Starting phenix.real_space_refine on Fri Jul 3 10:31:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v7s_64822/07_2026/9v7s_64822.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v7s_64822/07_2026/9v7s_64822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v7s_64822/07_2026/9v7s_64822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v7s_64822/07_2026/9v7s_64822.map" model { file = "/net/cci-nas-00/data/ceres_data/9v7s_64822/07_2026/9v7s_64822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v7s_64822/07_2026/9v7s_64822.cif" } resolution = 2.5 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= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 65 5.49 5 Mg 2 5.21 5 S 30 5.16 5 C 8236 2.51 5 N 2451 2.21 5 O 2637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13421 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 6038 Classifications: {'peptide': 757} Link IDs: {'PTRANS': 42, 'TRANS': 714} Chain: "B" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 379 Classifications: {'DNA': 18} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 17} Chain: "C" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 308 Classifications: {'RNA': 15} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 9} Link IDs: {'rna3p': 14} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 6019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 6019 Classifications: {'peptide': 755} Link IDs: {'PTRANS': 42, 'TRANS': 712} Chain: "b" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 359 Classifications: {'DNA': 17} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Chain: "c" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 308 Classifications: {'RNA': 15} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 8} Link IDs: {'rna3p': 14} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 3.25, per 1000 atoms: 0.24 Number of scatterers: 13421 At special positions: 0 Unit cell: (89.355, 102.12, 129.352, 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 30 16.00 P 65 15.00 Mg 2 11.99 O 2637 8.00 N 2451 7.00 C 8236 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: 1.21 Conformation dependent library (CDL) restraints added in 545.6 milliseconds 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2808 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 17 sheets defined 33.5% alpha, 23.8% beta 20 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 37 through 54 Processing helix chain 'A' and resid 109 through 130 removed outlier: 3.545A pdb=" N ARG A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 312 through 325 Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 372 through 392 removed outlier: 4.391A pdb=" N MET A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 431 Processing helix chain 'A' and resid 451 through 464 Processing helix chain 'A' and resid 482 through 491 Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 516 through 530 Processing helix chain 'A' and resid 587 through 606 Processing helix chain 'A' and resid 621 through 639 Processing helix chain 'A' and resid 697 through 703 Processing helix chain 'A' and resid 723 through 735 Processing helix chain 'A' and resid 749 through 753 Processing helix chain 'a' and resid 37 through 54 Processing helix chain 'a' and resid 104 through 108 removed outlier: 3.983A pdb=" N ALA a 108 " --> pdb=" O PRO a 105 " (cutoff:3.500A) Processing helix chain 'a' and resid 109 through 130 Processing helix chain 'a' and resid 190 through 194 Processing helix chain 'a' and resid 195 through 202 Processing helix chain 'a' and resid 203 through 208 Processing helix chain 'a' and resid 212 through 216 removed outlier: 3.715A pdb=" N ARG a 216 " --> pdb=" O ALA a 213 " (cutoff:3.500A) Processing helix chain 'a' and resid 254 through 262 Processing helix chain 'a' and resid 299 through 304 Processing helix chain 'a' and resid 312 through 325 Processing helix chain 'a' and resid 360 through 362 No H-bonds generated for 'chain 'a' and resid 360 through 362' Processing helix chain 'a' and resid 372 through 392 removed outlier: 3.515A pdb=" N GLN a 382 " --> pdb=" O ASN a 378 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N MET a 385 " --> pdb=" O ARG a 381 " (cutoff:3.500A) Processing helix chain 'a' and resid 411 through 431 Processing helix chain 'a' and resid 447 through 450 Processing helix chain 'a' and resid 451 through 464 Processing helix chain 'a' and resid 482 through 491 Processing helix chain 'a' and resid 501 through 510 Processing helix chain 'a' and resid 516 through 530 Processing helix chain 'a' and resid 587 through 606 Processing helix chain 'a' and resid 621 through 639 removed outlier: 3.508A pdb=" N GLY a 639 " --> pdb=" O LEU a 635 " (cutoff:3.500A) Processing helix chain 'a' and resid 697 through 703 Processing helix chain 'a' and resid 723 through 735 Processing helix chain 'a' and resid 749 through 753 Processing sheet with id=AA1, first strand: chain 'A' and resid 344 through 346 removed outlier: 3.514A pdb=" N PHE A 344 " --> pdb=" O ALA A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 135 through 139 removed outlier: 6.678A pdb=" N LEU A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ARG A 162 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL A 330 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60 removed outlier: 3.933A pdb=" N ALA A 67 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N PHE A 21 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL A 101 " --> pdb=" O PHE A 21 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LEU A 23 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLU A 99 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N VAL A 25 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 284 through 287 removed outlier: 7.377A pdb=" N ALA A 272 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 234 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ARG A 276 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N PHE A 232 " --> pdb=" O ARG A 276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 244 through 247 Processing sheet with id=AA6, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AA7, first strand: chain 'A' and resid 436 through 442 removed outlier: 6.936A pdb=" N LEU A 402 " --> pdb=" O ARG A 438 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ILE A 440 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU A 404 " --> pdb=" O ILE A 440 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N TYR A 442 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TYR A 406 " --> pdb=" O TYR A 442 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ASP A 401 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL A 472 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL A 403 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL A 474 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU A 405 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 568 through 574 removed outlier: 6.241A pdb=" N LEU A 551 " --> pdb=" O ALA A 617 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL A 649 " --> pdb=" O THR A 714 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER A 679 " --> pdb=" O THR A 691 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'a' and resid 344 through 346 removed outlier: 3.597A pdb=" N PHE a 344 " --> pdb=" O ALA a 8 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU a 6 " --> pdb=" O THR a 346 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'a' and resid 135 through 139 removed outlier: 6.660A pdb=" N LEU a 142 " --> pdb=" O LYS a 138 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ARG a 162 " --> pdb=" O ARG a 145 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS a 174 " --> pdb=" O LEU a 171 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a' and resid 58 through 60 removed outlier: 3.856A pdb=" N ALA a 67 " --> pdb=" O THR a 60 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N VAL a 25 " --> pdb=" O ILE a 97 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG a 90 " --> pdb=" O ASP a 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 283 through 287 removed outlier: 7.378A pdb=" N ALA a 272 " --> pdb=" O THR a 236 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY a 234 " --> pdb=" O PHE a 274 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ARG a 276 " --> pdb=" O PHE a 232 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N PHE a 232 " --> pdb=" O ARG a 276 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'a' and resid 244 through 247 Processing sheet with id=AB5, first strand: chain 'a' and resid 331 through 332 Processing sheet with id=AB6, first strand: chain 'a' and resid 364 through 365 Processing sheet with id=AB7, first strand: chain 'a' and resid 436 through 442 removed outlier: 6.869A pdb=" N LEU a 402 " --> pdb=" O ARG a 438 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N ILE a 440 " --> pdb=" O LEU a 402 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU a 404 " --> pdb=" O ILE a 440 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N TYR a 442 " --> pdb=" O LEU a 404 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR a 406 " --> pdb=" O TYR a 442 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASP a 401 " --> pdb=" O LEU a 470 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL a 472 " --> pdb=" O ASP a 401 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL a 403 " --> pdb=" O VAL a 472 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL a 474 " --> pdb=" O VAL a 403 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU a 405 " --> pdb=" O VAL a 474 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'a' and resid 568 through 575 removed outlier: 6.240A pdb=" N LEU a 551 " --> pdb=" O ALA a 617 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU a 612 " --> pdb=" O GLY a 648 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL a 650 " --> pdb=" O LEU a 612 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL a 614 " --> pdb=" O VAL a 650 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL a 652 " --> pdb=" O VAL a 614 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG a 616 " --> pdb=" O VAL a 652 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL a 649 " --> pdb=" O THR a 714 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU a 687 " --> pdb=" O LEU a 683 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER a 679 " --> pdb=" O THR a 691 " (cutoff:3.500A) 557 hydrogen bonds defined for protein. 1554 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 2.78 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3516 1.33 - 1.45: 2762 1.45 - 1.57: 7383 1.57 - 1.69: 126 1.69 - 1.81: 46 Bond restraints: 13833 Sorted by residual: bond pdb=" C3' DT b 14 " pdb=" C2' DT b 14 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DT B 14 " pdb=" C2' DT B 14 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.75e+00 bond pdb=" C3' DT B 18 " pdb=" C2' DT B 18 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.76e+00 bond pdb=" C3' DT B 16 " pdb=" C2' DT B 16 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.10e+00 bond pdb=" C3' DG b 15 " pdb=" C2' DG b 15 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.89e+00 ... (remaining 13828 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 18704 1.80 - 3.60: 329 3.60 - 5.40: 22 5.40 - 7.19: 1 7.19 - 8.99: 1 Bond angle restraints: 19057 Sorted by residual: angle pdb=" O5' C C 5 " pdb=" C5' C C 5 " pdb=" C4' C C 5 " ideal model delta sigma weight residual 109.40 116.30 -6.90 8.00e-01 1.56e+00 7.43e+01 angle pdb=" O4' C C 5 " pdb=" C1' C C 5 " pdb=" N1 C C 5 " ideal model delta sigma weight residual 108.50 112.12 -3.62 7.00e-01 2.04e+00 2.68e+01 angle pdb=" O4' DG b 4 " pdb=" C4' DG b 4 " pdb=" C3' DG b 4 " ideal model delta sigma weight residual 106.00 103.34 2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT b 16 " pdb=" C4 DT b 16 " pdb=" O4 DT b 16 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT b 14 " pdb=" C4 DT b 14 " pdb=" O4 DT b 14 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 ... (remaining 19052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.06: 7586 28.06 - 56.13: 575 56.13 - 84.19: 86 84.19 - 112.26: 6 112.26 - 140.32: 2 Dihedral angle restraints: 8255 sinusoidal: 3895 harmonic: 4360 Sorted by residual: dihedral pdb=" CA PHE a 21 " pdb=" C PHE a 21 " pdb=" N ARG a 22 " pdb=" CA ARG a 22 " ideal model delta harmonic sigma weight residual -180.00 -159.43 -20.57 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" C4' DT b 13 " pdb=" C3' DT b 13 " pdb=" O3' DT b 13 " pdb=" P DT b 14 " ideal model delta sinusoidal sigma weight residual 220.00 79.68 140.32 1 3.50e+01 8.16e-04 1.39e+01 dihedral pdb=" C4' DT B 13 " pdb=" C3' DT B 13 " pdb=" O3' DT B 13 " pdb=" P DT B 14 " ideal model delta sinusoidal sigma weight residual 220.00 84.95 135.05 1 3.50e+01 8.16e-04 1.34e+01 ... (remaining 8252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1682 0.046 - 0.093: 302 0.093 - 0.139: 133 0.139 - 0.185: 7 0.185 - 0.232: 1 Chirality restraints: 2125 Sorted by residual: chirality pdb=" C4' C C 5 " pdb=" C5' C C 5 " pdb=" O4' C C 5 " pdb=" C3' C C 5 " both_signs ideal model delta sigma weight residual False -2.50 -2.27 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C2' C C 5 " pdb=" C3' C C 5 " pdb=" O2' C C 5 " pdb=" C1' C C 5 " both_signs ideal model delta sigma weight residual False -2.62 -2.79 0.17 2.00e-01 2.50e+01 7.23e-01 chirality pdb=" C2' C c 5 " pdb=" C3' C c 5 " pdb=" O2' C c 5 " pdb=" C1' C c 5 " both_signs ideal model delta sigma weight residual False -2.62 -2.78 0.17 2.00e-01 2.50e+01 6.93e-01 ... (remaining 2122 not shown) Planarity restraints: 2268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 607 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO A 608 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 608 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 608 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 308 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO A 309 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 309 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 309 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL a 266 " 0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO a 267 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO a 267 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO a 267 " 0.021 5.00e-02 4.00e+02 ... (remaining 2265 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 96 2.62 - 3.19: 10221 3.19 - 3.76: 20351 3.76 - 4.33: 30131 4.33 - 4.90: 47650 Nonbonded interactions: 108449 Sorted by model distance: nonbonded pdb=" OE1 GLN a 497 " pdb="MG MG a 801 " model vdw 2.053 2.170 nonbonded pdb=" O LEU A 524 " pdb=" OG1 THR A 528 " model vdw 2.211 3.040 nonbonded pdb=" OD2 ASP a 126 " pdb=" O HOH a 901 " model vdw 2.233 3.040 nonbonded pdb=" NZ LYS a 417 " pdb=" OE1 GLN a 420 " model vdw 2.254 3.120 nonbonded pdb=" NZ LYS A 4 " pdb=" OE2 GLU A 374 " model vdw 2.261 3.120 ... (remaining 108444 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' and (resid 4 through 758 or resid 801)) selection = chain 'a' } ncs_group { reference = (chain 'B' and resid 1 through 17) selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } 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: 1.570 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.630 Find NCS groups from input model: 0.260 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:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 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 0.058 13833 Z= 0.229 Angle : 0.544 8.993 19057 Z= 0.377 Chirality : 0.043 0.232 2125 Planarity : 0.005 0.042 2268 Dihedral : 18.597 140.324 5447 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.33 % Allowed : 19.80 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.22), residues: 1508 helix: 1.80 (0.24), residues: 443 sheet: 1.10 (0.27), residues: 380 loop : -0.20 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 712 TYR 0.024 0.002 TYR a 380 PHE 0.012 0.001 PHE a 662 TRP 0.014 0.001 TRP a 620 HIS 0.004 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.23 (13833) covalent geometry : angle 0.54421 / 0.38 (19057) hydrogen bonds : bond 0.18568 / 12.10 ( 606) hydrogen bonds : angle 6.20982 / 4.39 ( 1652) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.457 Fit side-chains REVERT: A 390 GLU cc_start: 0.7142 (tt0) cc_final: 0.6919 (tt0) REVERT: A 758 ARG cc_start: 0.5212 (OUTLIER) cc_final: 0.4380 (ptt-90) REVERT: a 580 ARG cc_start: 0.7307 (ptt180) cc_final: 0.6785 (ptp-170) outliers start: 30 outliers final: 23 residues processed: 164 average time/residue: 0.6426 time to fit residues: 114.5300 Evaluate side-chains 162 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain a residue 14 THR Chi-restraints excluded: chain a residue 43 ASN Chi-restraints excluded: chain a residue 83 THR Chi-restraints excluded: chain a residue 134 LYS Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 184 THR Chi-restraints excluded: chain a residue 192 SER Chi-restraints excluded: chain a residue 208 SER Chi-restraints excluded: chain a residue 240 VAL Chi-restraints excluded: chain a residue 301 GLU Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain a residue 466 ASP Chi-restraints excluded: chain a residue 671 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 361 ASN a 572 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.165379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.135506 restraints weight = 12605.910| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.34 r_work: 0.3445 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.0714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.132 13833 Z= 0.293 Angle : 0.760 7.625 19057 Z= 0.414 Chirality : 0.053 0.292 2125 Planarity : 0.007 0.057 2268 Dihedral : 15.660 144.082 2537 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.66 % Allowed : 17.47 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.21), residues: 1508 helix: 1.35 (0.24), residues: 451 sheet: 0.77 (0.26), residues: 397 loop : -0.46 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 316 TYR 0.030 0.003 TYR A 380 PHE 0.025 0.003 PHE a 545 TRP 0.018 0.003 TRP a 620 HIS 0.006 0.001 HIS a 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00676 / 0.29 (13833) covalent geometry : angle 0.76028 / 0.41 (19057) hydrogen bonds : bond 0.07888 / 5.30 ( 606) hydrogen bonds : angle 5.07299 / 3.58 ( 1652) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 140 time to evaluate : 0.333 Fit side-chains REVERT: A 51 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7608 (ttmt) REVERT: A 94 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8200 (mm) REVERT: A 128 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7059 (t80) REVERT: A 193 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.6698 (mp0) REVERT: A 387 MET cc_start: 0.8716 (mmm) cc_final: 0.8504 (mmm) REVERT: a 34 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7038 (mpp) REVERT: a 580 ARG cc_start: 0.7430 (ptt180) cc_final: 0.6504 (ptp-170) outliers start: 60 outliers final: 32 residues processed: 175 average time/residue: 0.6718 time to fit residues: 127.0656 Evaluate side-chains 176 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain a residue 34 MET Chi-restraints excluded: chain a residue 77 THR Chi-restraints excluded: chain a residue 83 THR Chi-restraints excluded: chain a residue 100 THR Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 184 THR Chi-restraints excluded: chain a residue 208 SER Chi-restraints excluded: chain a residue 240 VAL Chi-restraints excluded: chain a residue 301 GLU Chi-restraints excluded: chain a residue 331 SER Chi-restraints excluded: chain a residue 607 VAL Chi-restraints excluded: chain a residue 643 LYS Chi-restraints excluded: chain a residue 646 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 82 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 128 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.166439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.134682 restraints weight = 12717.504| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.50 r_work: 0.3429 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13833 Z= 0.137 Angle : 0.534 5.868 19057 Z= 0.306 Chirality : 0.043 0.234 2125 Planarity : 0.005 0.052 2268 Dihedral : 15.245 144.212 2518 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.65 % Allowed : 18.01 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.22), residues: 1508 helix: 1.87 (0.24), residues: 453 sheet: 0.90 (0.26), residues: 401 loop : -0.24 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 712 TYR 0.021 0.002 TYR a 380 PHE 0.011 0.001 PHE a 545 TRP 0.016 0.001 TRP a 136 HIS 0.004 0.001 HIS a 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 (13833) covalent geometry : angle 0.53363 / 0.31 (19057) hydrogen bonds : bond 0.05201 / 3.49 ( 606) hydrogen bonds : angle 4.68928 / 3.31 ( 1652) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 135 time to evaluate : 0.475 Fit side-chains REVERT: A 22 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6932 (ttp-110) REVERT: A 51 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7411 (ttmt) REVERT: A 62 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7362 (mtp85) REVERT: A 128 PHE cc_start: 0.7852 (OUTLIER) cc_final: 0.6868 (t80) REVERT: A 301 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7636 (mp0) REVERT: a 580 ARG cc_start: 0.7303 (ptt180) cc_final: 0.6317 (ptp-170) REVERT: a 630 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6723 (tm-30) outliers start: 47 outliers final: 27 residues processed: 166 average time/residue: 0.6443 time to fit residues: 116.0924 Evaluate side-chains 167 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain a residue 14 THR Chi-restraints excluded: chain a residue 77 THR Chi-restraints excluded: chain a residue 83 THR Chi-restraints excluded: chain a residue 100 THR Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 184 THR Chi-restraints excluded: chain a residue 240 VAL Chi-restraints excluded: chain a residue 244 THR Chi-restraints excluded: chain a residue 301 GLU Chi-restraints excluded: chain a residue 331 SER Chi-restraints excluded: chain a residue 341 HIS Chi-restraints excluded: chain a residue 366 THR Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain a residue 630 GLU Chi-restraints excluded: chain a residue 643 LYS Chi-restraints excluded: chain a residue 671 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 76 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 chunk 101 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 96 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 GLN a 361 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.163284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.131184 restraints weight = 12645.567| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.50 r_work: 0.3376 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 13833 Z= 0.237 Angle : 0.680 7.235 19057 Z= 0.374 Chirality : 0.049 0.272 2125 Planarity : 0.006 0.059 2268 Dihedral : 15.363 143.326 2514 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.81 % Allowed : 17.47 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.21), residues: 1508 helix: 1.59 (0.24), residues: 452 sheet: 0.87 (0.26), residues: 393 loop : -0.41 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG a 316 TYR 0.028 0.003 TYR A 380 PHE 0.020 0.002 PHE a 545 TRP 0.017 0.003 TRP a 620 HIS 0.006 0.001 HIS a 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.24 (13833) covalent geometry : angle 0.68047 / 0.37 (19057) hydrogen bonds : bond 0.06733 / 4.53 ( 606) hydrogen bonds : angle 4.76985 / 3.36 ( 1652) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 132 time to evaluate : 0.531 Fit side-chains REVERT: A 94 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8121 (mm) REVERT: A 128 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7005 (t80) REVERT: A 193 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.6662 (mp0) REVERT: A 301 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7589 (mt-10) REVERT: a 34 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7114 (mpp) REVERT: a 212 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6461 (pp20) REVERT: a 225 LYS cc_start: 0.6159 (OUTLIER) cc_final: 0.5936 (tptm) REVERT: a 580 ARG cc_start: 0.7327 (ptt180) cc_final: 0.6358 (ptp-170) outliers start: 62 outliers final: 38 residues processed: 171 average time/residue: 0.6288 time to fit residues: 116.6067 Evaluate side-chains 182 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 137 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain a residue 14 THR Chi-restraints excluded: chain a residue 34 MET Chi-restraints excluded: chain a residue 77 THR Chi-restraints excluded: chain a residue 83 THR Chi-restraints excluded: chain a residue 100 THR Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 184 THR Chi-restraints excluded: chain a residue 212 GLU Chi-restraints excluded: chain a residue 225 LYS Chi-restraints excluded: chain a residue 240 VAL Chi-restraints excluded: chain a residue 244 THR Chi-restraints excluded: chain a residue 301 GLU Chi-restraints excluded: chain a residue 331 SER Chi-restraints excluded: chain a residue 341 HIS Chi-restraints excluded: chain a residue 366 THR Chi-restraints excluded: chain a residue 385 MET Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain a residue 607 VAL Chi-restraints excluded: chain a residue 643 LYS Chi-restraints excluded: chain a residue 646 GLN Chi-restraints excluded: chain a residue 664 VAL Chi-restraints excluded: chain a residue 671 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 120 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.166138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.134435 restraints weight = 12619.878| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.49 r_work: 0.3420 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13833 Z= 0.138 Angle : 0.538 5.977 19057 Z= 0.306 Chirality : 0.043 0.234 2125 Planarity : 0.005 0.052 2268 Dihedral : 15.174 143.805 2514 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.88 % Allowed : 18.79 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.22), residues: 1508 helix: 1.93 (0.25), residues: 452 sheet: 0.91 (0.26), residues: 397 loop : -0.27 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 567 TYR 0.022 0.002 TYR a 380 PHE 0.012 0.001 PHE a 545 TRP 0.016 0.001 TRP a 136 HIS 0.003 0.001 HIS a 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (13833) covalent geometry : angle 0.53759 / 0.31 (19057) hydrogen bonds : bond 0.05020 / 3.37 ( 606) hydrogen bonds : angle 4.56635 / 3.23 ( 1652) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 136 time to evaluate : 0.522 Fit side-chains REVERT: A 22 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6932 (ttp-110) REVERT: A 62 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7420 (mtp85) REVERT: A 94 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8103 (mm) REVERT: A 128 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7023 (t80) REVERT: A 301 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: A 758 ARG cc_start: 0.5108 (OUTLIER) cc_final: 0.3992 (ptt-90) REVERT: a 34 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7065 (mpp) REVERT: a 58 VAL cc_start: 0.8604 (m) cc_final: 0.8375 (t) REVERT: a 212 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6234 (pp20) REVERT: a 580 ARG cc_start: 0.7301 (ptt180) cc_final: 0.6368 (ptp-170) outliers start: 50 outliers final: 30 residues processed: 167 average time/residue: 0.6672 time to fit residues: 120.4620 Evaluate side-chains 173 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain a residue 14 THR Chi-restraints excluded: chain a residue 21 PHE Chi-restraints excluded: chain a residue 34 MET Chi-restraints excluded: chain a residue 55 GLN Chi-restraints excluded: chain a residue 77 THR Chi-restraints excluded: chain a residue 100 THR Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 212 GLU Chi-restraints excluded: chain a residue 240 VAL Chi-restraints excluded: chain a residue 244 THR Chi-restraints excluded: chain a residue 301 GLU Chi-restraints excluded: chain a residue 331 SER Chi-restraints excluded: chain a residue 341 HIS Chi-restraints excluded: chain a residue 366 THR Chi-restraints excluded: chain a residue 398 SER Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain a residue 643 LYS Chi-restraints excluded: chain a residue 671 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 78 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.165446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.133625 restraints weight = 12587.525| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.49 r_work: 0.3411 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13833 Z= 0.157 Angle : 0.561 6.247 19057 Z= 0.316 Chirality : 0.044 0.230 2125 Planarity : 0.005 0.054 2268 Dihedral : 15.149 143.176 2511 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.43 % Allowed : 18.56 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.22), residues: 1508 helix: 1.95 (0.24), residues: 452 sheet: 0.90 (0.26), residues: 391 loop : -0.27 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 712 TYR 0.023 0.002 TYR a 380 PHE 0.013 0.002 PHE a 545 TRP 0.015 0.002 TRP a 620 HIS 0.003 0.001 HIS a 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (13833) covalent geometry : angle 0.56055 / 0.32 (19057) hydrogen bonds : bond 0.05273 / 3.53 ( 606) hydrogen bonds : angle 4.54411 / 3.21 ( 1652) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 138 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 22 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.6917 (ttp-110) REVERT: A 62 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7327 (mtt90) REVERT: A 94 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8113 (mm) REVERT: A 128 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.6943 (t80) REVERT: A 226 ILE cc_start: 0.6664 (OUTLIER) cc_final: 0.6012 (mm) REVERT: A 301 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: A 758 ARG cc_start: 0.5092 (OUTLIER) cc_final: 0.3971 (ptt-90) REVERT: a 34 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7032 (mpp) REVERT: a 58 VAL cc_start: 0.8610 (m) cc_final: 0.8394 (t) REVERT: a 580 ARG cc_start: 0.7307 (ptt180) cc_final: 0.6429 (ptp-170) outliers start: 57 outliers final: 36 residues processed: 175 average time/residue: 0.6331 time to fit residues: 119.9626 Evaluate side-chains 181 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 137 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain a residue 14 THR Chi-restraints excluded: chain a residue 21 PHE Chi-restraints excluded: chain a residue 34 MET Chi-restraints excluded: chain a residue 77 THR Chi-restraints excluded: chain a residue 100 THR Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 184 THR Chi-restraints excluded: chain a residue 240 VAL Chi-restraints excluded: chain a residue 244 THR Chi-restraints excluded: chain a residue 301 GLU Chi-restraints excluded: chain a residue 331 SER Chi-restraints excluded: chain a residue 341 HIS Chi-restraints excluded: chain a residue 366 THR Chi-restraints excluded: chain a residue 398 SER Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain a residue 643 LYS Chi-restraints excluded: chain a residue 664 VAL Chi-restraints excluded: chain a residue 671 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 36 optimal weight: 0.5980 chunk 112 optimal weight: 0.4980 chunk 1 optimal weight: 9.9990 chunk 152 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 147 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 146 optimal weight: 0.0980 chunk 12 optimal weight: 4.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.165687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.133839 restraints weight = 12581.612| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.49 r_work: 0.3417 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13833 Z= 0.154 Angle : 0.554 6.121 19057 Z= 0.312 Chirality : 0.044 0.233 2125 Planarity : 0.005 0.054 2268 Dihedral : 15.127 143.012 2511 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.43 % Allowed : 18.63 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.22), residues: 1508 helix: 1.96 (0.24), residues: 452 sheet: 0.86 (0.26), residues: 393 loop : -0.27 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 712 TYR 0.023 0.002 TYR a 380 PHE 0.013 0.002 PHE a 545 TRP 0.016 0.002 TRP a 620 HIS 0.003 0.001 HIS a 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (13833) covalent geometry : angle 0.55384 / 0.31 (19057) hydrogen bonds : bond 0.05160 / 3.46 ( 606) hydrogen bonds : angle 4.52223 / 3.19 ( 1652) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 138 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 22 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6958 (ttp-110) REVERT: A 51 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7618 (ttmp) REVERT: A 62 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7352 (mtt90) REVERT: A 94 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8110 (mm) REVERT: A 128 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.6945 (t80) REVERT: A 193 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.6674 (mp0) REVERT: A 226 ILE cc_start: 0.6622 (OUTLIER) cc_final: 0.5972 (mm) REVERT: A 301 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7615 (mt-10) REVERT: A 758 ARG cc_start: 0.5056 (OUTLIER) cc_final: 0.4042 (ptt-90) REVERT: a 34 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7040 (mpp) REVERT: a 58 VAL cc_start: 0.8610 (m) cc_final: 0.8372 (t) REVERT: a 580 ARG cc_start: 0.7312 (ptt180) cc_final: 0.6441 (ptp-170) outliers start: 57 outliers final: 36 residues processed: 177 average time/residue: 0.6422 time to fit residues: 123.2264 Evaluate side-chains 183 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 137 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain a residue 14 THR Chi-restraints excluded: chain a residue 21 PHE Chi-restraints excluded: chain a residue 34 MET Chi-restraints excluded: chain a residue 43 ASN Chi-restraints excluded: chain a residue 77 THR Chi-restraints excluded: chain a residue 100 THR Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 184 THR Chi-restraints excluded: chain a residue 240 VAL Chi-restraints excluded: chain a residue 244 THR Chi-restraints excluded: chain a residue 301 GLU Chi-restraints excluded: chain a residue 331 SER Chi-restraints excluded: chain a residue 341 HIS Chi-restraints excluded: chain a residue 366 THR Chi-restraints excluded: chain a residue 398 SER Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain a residue 643 LYS Chi-restraints excluded: chain a residue 664 VAL Chi-restraints excluded: chain a residue 671 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 12 optimal weight: 4.9990 chunk 151 optimal weight: 0.0060 chunk 48 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.167994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.136553 restraints weight = 12516.120| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.49 r_work: 0.3470 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 13833 Z= 0.119 Angle : 0.495 5.303 19057 Z= 0.284 Chirality : 0.042 0.224 2125 Planarity : 0.005 0.050 2268 Dihedral : 15.018 142.742 2511 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.18 % Allowed : 20.03 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.22), residues: 1508 helix: 2.19 (0.24), residues: 452 sheet: 0.97 (0.27), residues: 394 loop : -0.15 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 712 TYR 0.019 0.001 TYR a 380 PHE 0.009 0.001 PHE a 545 TRP 0.015 0.001 TRP a 136 HIS 0.003 0.001 HIS a 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (13833) covalent geometry : angle 0.49497 / 0.28 (19057) hydrogen bonds : bond 0.04253 / 2.85 ( 606) hydrogen bonds : angle 4.39320 / 3.11 ( 1652) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 136 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 62 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7448 (mtp85) REVERT: A 94 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8080 (mm) REVERT: A 128 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.6810 (t80) REVERT: A 226 ILE cc_start: 0.6645 (OUTLIER) cc_final: 0.5980 (mm) REVERT: A 301 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: A 758 ARG cc_start: 0.4930 (OUTLIER) cc_final: 0.3980 (ptt-90) REVERT: a 34 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.6993 (mpp) REVERT: a 225 LYS cc_start: 0.6039 (OUTLIER) cc_final: 0.5813 (tptm) REVERT: a 481 GLU cc_start: 0.7138 (mp0) cc_final: 0.6798 (mp0) REVERT: a 580 ARG cc_start: 0.7266 (ptt180) cc_final: 0.6395 (ptp-170) outliers start: 41 outliers final: 24 residues processed: 165 average time/residue: 0.6935 time to fit residues: 123.8739 Evaluate side-chains 164 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain a residue 21 PHE Chi-restraints excluded: chain a residue 34 MET Chi-restraints excluded: chain a residue 100 THR Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 225 LYS Chi-restraints excluded: chain a residue 240 VAL Chi-restraints excluded: chain a residue 244 THR Chi-restraints excluded: chain a residue 301 GLU Chi-restraints excluded: chain a residue 331 SER Chi-restraints excluded: chain a residue 341 HIS Chi-restraints excluded: chain a residue 366 THR Chi-restraints excluded: chain a residue 398 SER Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain a residue 664 VAL Chi-restraints excluded: chain a residue 671 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 91 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 130 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 361 ASN a 449 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.167775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.136209 restraints weight = 12660.226| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.49 r_work: 0.3460 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 13833 Z= 0.124 Angle : 0.502 5.340 19057 Z= 0.285 Chirality : 0.042 0.220 2125 Planarity : 0.005 0.048 2268 Dihedral : 14.980 142.101 2509 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.87 % Allowed : 20.11 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.22), residues: 1508 helix: 2.21 (0.24), residues: 452 sheet: 0.99 (0.27), residues: 394 loop : -0.13 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 157 TYR 0.020 0.001 TYR a 380 PHE 0.014 0.001 PHE A 469 TRP 0.014 0.001 TRP a 136 HIS 0.004 0.001 HIS a 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (13833) covalent geometry : angle 0.50222 / 0.29 (19057) hydrogen bonds : bond 0.04358 / 2.90 ( 606) hydrogen bonds : angle 4.36459 / 3.09 ( 1652) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 62 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7432 (mtp85) REVERT: A 94 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8060 (mm) REVERT: A 128 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.6739 (t80) REVERT: A 226 ILE cc_start: 0.6654 (OUTLIER) cc_final: 0.6288 (tp) REVERT: A 758 ARG cc_start: 0.4979 (OUTLIER) cc_final: 0.3952 (ptt-90) REVERT: a 34 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.6985 (mpp) REVERT: a 212 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6320 (pp20) REVERT: a 240 VAL cc_start: 0.5779 (OUTLIER) cc_final: 0.5468 (m) REVERT: a 282 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6971 (m-30) REVERT: a 481 GLU cc_start: 0.7110 (mp0) cc_final: 0.6796 (mp0) REVERT: a 580 ARG cc_start: 0.7276 (ptt180) cc_final: 0.6412 (ptp-110) outliers start: 37 outliers final: 28 residues processed: 161 average time/residue: 0.6295 time to fit residues: 110.0156 Evaluate side-chains 171 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain a residue 14 THR Chi-restraints excluded: chain a residue 21 PHE Chi-restraints excluded: chain a residue 34 MET Chi-restraints excluded: chain a residue 77 THR Chi-restraints excluded: chain a residue 100 THR Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 212 GLU Chi-restraints excluded: chain a residue 240 VAL Chi-restraints excluded: chain a residue 244 THR Chi-restraints excluded: chain a residue 282 ASP Chi-restraints excluded: chain a residue 301 GLU Chi-restraints excluded: chain a residue 331 SER Chi-restraints excluded: chain a residue 341 HIS Chi-restraints excluded: chain a residue 366 THR Chi-restraints excluded: chain a residue 398 SER Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain a residue 664 VAL Chi-restraints excluded: chain a residue 671 SER Chi-restraints excluded: chain a residue 729 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 27 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 85 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 103 optimal weight: 20.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 361 ASN a 449 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.166267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.134528 restraints weight = 12527.449| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.49 r_work: 0.3420 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13833 Z= 0.152 Angle : 0.544 5.949 19057 Z= 0.305 Chirality : 0.044 0.235 2125 Planarity : 0.005 0.051 2268 Dihedral : 15.020 141.937 2509 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.34 % Allowed : 19.88 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.22), residues: 1508 helix: 2.10 (0.24), residues: 452 sheet: 0.92 (0.27), residues: 393 loop : -0.18 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 712 TYR 0.023 0.002 TYR a 380 PHE 0.015 0.002 PHE A 469 TRP 0.013 0.002 TRP a 620 HIS 0.004 0.001 HIS a 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (13833) covalent geometry : angle 0.54411 / 0.31 (19057) hydrogen bonds : bond 0.04894 / 3.27 ( 606) hydrogen bonds : angle 4.42834 / 3.13 ( 1652) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 133 time to evaluate : 0.378 Fit side-chains REVERT: A 62 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7432 (mtp85) REVERT: A 94 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.8074 (mm) REVERT: A 128 PHE cc_start: 0.7881 (OUTLIER) cc_final: 0.6893 (t80) REVERT: A 226 ILE cc_start: 0.6607 (OUTLIER) cc_final: 0.6257 (tp) REVERT: A 301 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7637 (mt-10) REVERT: A 758 ARG cc_start: 0.4992 (OUTLIER) cc_final: 0.4021 (ptt-90) REVERT: a 34 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7009 (mpp) REVERT: a 240 VAL cc_start: 0.5799 (OUTLIER) cc_final: 0.5505 (m) REVERT: a 282 ASP cc_start: 0.7213 (OUTLIER) cc_final: 0.6990 (m-30) REVERT: a 481 GLU cc_start: 0.7147 (mp0) cc_final: 0.6788 (mp0) REVERT: a 580 ARG cc_start: 0.7272 (ptt180) cc_final: 0.6410 (ptp-110) outliers start: 43 outliers final: 28 residues processed: 161 average time/residue: 0.6333 time to fit residues: 110.3713 Evaluate side-chains 169 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain a residue 14 THR Chi-restraints excluded: chain a residue 21 PHE Chi-restraints excluded: chain a residue 34 MET Chi-restraints excluded: chain a residue 77 THR Chi-restraints excluded: chain a residue 100 THR Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 240 VAL Chi-restraints excluded: chain a residue 244 THR Chi-restraints excluded: chain a residue 282 ASP Chi-restraints excluded: chain a residue 301 GLU Chi-restraints excluded: chain a residue 331 SER Chi-restraints excluded: chain a residue 341 HIS Chi-restraints excluded: chain a residue 366 THR Chi-restraints excluded: chain a residue 398 SER Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain a residue 643 LYS Chi-restraints excluded: chain a residue 664 VAL Chi-restraints excluded: chain a residue 671 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 112 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 361 ASN a 449 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.165689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.133842 restraints weight = 12592.352| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.49 r_work: 0.3416 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13833 Z= 0.157 Angle : 0.559 6.344 19057 Z= 0.313 Chirality : 0.044 0.233 2125 Planarity : 0.005 0.051 2268 Dihedral : 14.996 142.226 2509 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.18 % Allowed : 20.19 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.22), residues: 1508 helix: 2.04 (0.24), residues: 452 sheet: 0.87 (0.27), residues: 393 loop : -0.22 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 712 TYR 0.023 0.002 TYR a 380 PHE 0.015 0.002 PHE A 469 TRP 0.014 0.002 TRP a 620 HIS 0.004 0.001 HIS a 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (13833) covalent geometry : angle 0.55916 / 0.31 (19057) hydrogen bonds : bond 0.05171 / 3.47 ( 606) hydrogen bonds : angle 4.48153 / 3.17 ( 1652) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4612.51 seconds wall clock time: 79 minutes 10.01 seconds (4750.01 seconds total)