.118 81.488 2720 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.22 % Favored : 94.61 % Rotamer: Outliers : 1.29 % Allowed : 9.79 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.95 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.18), residues: 2432 helix: 1.78 (0.14), residues: 1476 sheet: -3.77 (0.44), residues: 88 loop : -1.87 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 701 TYR 0.022 0.002 TYR B 338 PHE 0.008 0.001 PHE C 462 TRP 0.007 0.001 TRP D 173 HIS 0.004 0.001 HIS B 408 Details of bonding type rmsd covalent geometry : bond 0.00381 (20556) covalent geometry : angle 0.52031 (27884) hydrogen bonds : bond 0.04712 ( 1068) hydrogen bonds : angle 4.43928 ( 3114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 211 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 PHE cc_start: 0.6300 (m-80) cc_final: 0.5950 (m-80) REVERT: C 539 TYR cc_start: 0.8244 (t80) cc_final: 0.8023 (t80) REVERT: D 539 TYR cc_start: 0.8230 (t80) cc_final: 0.7894 (t80) outliers start: 28 outliers final: 24 residues processed: 233 average time/residue: 0.3376 time to fit residues: 124.4044 Evaluate side-chains 232 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 462 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 462 PHE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 540 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 60 optimal weight: 7.9990 chunk 197 optimal weight: 0.5980 chunk 214 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 219 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.153333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.116797 restraints weight = 104402.508| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 3.09 r_work: 0.3618 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20556 Z= 0.190 Angle : 0.532 6.085 27884 Z= 0.284 Chirality : 0.036 0.230 3140 Planarity : 0.006 0.124 3440 Dihedral : 6.227 82.972 2720 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.55 % Favored : 94.28 % Rotamer: Outliers : 1.42 % Allowed : 11.81 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.95 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.18), residues: 2432 helix: 1.70 (0.14), residues: 1476 sheet: -3.81 (0.43), residues: 88 loop : -1.85 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 74 TYR 0.022 0.002 TYR B 338 PHE 0.010 0.001 PHE C 70 TRP 0.009 0.001 TRP D 173 HIS 0.004 0.001 HIS B 408 Details of bonding type rmsd covalent geometry : bond 0.00421 (20556) covalent geometry : angle 0.53250 (27884) hydrogen bonds : bond 0.04861 ( 1068) hydrogen bonds : angle 4.46720 ( 3114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 206 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 PHE cc_start: 0.6119 (m-80) cc_final: 0.5795 (m-80) REVERT: C 539 TYR cc_start: 0.8271 (t80) cc_final: 0.8004 (t80) REVERT: D 539 TYR cc_start: 0.8302 (t80) cc_final: 0.8023 (t80) outliers start: 31 outliers final: 27 residues processed: 232 average time/residue: 0.3510 time to fit residues: 125.5959 Evaluate side-chains 226 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 199 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 552 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 87 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 184 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 213 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 210 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.154566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.117581 restraints weight = 104306.229| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 3.12 r_work: 0.3637 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20556 Z= 0.142 Angle : 0.499 5.702 27884 Z= 0.265 Chirality : 0.035 0.216 3140 Planarity : 0.005 0.121 3440 Dihedral : 6.083 84.732 2720 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.22 % Favored : 94.61 % Rotamer: Outliers : 1.52 % Allowed : 12.82 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.95 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.18), residues: 2432 helix: 1.89 (0.14), residues: 1472 sheet: -3.61 (0.45), residues: 84 loop : -1.83 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 74 TYR 0.020 0.001 TYR A 338 PHE 0.008 0.001 PHE D 70 TRP 0.009 0.001 TRP D 173 HIS 0.003 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00312 (20556) covalent geometry : angle 0.49880 (27884) hydrogen bonds : bond 0.04431 ( 1068) hydrogen bonds : angle 4.31167 ( 3114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 539 TYR cc_start: 0.8236 (t80) cc_final: 0.8032 (t80) REVERT: B 70 PHE cc_start: 0.6109 (m-80) cc_final: 0.5766 (m-80) REVERT: C 539 TYR cc_start: 0.8160 (t80) cc_final: 0.7905 (t80) outliers start: 33 outliers final: 30 residues processed: 231 average time/residue: 0.3252 time to fit residues: 117.8982 Evaluate side-chains 232 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 552 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 191 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 197 optimal weight: 7.9990 chunk 141 optimal weight: 0.7980 chunk 109 optimal weight: 9.9990 chunk 119 optimal weight: 0.0570 chunk 240 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 231 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 overall best weight: 3.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.153702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.116657 restraints weight = 104166.869| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 3.14 r_work: 0.3623 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 20556 Z= 0.164 Angle : 0.511 6.518 27884 Z= 0.272 Chirality : 0.035 0.208 3140 Planarity : 0.005 0.122 3440 Dihedral : 6.067 82.975 2720 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.98 % Favored : 94.86 % Rotamer: Outliers : 1.61 % Allowed : 13.33 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.95 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.18), residues: 2432 helix: 1.84 (0.14), residues: 1472 sheet: -3.70 (0.44), residues: 88 loop : -1.83 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 74 TYR 0.022 0.001 TYR A 338 PHE 0.009 0.001 PHE C 76 TRP 0.010 0.001 TRP D 173 HIS 0.003 0.001 HIS B 365 Details of bonding type rmsd covalent geometry : bond 0.00362 (20556) covalent geometry : angle 0.51122 (27884) hydrogen bonds : bond 0.04567 ( 1068) hydrogen bonds : angle 4.35119 ( 3114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 539 TYR cc_start: 0.8302 (t80) cc_final: 0.8096 (t80) REVERT: B 70 PHE cc_start: 0.6151 (m-80) cc_final: 0.5855 (m-80) REVERT: B 539 TYR cc_start: 0.8299 (t80) cc_final: 0.8085 (t80) REVERT: C 539 TYR cc_start: 0.8254 (t80) cc_final: 0.8001 (t80) outliers start: 35 outliers final: 32 residues processed: 230 average time/residue: 0.3036 time to fit residues: 111.5141 Evaluate side-chains 234 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 202 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 552 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 217 optimal weight: 9.9990 chunk 229 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 240 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 190 optimal weight: 9.9990 chunk 236 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.154271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.117865 restraints weight = 104172.823| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 3.09 r_work: 0.3629 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20556 Z= 0.140 Angle : 0.496 6.592 27884 Z= 0.262 Chirality : 0.035 0.204 3140 Planarity : 0.005 0.121 3440 Dihedral : 5.985 84.094 2720 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.93 % Favored : 94.90 % Rotamer: Outliers : 1.52 % Allowed : 13.79 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.95 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.18), residues: 2432 helix: 2.05 (0.14), residues: 1452 sheet: -3.50 (0.46), residues: 84 loop : -1.83 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 74 TYR 0.021 0.001 TYR A 338 PHE 0.009 0.001 PHE C 76 TRP 0.011 0.001 TRP D 173 HIS 0.003 0.001 HIS B 516 Details of bonding type rmsd covalent geometry : bond 0.00306 (20556) covalent geometry : angle 0.49564 (27884) hydrogen bonds : bond 0.04336 ( 1068) hydrogen bonds : angle 4.25273 ( 3114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 PHE cc_start: 0.6014 (m-80) cc_final: 0.5700 (m-80) REVERT: C 539 TYR cc_start: 0.8142 (t80) cc_final: 0.7922 (t80) outliers start: 33 outliers final: 32 residues processed: 231 average time/residue: 0.3039 time to fit residues: 112.3436 Evaluate side-chains 233 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 552 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 136 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 87 optimal weight: 0.0980 chunk 228 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 219 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.155278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.118336 restraints weight = 104003.416| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 3.17 r_work: 0.3646 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20556 Z= 0.114 Angle : 0.481 6.683 27884 Z= 0.253 Chirality : 0.034 0.203 3140 Planarity : 0.005 0.119 3440 Dihedral : 5.861 83.658 2720 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.69 % Favored : 95.15 % Rotamer: Outliers : 1.61 % Allowed : 13.69 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.95 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.18), residues: 2432 helix: 2.15 (0.14), residues: 1452 sheet: -3.40 (0.47), residues: 84 loop : -1.78 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 74 TYR 0.020 0.001 TYR A 338 PHE 0.009 0.001 PHE C 76 TRP 0.012 0.001 TRP D 173 HIS 0.003 0.001 HIS B 516 Details of bonding type rmsd covalent geometry : bond 0.00246 (20556) covalent geometry : angle 0.48077 (27884) hydrogen bonds : bond 0.04088 ( 1068) hydrogen bonds : angle 4.15407 ( 3114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 PHE cc_start: 0.6023 (m-80) cc_final: 0.5723 (m-80) REVERT: C 117 MET cc_start: 0.5969 (mtt) cc_final: 0.5688 (mtt) outliers start: 35 outliers final: 35 residues processed: 234 average time/residue: 0.3147 time to fit residues: 118.0171 Evaluate side-chains 237 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 202 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 552 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 109 optimal weight: 0.2980 chunk 56 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 121 optimal weight: 8.9990 chunk 241 optimal weight: 10.0000 chunk 169 optimal weight: 3.9990 chunk 189 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 51 optimal weight: 0.0170 overall best weight: 1.8624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.155569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.118822 restraints weight = 103505.741| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 3.14 r_work: 0.3647 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20556 Z= 0.115 Angle : 0.480 6.739 27884 Z= 0.252 Chirality : 0.034 0.201 3140 Planarity : 0.005 0.118 3440 Dihedral : 5.747 82.133 2720 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.48 % Favored : 95.35 % Rotamer: Outliers : 1.42 % Allowed : 13.79 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.95 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.18), residues: 2432 helix: 2.19 (0.14), residues: 1456 sheet: -3.32 (0.49), residues: 84 loop : -1.77 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 74 TYR 0.020 0.001 TYR A 338 PHE 0.010 0.001 PHE A 76 TRP 0.013 0.001 TRP D 173 HIS 0.003 0.001 HIS B 516 Details of bonding type rmsd covalent geometry : bond 0.00248 (20556) covalent geometry : angle 0.47976 (27884) hydrogen bonds : bond 0.03966 ( 1068) hydrogen bonds : angle 4.08301 ( 3114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 211 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 MET cc_start: 0.7868 (mmp) cc_final: 0.7667 (mmp) REVERT: A 539 TYR cc_start: 0.8213 (t80) cc_final: 0.7929 (t80) REVERT: A 604 GLU cc_start: 0.8289 (tp30) cc_final: 0.7902 (tp30) REVERT: B 70 PHE cc_start: 0.5973 (m-80) cc_final: 0.5670 (m-80) REVERT: B 265 MET cc_start: 0.7867 (mmp) cc_final: 0.7658 (mmp) REVERT: B 539 TYR cc_start: 0.8184 (t80) cc_final: 0.7717 (t80) REVERT: C 117 MET cc_start: 0.6053 (mtt) cc_final: 0.5820 (mtt) REVERT: D 539 TYR cc_start: 0.8261 (t80) cc_final: 0.7996 (t80) REVERT: D 604 GLU cc_start: 0.8306 (tp30) cc_final: 0.7921 (tp30) outliers start: 31 outliers final: 28 residues processed: 232 average time/residue: 0.3105 time to fit residues: 115.4792 Evaluate side-chains 235 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 207 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 540 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 146 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 236 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 180 optimal weight: 6.9990 chunk 199 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.154742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.117906 restraints weight = 104472.511| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 3.12 r_work: 0.3639 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20556 Z= 0.141 Angle : 0.496 6.710 27884 Z= 0.261 Chirality : 0.035 0.198 3140 Planarity : 0.005 0.119 3440 Dihedral : 5.788 80.896 2720 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.52 % Favored : 95.27 % Rotamer: Outliers : 1.38 % Allowed : 13.88 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.95 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.18), residues: 2432 helix: 2.12 (0.14), residues: 1456 sheet: -3.34 (0.49), residues: 84 loop : -1.76 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 74 TYR 0.021 0.001 TYR A 338 PHE 0.009 0.001 PHE C 76 TRP 0.012 0.001 TRP D 173 HIS 0.002 0.001 HIS A 365 Details of bonding type rmsd covalent geometry : bond 0.00309 (20556) covalent geometry : angle 0.49566 (27884) hydrogen bonds : bond 0.04170 ( 1068) hydrogen bonds : angle 4.14679 ( 3114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8338.09 seconds wall clock time: 142 minutes 22.26 seconds (8542.26 seconds total)