Starting phenix.real_space_refine on Thu Aug 6 05:11:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v7s_64822/08_2026/9v7s_64822.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v7s_64822/08_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_64822/08_2026/9v7s_64822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v7s_64822/08_2026/9v7s_64822.map" model { file = "/net/cci-nas-00/data/ceres_data/9v7s_64822/08_2026/9v7s_64822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v7s_64822/08_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-2.2rc3-6140/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: 2.74, per 1000 atoms: 0.20 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: 0.99 Conformation dependent library (CDL) restraints added in 627.6 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: 1.42 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: 2.84 Time building geometry restraints manager: 1.38 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: 18623 1.80 - 3.60: 410 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: 1651 0.046 - 0.093: 306 0.093 - 0.139: 159 0.139 - 0.185: 8 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.930 Find NCS groups from input model: 0.230 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:9.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.380 ------------------------------------------------------------------------------- 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= 0.231 Angle : 0.568 8.993 19057 Z= 0.398 Chirality : 0.045 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 0.00343 / 0.23 (13833) covalent geometry : angle 0.56773 / 0.40 (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 : 0.294 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: 0.6352 time to fit residues: 112.9547 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 : 0.518 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.162496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.130284 restraints weight = 12586.579| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.52 r_work: 0.3366 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.0733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.134 13833 Z= 0.298 Angle : 0.780 7.821 19057 Z= 0.421 Chirality : 0.054 0.309 2125 Planarity : 0.007 0.059 2268 Dihedral : 15.632 143.736 2537 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.74 % Allowed : 17.24 % Favored : 78.03 % 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: 0.58 (0.21), residues: 1508 helix: 1.33 (0.24), residues: 451 sheet: 0.77 (0.26), residues: 397 loop : -0.47 (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 0.002 HIS a 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.30 (13833) covalent geometry : angle 0.78026 / 0.42 (19057) hydrogen bonds : bond 0.07682 / 5.18 ( 606) hydrogen bonds : angle 5.04167 / 3.56 ( 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 201 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 140 time to evaluate : 0.433 Fit side-chains REVERT: A 51 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7536 (ttmt) REVERT: A 94 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8135 (mm) REVERT: A 114 GLN cc_start: 0.7891 (tt0) cc_final: 0.7690 (tt0) REVERT: A 128 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.7055 (t80) REVERT: A 193 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.6670 (mp0) REVERT: A 387 MET cc_start: 0.8720 (mmm) cc_final: 0.8502 (mmm) REVERT: A 630 GLU cc_start: 0.7949 (mp0) cc_final: 0.7730 (mp0) REVERT: a 34 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7067 (mpp) REVERT: a 580 ARG cc_start: 0.7356 (ptt180) cc_final: 0.6399 (ptp-170) outliers start: 61 outliers final: 32 residues processed: 175 average time/residue: 0.6132 time to fit residues: 116.2163 Evaluate side-chains 175 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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: 0.3980 chunk 91 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.168123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.136731 restraints weight = 12720.213| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.49 r_work: 0.3454 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 13833 Z= 0.125 Angle : 0.505 5.432 19057 Z= 0.290 Chirality : 0.042 0.229 2125 Planarity : 0.005 0.048 2268 Dihedral : 15.106 143.875 2518 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.03 % Allowed : 18.56 % Favored : 78.42 % 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: 1.16 (0.22), residues: 1508 helix: 2.04 (0.25), residues: 446 sheet: 0.96 (0.26), residues: 396 loop : -0.19 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 316 TYR 0.018 0.001 TYR a 380 PHE 0.010 0.001 PHE A 219 TRP 0.015 0.001 TRP a 136 HIS 0.004 0.001 HIS a 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (13833) covalent geometry : angle 0.50473 / 0.29 (19057) hydrogen bonds : bond 0.04671 / 3.14 ( 606) hydrogen bonds : angle 4.61595 / 3.26 ( 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 176 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 0.478 Fit side-chains REVERT: A 62 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7368 (mtp85) REVERT: A 128 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.6712 (t80) REVERT: A 301 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: a 58 VAL cc_start: 0.8586 (m) cc_final: 0.8325 (t) REVERT: a 580 ARG cc_start: 0.7246 (ptt180) cc_final: 0.6316 (ptp-170) REVERT: a 630 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6673 (tm-30) outliers start: 39 outliers final: 22 residues processed: 164 average time/residue: 0.6266 time to fit residues: 111.7237 Evaluate side-chains 158 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 77 THR Chi-restraints excluded: chain A residue 128 PHE 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 21 PHE 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 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 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: 8.9990 chunk 128 optimal weight: 8.9990 chunk 140 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3888 r_free = 0.3888 target = 0.164786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.132792 restraints weight = 12637.992| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.50 r_work: 0.3403 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 13833 Z= 0.182 Angle : 0.607 6.527 19057 Z= 0.337 Chirality : 0.046 0.246 2125 Planarity : 0.005 0.054 2268 Dihedral : 15.151 142.351 2512 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.96 % Allowed : 18.48 % Favored : 77.56 % 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: 1.02 (0.22), residues: 1508 helix: 1.86 (0.24), residues: 452 sheet: 0.91 (0.26), residues: 389 loop : -0.25 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 22 TYR 0.026 0.002 TYR A 380 PHE 0.016 0.002 PHE a 545 TRP 0.015 0.002 TRP a 136 HIS 0.004 0.001 HIS a 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (13833) covalent geometry : angle 0.60709 / 0.34 (19057) hydrogen bonds : bond 0.05807 / 3.90 ( 606) hydrogen bonds : angle 4.63138 / 3.27 ( 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 185 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 134 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: A 22 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6820 (ttp-110) REVERT: A 94 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8120 (mm) REVERT: A 128 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.6927 (t80) REVERT: A 301 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7674 (mp0) REVERT: a 34 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7072 (mpp) REVERT: a 212 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6409 (pp20) REVERT: a 580 ARG cc_start: 0.7343 (ptt180) cc_final: 0.6435 (ptp-170) outliers start: 51 outliers final: 29 residues processed: 165 average time/residue: 0.6529 time to fit residues: 116.8686 Evaluate side-chains 168 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 94 ILE Chi-restraints excluded: chain A residue 128 PHE 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 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 676 MET 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 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 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 567 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 120 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 125 optimal weight: 0.5980 chunk 1 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.164961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.133033 restraints weight = 12600.988| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.49 r_work: 0.3405 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13833 Z= 0.174 Angle : 0.590 6.583 19057 Z= 0.329 Chirality : 0.046 0.244 2125 Planarity : 0.005 0.054 2268 Dihedral : 15.124 142.551 2511 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.43 % Allowed : 18.48 % Favored : 77.10 % 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: 0.96 (0.21), residues: 1508 helix: 1.82 (0.24), residues: 452 sheet: 0.86 (0.26), residues: 397 loop : -0.29 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 712 TYR 0.024 0.002 TYR a 380 PHE 0.015 0.002 PHE a 545 TRP 0.016 0.002 TRP a 136 HIS 0.004 0.001 HIS a 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (13833) covalent geometry : angle 0.59042 / 0.33 (19057) hydrogen bonds : bond 0.05624 / 3.78 ( 606) hydrogen bonds : angle 4.60727 / 3.25 ( 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 192 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 135 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 22 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.6840 (ttp-110) REVERT: A 62 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7417 (mtp85) REVERT: A 94 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8116 (mm) REVERT: A 128 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.7000 (t80) REVERT: A 193 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.6635 (mp0) REVERT: A 226 ILE cc_start: 0.6633 (OUTLIER) cc_final: 0.5975 (mm) REVERT: A 301 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: A 758 ARG cc_start: 0.5169 (OUTLIER) cc_final: 0.4035 (ptt-90) REVERT: a 34 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7080 (mpp) REVERT: a 212 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6368 (pp20) REVERT: a 225 LYS cc_start: 0.6095 (OUTLIER) cc_final: 0.5895 (tptm) REVERT: a 580 ARG cc_start: 0.7301 (ptt180) cc_final: 0.6429 (ptp-170) outliers start: 57 outliers final: 32 residues processed: 176 average time/residue: 0.5701 time to fit residues: 108.9428 Evaluate side-chains 178 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 135 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 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 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 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 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 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: 4.9990 chunk 78 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 69 optimal weight: 0.4980 chunk 43 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.164286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.132311 restraints weight = 12581.694| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.49 r_work: 0.3396 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 13833 Z= 0.192 Angle : 0.621 6.896 19057 Z= 0.343 Chirality : 0.047 0.245 2125 Planarity : 0.006 0.056 2268 Dihedral : 15.170 142.505 2511 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.74 % Allowed : 18.17 % Favored : 77.10 % 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: 0.91 (0.21), residues: 1508 helix: 1.75 (0.24), residues: 452 sheet: 0.87 (0.26), residues: 395 loop : -0.32 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 712 TYR 0.025 0.002 TYR A 380 PHE 0.017 0.002 PHE a 545 TRP 0.016 0.002 TRP a 136 HIS 0.004 0.001 HIS a 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (13833) covalent geometry : angle 0.62140 / 0.34 (19057) hydrogen bonds : bond 0.05983 / 4.02 ( 606) hydrogen bonds : angle 4.63637 / 3.27 ( 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 197 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 136 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 22 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6849 (ttp-110) REVERT: A 51 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7662 (ttmp) REVERT: A 62 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7351 (mtp85) REVERT: A 94 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8116 (mm) REVERT: A 128 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7017 (t80) REVERT: A 193 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.6646 (mp0) REVERT: A 226 ILE cc_start: 0.6657 (OUTLIER) cc_final: 0.5988 (mm) REVERT: A 301 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7673 (mp0) REVERT: A 758 ARG cc_start: 0.5147 (OUTLIER) cc_final: 0.4006 (ptt-90) REVERT: a 34 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7080 (mpp) REVERT: a 580 ARG cc_start: 0.7309 (ptt180) cc_final: 0.6416 (ptp-170) outliers start: 61 outliers final: 36 residues processed: 176 average time/residue: 0.5824 time to fit residues: 111.4247 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 : 0.477 ------------------------------------------------------------------------------- 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 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 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 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 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 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: 7.9990 chunk 112 optimal weight: 0.6980 chunk 1 optimal weight: 9.9990 chunk 152 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 58 optimal weight: 0.3980 chunk 146 optimal weight: 0.4980 chunk 12 optimal weight: 4.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.166198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.134417 restraints weight = 12602.046| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.49 r_work: 0.3420 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13833 Z= 0.142 Angle : 0.542 5.873 19057 Z= 0.306 Chirality : 0.043 0.238 2125 Planarity : 0.005 0.053 2268 Dihedral : 15.032 142.581 2511 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.35 % Allowed : 18.63 % 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: 1.10 (0.22), residues: 1508 helix: 1.99 (0.24), residues: 452 sheet: 0.91 (0.26), residues: 397 loop : -0.23 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 567 TYR 0.021 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 0.00298 / 0.14 (13833) covalent geometry : angle 0.54240 / 0.31 (19057) hydrogen bonds : bond 0.04960 / 3.32 ( 606) hydrogen bonds : angle 4.51103 / 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 193 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 137 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 22 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.6961 (ttp-110) REVERT: A 51 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7688 (ttmp) REVERT: A 62 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7344 (mtp85) REVERT: A 94 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8089 (mm) REVERT: A 128 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7048 (t80) REVERT: A 193 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.6625 (mp0) REVERT: A 758 ARG cc_start: 0.5062 (OUTLIER) cc_final: 0.4058 (ptt-90) REVERT: a 34 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7072 (mpp) REVERT: a 58 VAL cc_start: 0.8599 (m) cc_final: 0.8359 (t) REVERT: a 225 LYS cc_start: 0.6059 (OUTLIER) cc_final: 0.5853 (tptm) REVERT: a 282 ASP cc_start: 0.7210 (OUTLIER) cc_final: 0.6985 (m-30) REVERT: a 580 ARG cc_start: 0.7269 (ptt180) cc_final: 0.6397 (ptp-170) outliers start: 56 outliers final: 33 residues processed: 175 average time/residue: 0.5904 time to fit residues: 112.2240 Evaluate side-chains 179 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 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 240 VAL 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 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 638 ASP Chi-restraints excluded: chain A residue 671 SER 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 225 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 12 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.165933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.134184 restraints weight = 12518.577| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.49 r_work: 0.3413 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 13833 Z= 0.151 Angle : 0.555 6.068 19057 Z= 0.311 Chirality : 0.044 0.235 2125 Planarity : 0.005 0.051 2268 Dihedral : 15.007 142.228 2511 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.04 % Allowed : 19.33 % 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: 1.08 (0.22), residues: 1508 helix: 1.99 (0.24), residues: 452 sheet: 0.86 (0.26), residues: 399 loop : -0.23 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 567 TYR 0.022 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 0.00326 / 0.15 (13833) covalent geometry : angle 0.55513 / 0.31 (19057) hydrogen bonds : bond 0.05079 / 3.40 ( 606) hydrogen bonds : angle 4.50259 / 3.18 ( 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 186 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 134 time to evaluate : 0.447 Fit side-chains REVERT: A 22 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6916 (ttp-110) REVERT: A 51 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7688 (ttmp) REVERT: A 62 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7355 (mtp85) REVERT: A 94 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.8082 (mm) REVERT: A 128 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7048 (t80) REVERT: A 193 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.6607 (mp0) REVERT: A 226 ILE cc_start: 0.6616 (OUTLIER) cc_final: 0.5963 (mm) REVERT: A 758 ARG cc_start: 0.5040 (OUTLIER) cc_final: 0.4047 (ptt-90) REVERT: a 34 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7064 (mpp) REVERT: a 282 ASP cc_start: 0.7207 (OUTLIER) cc_final: 0.6983 (m-30) REVERT: a 580 ARG cc_start: 0.7274 (ptt180) cc_final: 0.6398 (ptp-170) outliers start: 52 outliers final: 33 residues processed: 170 average time/residue: 0.6280 time to fit residues: 116.0666 Evaluate side-chains 175 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 132 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 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 239 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 241 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 91 optimal weight: 0.3980 chunk 97 optimal weight: 6.9990 chunk 129 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.166507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.134713 restraints weight = 12694.097| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.50 r_work: 0.3443 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1039 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= 0.136 Angle : 0.534 5.760 19057 Z= 0.301 Chirality : 0.043 0.236 2125 Planarity : 0.005 0.050 2268 Dihedral : 14.939 142.194 2510 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.88 % Allowed : 19.25 % Favored : 76.86 % 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: 1.13 (0.22), residues: 1508 helix: 2.07 (0.24), residues: 452 sheet: 0.88 (0.26), residues: 393 loop : -0.22 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 567 TYR 0.021 0.002 TYR a 380 PHE 0.011 0.001 PHE a 545 TRP 0.015 0.001 TRP a 136 HIS 0.004 0.001 HIS a 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (13833) covalent geometry : angle 0.53421 / 0.30 (19057) hydrogen bonds : bond 0.04806 / 3.22 ( 606) hydrogen bonds : angle 4.46713 / 3.16 ( 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 184 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 134 time to evaluate : 0.469 Fit side-chains REVERT: A 51 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7672 (ttmp) REVERT: A 62 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7351 (mtp85) REVERT: A 94 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8083 (mm) REVERT: A 128 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.6926 (t80) REVERT: A 193 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.6628 (mp0) REVERT: A 226 ILE cc_start: 0.6576 (OUTLIER) cc_final: 0.5920 (mm) REVERT: A 758 ARG cc_start: 0.5008 (OUTLIER) cc_final: 0.4034 (ptt-90) REVERT: a 34 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7085 (mpp) REVERT: a 58 VAL cc_start: 0.8606 (m) cc_final: 0.8367 (t) REVERT: a 282 ASP cc_start: 0.7220 (OUTLIER) cc_final: 0.6996 (m-30) REVERT: a 481 GLU cc_start: 0.7175 (mp0) cc_final: 0.6831 (mp0) REVERT: a 580 ARG cc_start: 0.7291 (ptt180) cc_final: 0.6424 (ptp-170) outliers start: 50 outliers final: 35 residues processed: 169 average time/residue: 0.5770 time to fit residues: 106.1048 Evaluate side-chains 177 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 133 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 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 239 THR Chi-restraints excluded: chain A residue 240 VAL 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 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 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 184 THR 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 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 27 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.166336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.134590 restraints weight = 12559.196| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.49 r_work: 0.3418 rms_B_bonded: 2.09 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: 0.8442 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 13833 Z= 0.140 Angle : 0.539 5.828 19057 Z= 0.303 Chirality : 0.043 0.237 2125 Planarity : 0.005 0.050 2268 Dihedral : 14.923 141.926 2510 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.57 % Allowed : 19.72 % Favored : 76.71 % 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: 1.12 (0.22), residues: 1508 helix: 2.06 (0.24), residues: 452 sheet: 0.88 (0.27), residues: 393 loop : -0.22 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 567 TYR 0.022 0.002 TYR a 380 PHE 0.012 0.001 PHE a 545 TRP 0.015 0.001 TRP a 136 HIS 0.004 0.001 HIS a 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (13833) covalent geometry : angle 0.53917 / 0.30 (19057) hydrogen bonds : bond 0.04838 / 3.24 ( 606) hydrogen bonds : angle 4.45897 / 3.15 ( 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 177 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 131 time to evaluate : 0.535 Fit side-chains REVERT: A 51 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7706 (ttmp) REVERT: A 62 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7437 (mtp85) REVERT: A 94 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8075 (mm) REVERT: A 128 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.6904 (t80) REVERT: A 193 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.6654 (mp0) REVERT: A 226 ILE cc_start: 0.6571 (OUTLIER) cc_final: 0.5918 (mm) REVERT: A 758 ARG cc_start: 0.4998 (OUTLIER) cc_final: 0.4033 (ptt-90) REVERT: a 34 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7070 (mpp) REVERT: a 58 VAL cc_start: 0.8598 (m) cc_final: 0.8359 (t) REVERT: a 82 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6920 (mp) REVERT: a 282 ASP cc_start: 0.7209 (OUTLIER) cc_final: 0.6984 (m-30) REVERT: a 481 GLU cc_start: 0.7159 (mp0) cc_final: 0.6810 (mp0) REVERT: a 580 ARG cc_start: 0.7261 (ptt180) cc_final: 0.6385 (ptp-110) outliers start: 46 outliers final: 34 residues processed: 163 average time/residue: 0.5794 time to fit residues: 102.9589 Evaluate side-chains 175 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 131 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 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 239 THR Chi-restraints excluded: chain A residue 240 VAL 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 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 671 SER 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 82 LEU 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 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: 0.5980 chunk 51 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 126 optimal weight: 0.1980 chunk 107 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 a 449 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.170992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.142392 restraints weight = 12730.638| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.39 r_work: 0.3517 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 13833 Z= 0.109 Angle : 0.479 5.327 19057 Z= 0.273 Chirality : 0.041 0.226 2125 Planarity : 0.004 0.045 2268 Dihedral : 14.766 141.328 2510 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.48 % Allowed : 20.65 % Favored : 76.86 % 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: 1.37 (0.22), residues: 1508 helix: 2.28 (0.24), residues: 453 sheet: 1.02 (0.27), residues: 395 loop : -0.09 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 567 TYR 0.017 0.001 TYR a 380 PHE 0.009 0.001 PHE A 219 TRP 0.016 0.001 TRP a 136 HIS 0.005 0.001 HIS a 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.11 (13833) covalent geometry : angle 0.47875 / 0.27 (19057) hydrogen bonds : bond 0.03853 / 2.58 ( 606) hydrogen bonds : angle 4.31926 / 3.06 ( 1652) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4547.37 seconds wall clock time: 78 minutes 2.99 seconds (4682.99 seconds total)