Starting phenix.real_space_refine on Fri Aug 22 18:29:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yad_33709/08_2025/7yad_33709.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yad_33709/08_2025/7yad_33709.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yad_33709/08_2025/7yad_33709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yad_33709/08_2025/7yad_33709.map" model { file = "/net/cci-nas-00/data/ceres_data/7yad_33709/08_2025/7yad_33709.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yad_33709/08_2025/7yad_33709.cif" } resolution = 2.66 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= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 4267 2.51 5 N 1141 2.21 5 O 1291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6728 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 966 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "B" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 787 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Chain: "M" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1606 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 12, 'TRANS': 187} Chain: "C" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 979 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "D" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 815 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "E" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1499 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 10, 'TRANS': 174} Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.97, per 1000 atoms: 0.29 Number of scatterers: 6728 At special positions: 0 Unit cell: (111.89, 136.01, 88.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 1291 8.00 N 1141 7.00 C 4267 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.04 Simple disulfide: pdb=" SG CYS M 336 " - pdb=" SG CYS M 361 " distance=2.03 Simple disulfide: pdb=" SG CYS M 379 " - pdb=" SG CYS M 432 " distance=2.04 Simple disulfide: pdb=" SG CYS M 480 " - pdb=" SG CYS M 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.04 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " BETA1-6 " NAG F 1 " - " FUC F 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG G 1 " - " FUC G 3 " NAG-ASN " NAG F 1 " - " ASN M 343 " " NAG G 1 " - " ASN E 343 " Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 379.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1542 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 16 sheets defined 11.7% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.903A pdb=" N GLN A 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 87 through 91 removed outlier: 4.068A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 338 through 343 Processing helix chain 'M' and resid 349 through 353 removed outlier: 3.967A pdb=" N TRP M 353 " --> pdb=" O VAL M 350 " (cutoff:3.500A) Processing helix chain 'M' and resid 365 through 370 removed outlier: 3.879A pdb=" N TYR M 369 " --> pdb=" O TYR M 365 " (cutoff:3.500A) Processing helix chain 'M' and resid 384 through 390 removed outlier: 4.332A pdb=" N ASN M 388 " --> pdb=" O THR M 385 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU M 390 " --> pdb=" O LEU M 387 " (cutoff:3.500A) Processing helix chain 'M' and resid 405 through 410 removed outlier: 3.997A pdb=" N ARG M 408 " --> pdb=" O ASP M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 422 Processing helix chain 'M' and resid 438 through 443 removed outlier: 3.553A pdb=" N SER M 443 " --> pdb=" O ASN M 439 " (cutoff:3.500A) Processing helix chain 'M' and resid 502 through 505 Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.928A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 32 No H-bonds generated for 'chain 'D' and resid 30 through 32' Processing helix chain 'E' and resid 338 through 343 removed outlier: 3.617A pdb=" N PHE E 342 " --> pdb=" O PHE E 338 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN E 343 " --> pdb=" O ASP E 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 338 through 343' Processing helix chain 'E' and resid 383 through 390 removed outlier: 3.769A pdb=" N LEU E 387 " --> pdb=" O PRO E 384 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU E 390 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 410 removed outlier: 3.921A pdb=" N VAL E 407 " --> pdb=" O GLY E 404 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.761A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TRP A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY A 33 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASN A 116 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.761A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TRP A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY A 33 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 5 removed outlier: 5.702A pdb=" N THR B 70 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 10.633A pdb=" N GLN B 27 " --> pdb=" O SER B 68 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N SER B 68 " --> pdb=" O GLN B 27 " (cutoff:3.500A) removed outlier: 11.802A pdb=" N VAL B 29 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 11.915A pdb=" N SER B 66 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.800A pdb=" N ILE B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLN B 38 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU B 47 " --> pdb=" O GLN B 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 354 through 358 removed outlier: 3.625A pdb=" N ASN M 354 " --> pdb=" O SER M 399 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN M 394 " --> pdb=" O GLU M 516 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL M 433 " --> pdb=" O LYS M 378 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS M 378 " --> pdb=" O VAL M 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'M' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.756A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 83 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.716A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY C 33 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN C 116 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.716A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY C 33 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.845A pdb=" N ASP D 71 " --> pdb=" O SER D 68 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.225A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 86 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLN D 38 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU D 47 " --> pdb=" O GLN D 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.225A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN D 91 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.959A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA E 397 " --> pdb=" O LYS E 356 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 452 through 454 209 hydrogen bonds defined for protein. 525 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.99 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2149 1.35 - 1.47: 1932 1.47 - 1.60: 2784 1.60 - 1.72: 0 1.72 - 1.84: 35 Bond restraints: 6900 Sorted by residual: bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.69e+00 bond pdb=" CA ALA M 520 " pdb=" CB ALA M 520 " ideal model delta sigma weight residual 1.522 1.531 -0.008 7.00e-03 2.04e+04 1.45e+00 bond pdb=" C5 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.29e+00 bond pdb=" C5 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.427 -0.021 2.00e-02 2.50e+03 1.13e+00 ... (remaining 6895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 9169 1.59 - 3.19: 171 3.19 - 4.78: 28 4.78 - 6.38: 5 6.38 - 7.97: 1 Bond angle restraints: 9374 Sorted by residual: angle pdb=" C LEU D 13 " pdb=" N SER D 14 " pdb=" CA SER D 14 " ideal model delta sigma weight residual 120.49 128.46 -7.97 1.42e+00 4.96e-01 3.15e+01 angle pdb=" CA LYS E 386 " pdb=" CB LYS E 386 " pdb=" CG LYS E 386 " ideal model delta sigma weight residual 114.10 120.35 -6.25 2.00e+00 2.50e-01 9.75e+00 angle pdb=" C HIS E 505 " pdb=" N GLN E 506 " pdb=" CA GLN E 506 " ideal model delta sigma weight residual 120.68 125.29 -4.61 1.52e+00 4.33e-01 9.19e+00 angle pdb=" CA PRO D 81 " pdb=" N PRO D 81 " pdb=" CD PRO D 81 " ideal model delta sigma weight residual 112.00 108.19 3.81 1.40e+00 5.10e-01 7.40e+00 angle pdb=" CA CYS M 379 " pdb=" CB CYS M 379 " pdb=" SG CYS M 379 " ideal model delta sigma weight residual 114.40 120.41 -6.01 2.30e+00 1.89e-01 6.82e+00 ... (remaining 9369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 3727 17.19 - 34.39: 327 34.39 - 51.58: 56 51.58 - 68.77: 8 68.77 - 85.96: 3 Dihedral angle restraints: 4121 sinusoidal: 1683 harmonic: 2438 Sorted by residual: dihedral pdb=" CB CYS M 379 " pdb=" SG CYS M 379 " pdb=" SG CYS M 432 " pdb=" CB CYS M 432 " ideal model delta sinusoidal sigma weight residual 93.00 31.66 61.34 1 1.00e+01 1.00e-02 5.00e+01 dihedral pdb=" CA ALA M 520 " pdb=" C ALA M 520 " pdb=" N PRO M 521 " pdb=" CA PRO M 521 " ideal model delta harmonic sigma weight residual 180.00 151.66 28.34 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual -86.00 -129.46 43.46 1 1.00e+01 1.00e-02 2.63e+01 ... (remaining 4118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 630 0.032 - 0.064: 249 0.064 - 0.097: 80 0.097 - 0.129: 54 0.129 - 0.161: 6 Chirality restraints: 1019 Sorted by residual: chirality pdb=" CA PRO D 81 " pdb=" N PRO D 81 " pdb=" C PRO D 81 " pdb=" CB PRO D 81 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN E 343 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE B 76 " pdb=" N ILE B 76 " pdb=" C ILE B 76 " pdb=" CB ILE B 76 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 1016 not shown) Planarity restraints: 1205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 80 " 0.046 5.00e-02 4.00e+02 6.76e-02 7.32e+00 pdb=" N PRO D 81 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO D 81 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 81 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR E 385 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.56e+00 pdb=" C THR E 385 " 0.033 2.00e-02 2.50e+03 pdb=" O THR E 385 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS E 386 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA M 520 " 0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO M 521 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO M 521 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO M 521 " 0.021 5.00e-02 4.00e+02 ... (remaining 1202 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 230 2.71 - 3.26: 6147 3.26 - 3.81: 9889 3.81 - 4.35: 12177 4.35 - 4.90: 21925 Nonbonded interactions: 50368 Sorted by model distance: nonbonded pdb=" OD1 ASP E 442 " pdb=" OH TYR E 451 " model vdw 2.165 3.040 nonbonded pdb=" OH TYR M 369 " pdb=" O PRO M 384 " model vdw 2.175 3.040 nonbonded pdb=" NH2 ARG E 457 " pdb=" OD1 ASN E 460 " model vdw 2.219 3.120 nonbonded pdb=" O ASN M 439 " pdb=" OG SER M 443 " model vdw 2.242 3.040 nonbonded pdb=" OG SER B 12 " pdb=" OE2 GLU B 105 " model vdw 2.254 3.040 ... (remaining 50363 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and resid 1 through 124) } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 1 through 105) } ncs_group { reference = chain 'E' selection = (chain 'M' and resid 332 through 516) } ncs_group { reference = chain 'F' selection = chain 'G' } 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: 9.060 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.420 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 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 0.049 6916 Z= 0.156 Angle : 0.565 7.971 9412 Z= 0.296 Chirality : 0.044 0.161 1019 Planarity : 0.004 0.068 1203 Dihedral : 12.506 85.964 2549 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.55 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: -1.22 (0.28), residues: 836 helix: -3.96 (0.55), residues: 33 sheet: 0.49 (0.32), residues: 281 loop : -1.40 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 403 TYR 0.016 0.001 TYR C 100 PHE 0.011 0.001 PHE E 347 TRP 0.013 0.001 TRP C 50 HIS 0.004 0.002 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 6900) covalent geometry : angle 0.55483 ( 9374) SS BOND : bond 0.00528 ( 10) SS BOND : angle 1.25273 ( 20) hydrogen bonds : bond 0.28588 ( 183) hydrogen bonds : angle 10.44226 ( 525) link_BETA1-4 : bond 0.00189 ( 2) link_BETA1-4 : angle 1.94580 ( 6) link_BETA1-6 : bond 0.00125 ( 2) link_BETA1-6 : angle 1.86345 ( 6) link_NAG-ASN : bond 0.00341 ( 2) link_NAG-ASN : angle 2.60802 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 MET cc_start: 0.6596 (tmm) cc_final: 0.6215 (tmm) REVERT: D 71 ASP cc_start: 0.7084 (t70) cc_final: 0.6857 (t0) REVERT: D 82 GLU cc_start: 0.7055 (pm20) cc_final: 0.6744 (pm20) REVERT: E 386 LYS cc_start: 0.8775 (mmpt) cc_final: 0.8549 (mmpt) REVERT: E 438 SER cc_start: 0.8339 (p) cc_final: 0.8122 (p) REVERT: E 439 ASN cc_start: 0.7959 (t0) cc_final: 0.7691 (t0) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.4274 time to fit residues: 67.1671 Evaluate side-chains 137 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN B 92 HIS M 439 ASN M 450 ASN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.148855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.126033 restraints weight = 10424.596| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.46 r_work: 0.3681 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 6916 Z= 0.261 Angle : 0.614 6.346 9412 Z= 0.325 Chirality : 0.047 0.182 1019 Planarity : 0.005 0.046 1203 Dihedral : 5.328 35.865 1063 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.74 % Favored : 94.14 % Rotamer: Outliers : 1.12 % Allowed : 9.90 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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 aren not related in a simple way. whole: -1.22 (0.28), residues: 836 helix: -4.33 (0.37), residues: 47 sheet: 0.80 (0.32), residues: 273 loop : -1.45 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 408 TYR 0.021 0.002 TYR M 501 PHE 0.010 0.001 PHE E 392 TRP 0.015 0.002 TRP C 50 HIS 0.007 0.002 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00593 ( 6900) covalent geometry : angle 0.60165 ( 9374) SS BOND : bond 0.00826 ( 10) SS BOND : angle 1.75125 ( 20) hydrogen bonds : bond 0.04964 ( 183) hydrogen bonds : angle 7.32964 ( 525) link_BETA1-4 : bond 0.00199 ( 2) link_BETA1-4 : angle 1.79402 ( 6) link_BETA1-6 : bond 0.00682 ( 2) link_BETA1-6 : angle 1.71447 ( 6) link_NAG-ASN : bond 0.00344 ( 2) link_NAG-ASN : angle 2.92056 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 MET cc_start: 0.7386 (tmm) cc_final: 0.6888 (tmm) REVERT: D 82 GLU cc_start: 0.7512 (pm20) cc_final: 0.6959 (pm20) REVERT: E 439 ASN cc_start: 0.8361 (t0) cc_final: 0.8099 (t0) REVERT: E 501 TYR cc_start: 0.7746 (m-10) cc_final: 0.7447 (m-10) outliers start: 8 outliers final: 3 residues processed: 126 average time/residue: 0.4033 time to fit residues: 54.6342 Evaluate side-chains 128 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain E residue 434 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 62 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 78 optimal weight: 0.2980 chunk 44 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN B 43 GLN ** M 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 439 ASN M 450 ASN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.149275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.126813 restraints weight = 10395.759| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.44 r_work: 0.3692 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6916 Z= 0.191 Angle : 0.566 5.784 9412 Z= 0.297 Chirality : 0.045 0.186 1019 Planarity : 0.004 0.049 1203 Dihedral : 5.189 35.376 1063 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.26 % Favored : 94.62 % Rotamer: Outliers : 1.53 % Allowed : 12.69 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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 aren not related in a simple way. whole: -1.29 (0.27), residues: 836 helix: -4.74 (0.31), residues: 40 sheet: 0.82 (0.31), residues: 272 loop : -1.56 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 78 TYR 0.017 0.001 TYR M 351 PHE 0.007 0.001 PHE D 63 TRP 0.009 0.002 TRP A 50 HIS 0.004 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 6900) covalent geometry : angle 0.55536 ( 9374) SS BOND : bond 0.00674 ( 10) SS BOND : angle 1.49691 ( 20) hydrogen bonds : bond 0.04398 ( 183) hydrogen bonds : angle 6.76707 ( 525) link_BETA1-4 : bond 0.00211 ( 2) link_BETA1-4 : angle 1.74874 ( 6) link_BETA1-6 : bond 0.00387 ( 2) link_BETA1-6 : angle 1.53711 ( 6) link_NAG-ASN : bond 0.00310 ( 2) link_NAG-ASN : angle 2.63722 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 81 MET cc_start: 0.7434 (tmm) cc_final: 0.6979 (tmm) REVERT: D 82 GLU cc_start: 0.7486 (pm20) cc_final: 0.6952 (pm20) REVERT: E 439 ASN cc_start: 0.8333 (t0) cc_final: 0.8071 (t0) REVERT: E 501 TYR cc_start: 0.7718 (m-10) cc_final: 0.7469 (m-10) outliers start: 11 outliers final: 3 residues processed: 127 average time/residue: 0.3593 time to fit residues: 49.5018 Evaluate side-chains 122 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain D residue 7 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 34 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 64 optimal weight: 0.0370 chunk 67 optimal weight: 0.9980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 59 ASN B 43 GLN M 439 ASN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.149021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.126800 restraints weight = 10443.684| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.41 r_work: 0.3705 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6916 Z= 0.141 Angle : 0.527 6.582 9412 Z= 0.276 Chirality : 0.044 0.149 1019 Planarity : 0.004 0.048 1203 Dihedral : 4.955 34.652 1063 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.14 % Favored : 94.74 % Rotamer: Outliers : 1.53 % Allowed : 14.09 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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 aren not related in a simple way. whole: -1.15 (0.28), residues: 836 helix: -4.61 (0.36), residues: 32 sheet: 0.90 (0.31), residues: 272 loop : -1.52 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 408 TYR 0.022 0.001 TYR M 501 PHE 0.006 0.001 PHE E 375 TRP 0.010 0.001 TRP C 50 HIS 0.003 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6900) covalent geometry : angle 0.51821 ( 9374) SS BOND : bond 0.00525 ( 10) SS BOND : angle 1.30051 ( 20) hydrogen bonds : bond 0.03705 ( 183) hydrogen bonds : angle 6.27737 ( 525) link_BETA1-4 : bond 0.00268 ( 2) link_BETA1-4 : angle 1.69719 ( 6) link_BETA1-6 : bond 0.00271 ( 2) link_BETA1-6 : angle 1.51232 ( 6) link_NAG-ASN : bond 0.00280 ( 2) link_NAG-ASN : angle 2.37211 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 82 GLU cc_start: 0.7479 (pm20) cc_final: 0.6974 (pm20) REVERT: D 95 SER cc_start: 0.8418 (p) cc_final: 0.8150 (t) REVERT: E 439 ASN cc_start: 0.8309 (t0) cc_final: 0.8023 (t0) REVERT: E 501 TYR cc_start: 0.7682 (m-10) cc_final: 0.7397 (m-10) outliers start: 11 outliers final: 4 residues processed: 138 average time/residue: 0.3363 time to fit residues: 50.7042 Evaluate side-chains 138 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 134 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain D residue 7 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 45 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 0.0270 chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 59 optimal weight: 0.0970 chunk 60 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN ** M 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 439 ASN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.148051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.125514 restraints weight = 10587.752| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.50 r_work: 0.3693 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6916 Z= 0.148 Angle : 0.527 5.654 9412 Z= 0.275 Chirality : 0.044 0.149 1019 Planarity : 0.004 0.049 1203 Dihedral : 4.931 34.388 1063 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.26 % Favored : 94.62 % Rotamer: Outliers : 2.23 % Allowed : 14.23 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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 aren not related in a simple way. whole: -1.19 (0.28), residues: 836 helix: -4.74 (0.31), residues: 38 sheet: 0.88 (0.31), residues: 273 loop : -1.50 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 408 TYR 0.019 0.001 TYR M 351 PHE 0.010 0.001 PHE E 377 TRP 0.012 0.001 TRP C 50 HIS 0.004 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 6900) covalent geometry : angle 0.51750 ( 9374) SS BOND : bond 0.00590 ( 10) SS BOND : angle 1.34573 ( 20) hydrogen bonds : bond 0.03597 ( 183) hydrogen bonds : angle 6.09738 ( 525) link_BETA1-4 : bond 0.00226 ( 2) link_BETA1-4 : angle 1.73308 ( 6) link_BETA1-6 : bond 0.00263 ( 2) link_BETA1-6 : angle 1.51461 ( 6) link_NAG-ASN : bond 0.00284 ( 2) link_NAG-ASN : angle 2.44562 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 82 GLU cc_start: 0.7324 (pm20) cc_final: 0.6875 (pm20) REVERT: E 439 ASN cc_start: 0.8108 (t0) cc_final: 0.7790 (t0) REVERT: E 501 TYR cc_start: 0.7552 (m-10) cc_final: 0.7268 (m-10) outliers start: 16 outliers final: 5 residues processed: 145 average time/residue: 0.3134 time to fit residues: 49.6148 Evaluate side-chains 138 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 133 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain M residue 341 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain E residue 461 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 61 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN ** M 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 439 ASN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.148698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.126124 restraints weight = 10393.369| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.49 r_work: 0.3676 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6916 Z= 0.217 Angle : 0.575 6.842 9412 Z= 0.299 Chirality : 0.046 0.173 1019 Planarity : 0.004 0.051 1203 Dihedral : 5.098 34.516 1063 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.46 % Favored : 93.42 % Rotamer: Outliers : 2.37 % Allowed : 14.92 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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 aren not related in a simple way. whole: -1.23 (0.28), residues: 836 helix: -4.75 (0.31), residues: 38 sheet: 0.88 (0.31), residues: 273 loop : -1.55 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 408 TYR 0.020 0.002 TYR M 351 PHE 0.014 0.001 PHE B 72 TRP 0.016 0.002 TRP C 50 HIS 0.005 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 6900) covalent geometry : angle 0.56355 ( 9374) SS BOND : bond 0.00772 ( 10) SS BOND : angle 1.55010 ( 20) hydrogen bonds : bond 0.03977 ( 183) hydrogen bonds : angle 6.13579 ( 525) link_BETA1-4 : bond 0.00224 ( 2) link_BETA1-4 : angle 1.86638 ( 6) link_BETA1-6 : bond 0.00430 ( 2) link_BETA1-6 : angle 1.57108 ( 6) link_NAG-ASN : bond 0.00314 ( 2) link_NAG-ASN : angle 2.76062 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 MET cc_start: 0.7387 (tmm) cc_final: 0.6854 (tmm) REVERT: D 82 GLU cc_start: 0.7539 (pm20) cc_final: 0.7032 (pm20) REVERT: E 439 ASN cc_start: 0.8365 (t0) cc_final: 0.8127 (t0) REVERT: E 501 TYR cc_start: 0.7731 (m-10) cc_final: 0.7440 (m-10) outliers start: 17 outliers final: 11 residues processed: 147 average time/residue: 0.3347 time to fit residues: 53.8846 Evaluate side-chains 150 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 461 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 12 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 26 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 76 optimal weight: 0.0170 chunk 1 optimal weight: 0.1980 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN ** M 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 439 ASN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.151501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.128768 restraints weight = 10359.457| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 2.50 r_work: 0.3705 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6916 Z= 0.112 Angle : 0.533 5.815 9412 Z= 0.276 Chirality : 0.044 0.153 1019 Planarity : 0.004 0.053 1203 Dihedral : 4.848 34.453 1063 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.14 % Favored : 94.74 % Rotamer: Outliers : 1.81 % Allowed : 16.74 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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 aren not related in a simple way. whole: -1.14 (0.28), residues: 836 helix: -4.75 (0.31), residues: 38 sheet: 0.91 (0.31), residues: 283 loop : -1.50 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 408 TYR 0.022 0.001 TYR M 351 PHE 0.009 0.001 PHE E 377 TRP 0.014 0.001 TRP C 50 HIS 0.003 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 6900) covalent geometry : angle 0.52559 ( 9374) SS BOND : bond 0.00537 ( 10) SS BOND : angle 1.20140 ( 20) hydrogen bonds : bond 0.03222 ( 183) hydrogen bonds : angle 5.90059 ( 525) link_BETA1-4 : bond 0.00240 ( 2) link_BETA1-4 : angle 1.67749 ( 6) link_BETA1-6 : bond 0.00169 ( 2) link_BETA1-6 : angle 1.46204 ( 6) link_NAG-ASN : bond 0.00317 ( 2) link_NAG-ASN : angle 2.20696 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 81 MET cc_start: 0.7058 (tmm) cc_final: 0.6561 (tmm) REVERT: D 82 GLU cc_start: 0.7318 (pm20) cc_final: 0.6903 (pm20) REVERT: E 439 ASN cc_start: 0.8084 (t0) cc_final: 0.7754 (t0) REVERT: E 501 TYR cc_start: 0.7540 (m-10) cc_final: 0.7217 (m-10) outliers start: 13 outliers final: 6 residues processed: 141 average time/residue: 0.3256 time to fit residues: 50.2346 Evaluate side-chains 142 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 136 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain E residue 461 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 28 optimal weight: 1.9990 chunk 80 optimal weight: 0.1980 chunk 16 optimal weight: 0.9990 chunk 48 optimal weight: 0.0670 chunk 49 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 4 optimal weight: 0.1980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN ** M 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.149173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.126744 restraints weight = 10465.616| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.48 r_work: 0.3710 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6916 Z= 0.119 Angle : 0.537 10.106 9412 Z= 0.275 Chirality : 0.044 0.160 1019 Planarity : 0.004 0.052 1203 Dihedral : 4.762 34.440 1063 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.02 % Favored : 94.86 % Rotamer: Outliers : 1.12 % Allowed : 17.71 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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 aren not related in a simple way. whole: -1.09 (0.28), residues: 836 helix: -4.74 (0.31), residues: 38 sheet: 0.92 (0.31), residues: 285 loop : -1.46 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 408 TYR 0.023 0.001 TYR M 351 PHE 0.009 0.001 PHE E 377 TRP 0.018 0.001 TRP C 50 HIS 0.003 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 6900) covalent geometry : angle 0.52938 ( 9374) SS BOND : bond 0.00546 ( 10) SS BOND : angle 1.20372 ( 20) hydrogen bonds : bond 0.03258 ( 183) hydrogen bonds : angle 5.79571 ( 525) link_BETA1-4 : bond 0.00248 ( 2) link_BETA1-4 : angle 1.68855 ( 6) link_BETA1-6 : bond 0.00148 ( 2) link_BETA1-6 : angle 1.47524 ( 6) link_NAG-ASN : bond 0.00256 ( 2) link_NAG-ASN : angle 2.26039 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 441 LEU cc_start: 0.8540 (mt) cc_final: 0.8332 (tt) REVERT: C 81 MET cc_start: 0.7055 (tmm) cc_final: 0.6567 (tmm) REVERT: C 119 GLN cc_start: 0.7138 (OUTLIER) cc_final: 0.6929 (pm20) REVERT: D 82 GLU cc_start: 0.7339 (pm20) cc_final: 0.6903 (pm20) REVERT: E 439 ASN cc_start: 0.8070 (t0) cc_final: 0.7750 (t0) REVERT: E 501 TYR cc_start: 0.7525 (m-10) cc_final: 0.7230 (m-10) outliers start: 8 outliers final: 5 residues processed: 142 average time/residue: 0.3166 time to fit residues: 49.2033 Evaluate side-chains 144 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 138 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain E residue 461 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 63 optimal weight: 0.3980 chunk 72 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 67 optimal weight: 0.4980 chunk 5 optimal weight: 0.0770 chunk 59 optimal weight: 0.0980 chunk 79 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN ** M 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 439 ASN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.149269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.126927 restraints weight = 10506.017| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.48 r_work: 0.3713 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6916 Z= 0.119 Angle : 0.542 13.098 9412 Z= 0.275 Chirality : 0.044 0.159 1019 Planarity : 0.004 0.052 1203 Dihedral : 4.718 34.567 1063 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.14 % Favored : 94.74 % Rotamer: Outliers : 1.39 % Allowed : 17.71 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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 aren not related in a simple way. whole: -1.05 (0.28), residues: 836 helix: -4.71 (0.31), residues: 38 sheet: 0.92 (0.31), residues: 288 loop : -1.42 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 408 TYR 0.023 0.001 TYR M 351 PHE 0.011 0.001 PHE E 377 TRP 0.016 0.001 TRP C 50 HIS 0.004 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 6900) covalent geometry : angle 0.53482 ( 9374) SS BOND : bond 0.00516 ( 10) SS BOND : angle 1.18849 ( 20) hydrogen bonds : bond 0.03195 ( 183) hydrogen bonds : angle 5.73939 ( 525) link_BETA1-4 : bond 0.00272 ( 2) link_BETA1-4 : angle 1.64953 ( 6) link_BETA1-6 : bond 0.00154 ( 2) link_BETA1-6 : angle 1.47722 ( 6) link_NAG-ASN : bond 0.00239 ( 2) link_NAG-ASN : angle 2.19296 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8049 (ttm) cc_final: 0.7842 (ttp) REVERT: C 81 MET cc_start: 0.7018 (tmm) cc_final: 0.6531 (tmm) REVERT: C 119 GLN cc_start: 0.7119 (OUTLIER) cc_final: 0.6916 (pm20) REVERT: D 82 GLU cc_start: 0.7323 (pm20) cc_final: 0.6891 (pm20) REVERT: E 439 ASN cc_start: 0.8055 (t0) cc_final: 0.7743 (t0) REVERT: E 501 TYR cc_start: 0.7515 (m-10) cc_final: 0.7239 (m-10) outliers start: 10 outliers final: 5 residues processed: 134 average time/residue: 0.3386 time to fit residues: 49.5699 Evaluate side-chains 135 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 129 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain E residue 461 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 0.6980 chunk 69 optimal weight: 0.0570 chunk 61 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 1 optimal weight: 0.0370 chunk 0 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN M 388 ASN ** M 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.149236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.126925 restraints weight = 10502.851| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.48 r_work: 0.3712 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6916 Z= 0.132 Angle : 0.569 14.028 9412 Z= 0.287 Chirality : 0.044 0.169 1019 Planarity : 0.004 0.051 1203 Dihedral : 4.745 34.677 1063 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.50 % Favored : 94.38 % Rotamer: Outliers : 1.53 % Allowed : 17.85 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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 aren not related in a simple way. whole: -0.93 (0.28), residues: 836 helix: -4.57 (0.37), residues: 32 sheet: 1.07 (0.31), residues: 275 loop : -1.38 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 408 TYR 0.023 0.001 TYR M 351 PHE 0.010 0.001 PHE E 377 TRP 0.019 0.001 TRP C 50 HIS 0.004 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 6900) covalent geometry : angle 0.56166 ( 9374) SS BOND : bond 0.00505 ( 10) SS BOND : angle 1.19444 ( 20) hydrogen bonds : bond 0.03243 ( 183) hydrogen bonds : angle 5.72254 ( 525) link_BETA1-4 : bond 0.00223 ( 2) link_BETA1-4 : angle 1.66690 ( 6) link_BETA1-6 : bond 0.00204 ( 2) link_BETA1-6 : angle 1.48329 ( 6) link_NAG-ASN : bond 0.00235 ( 2) link_NAG-ASN : angle 2.23689 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 81 MET cc_start: 0.7042 (tmm) cc_final: 0.6553 (tmm) REVERT: C 119 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6932 (pm20) REVERT: D 82 GLU cc_start: 0.7344 (pm20) cc_final: 0.6898 (pm20) REVERT: E 439 ASN cc_start: 0.8064 (t0) cc_final: 0.7747 (t0) REVERT: E 501 TYR cc_start: 0.7525 (m-10) cc_final: 0.7247 (m-10) outliers start: 11 outliers final: 7 residues processed: 135 average time/residue: 0.3263 time to fit residues: 48.1733 Evaluate side-chains 137 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 461 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.0670 chunk 52 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 0.0970 chunk 2 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN M 388 ASN ** M 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 439 ASN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN D 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.148271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.126005 restraints weight = 10447.561| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.46 r_work: 0.3699 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6916 Z= 0.165 Angle : 0.581 13.884 9412 Z= 0.295 Chirality : 0.045 0.169 1019 Planarity : 0.004 0.051 1203 Dihedral : 4.848 34.616 1063 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.62 % Favored : 94.26 % Rotamer: Outliers : 1.81 % Allowed : 17.71 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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 aren not related in a simple way. whole: -1.08 (0.28), residues: 836 helix: -4.73 (0.32), residues: 38 sheet: 1.08 (0.31), residues: 272 loop : -1.49 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 408 TYR 0.023 0.001 TYR M 351 PHE 0.010 0.001 PHE E 377 TRP 0.017 0.002 TRP C 50 HIS 0.005 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 6900) covalent geometry : angle 0.57293 ( 9374) SS BOND : bond 0.00652 ( 10) SS BOND : angle 1.35325 ( 20) hydrogen bonds : bond 0.03466 ( 183) hydrogen bonds : angle 5.78085 ( 525) link_BETA1-4 : bond 0.00205 ( 2) link_BETA1-4 : angle 1.76198 ( 6) link_BETA1-6 : bond 0.00293 ( 2) link_BETA1-6 : angle 1.49612 ( 6) link_NAG-ASN : bond 0.00264 ( 2) link_NAG-ASN : angle 2.47776 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3108.00 seconds wall clock time: 53 minutes 53.29 seconds (3233.29 seconds total)