Starting phenix.real_space_refine on Thu Jul 2 17:10:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ty4_26165/07_2026/7ty4_26165.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ty4_26165/07_2026/7ty4_26165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ty4_26165/07_2026/7ty4_26165.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ty4_26165/07_2026/7ty4_26165.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ty4_26165/07_2026/7ty4_26165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ty4_26165/07_2026/7ty4_26165.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ty4_26165/07_2026/7ty4_26165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ty4_26165/07_2026/7ty4_26165.map" } resolution = 2.99 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= 0.043 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 36 5.16 5 C 5798 2.51 5 N 1310 2.21 5 O 1490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8636 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4067 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 29, 'TRANS': 485} Chain breaks: 1 Chain: "B" Number of atoms: 4067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4067 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 29, 'TRANS': 485} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 187 Unusual residues: {'CLR': 1, 'PC1': 1, 'Y01': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 187 Unusual residues: {'CLR': 1, 'PC1': 1, 'Y01': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Time building chain proxies: 1.49, per 1000 atoms: 0.17 Number of scatterers: 8636 At special positions: 0 Unit cell: (112.98, 97.916, 83.928, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 2 15.00 O 1490 8.00 N 1310 7.00 C 5798 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 642 " " NAG D 1 " - " ASN B 642 " Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 215.1 milliseconds 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1916 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 4 sheets defined 74.6% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 379 through 390 Processing helix chain 'A' and resid 392 through 399 Processing helix chain 'A' and resid 402 through 432 removed outlier: 3.501A pdb=" N LEU A 406 " --> pdb=" O SER A 402 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) Proline residue: A 419 - end of helix removed outlier: 3.626A pdb=" N GLY A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 455 Processing helix chain 'A' and resid 465 through 483 Processing helix chain 'A' and resid 485 through 507 removed outlier: 3.859A pdb=" N VAL A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TRP A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 515 Processing helix chain 'A' and resid 517 through 547 removed outlier: 3.511A pdb=" N LEU A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 543 " --> pdb=" O LYS A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 593 Processing helix chain 'A' and resid 598 through 608 Processing helix chain 'A' and resid 608 through 623 removed outlier: 3.509A pdb=" N MET A 617 " --> pdb=" O SER A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 646 Processing helix chain 'A' and resid 660 through 667 removed outlier: 4.022A pdb=" N MET A 664 " --> pdb=" O PRO A 660 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 665 " --> pdb=" O ILE A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 690 Processing helix chain 'A' and resid 701 through 719 removed outlier: 3.756A pdb=" N LEU A 718 " --> pdb=" O GLY A 714 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE A 719 " --> pdb=" O VAL A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 738 Processing helix chain 'A' and resid 760 through 773 Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 784 through 799 removed outlier: 3.722A pdb=" N LEU A 788 " --> pdb=" O PRO A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 812 removed outlier: 3.535A pdb=" N LEU A 811 " --> pdb=" O ASP A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 819 removed outlier: 3.824A pdb=" N HIS A 819 " --> pdb=" O PRO A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 827 Processing helix chain 'A' and resid 829 through 853 Processing helix chain 'A' and resid 858 through 865 removed outlier: 3.605A pdb=" N LEU A 865 " --> pdb=" O PHE A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 872 Processing helix chain 'A' and resid 873 through 878 removed outlier: 3.606A pdb=" N ILE A 877 " --> pdb=" O LEU A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 887 Processing helix chain 'B' and resid 379 through 390 Processing helix chain 'B' and resid 392 through 399 Processing helix chain 'B' and resid 402 through 432 removed outlier: 3.501A pdb=" N LEU B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B 414 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Proline residue: B 419 - end of helix removed outlier: 3.626A pdb=" N GLY B 424 " --> pdb=" O ALA B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 455 Processing helix chain 'B' and resid 465 through 483 Processing helix chain 'B' and resid 485 through 507 removed outlier: 3.859A pdb=" N VAL B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TRP B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 493 " --> pdb=" O GLY B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 515 Processing helix chain 'B' and resid 517 through 547 removed outlier: 3.509A pdb=" N LEU B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 543 " --> pdb=" O LYS B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 593 Processing helix chain 'B' and resid 598 through 608 Processing helix chain 'B' and resid 608 through 623 removed outlier: 3.509A pdb=" N MET B 617 " --> pdb=" O SER B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 646 Processing helix chain 'B' and resid 660 through 667 removed outlier: 4.023A pdb=" N MET B 664 " --> pdb=" O PRO B 660 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B 665 " --> pdb=" O ILE B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 690 Processing helix chain 'B' and resid 701 through 719 removed outlier: 3.757A pdb=" N LEU B 718 " --> pdb=" O GLY B 714 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE B 719 " --> pdb=" O VAL B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 738 Processing helix chain 'B' and resid 760 through 773 Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 784 through 799 removed outlier: 3.724A pdb=" N LEU B 788 " --> pdb=" O PRO B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 812 removed outlier: 3.534A pdb=" N LEU B 811 " --> pdb=" O ASP B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 819 removed outlier: 3.824A pdb=" N HIS B 819 " --> pdb=" O PRO B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 827 Processing helix chain 'B' and resid 829 through 853 Processing helix chain 'B' and resid 858 through 865 removed outlier: 3.605A pdb=" N LEU B 865 " --> pdb=" O PHE B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 872 Processing helix chain 'B' and resid 873 through 878 removed outlier: 3.607A pdb=" N ILE B 877 " --> pdb=" O LEU B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 887 Processing sheet with id=AA1, first strand: chain 'A' and resid 461 through 463 removed outlier: 4.792A pdb=" N VAL A 461 " --> pdb=" O THR A 727 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 739 through 742 removed outlier: 7.659A pdb=" N VAL A 740 " --> pdb=" O GLN A 754 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN A 754 " --> pdb=" O VAL A 740 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN A 752 " --> pdb=" O GLY A 742 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 461 through 463 removed outlier: 4.792A pdb=" N VAL B 461 " --> pdb=" O THR B 727 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 739 through 742 removed outlier: 7.661A pdb=" N VAL B 740 " --> pdb=" O GLN B 754 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN B 754 " --> pdb=" O VAL B 740 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN B 752 " --> pdb=" O GLY B 742 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1518 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: 0.93 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1254 1.32 - 1.45: 2267 1.45 - 1.57: 5201 1.57 - 1.69: 4 1.69 - 1.82: 66 Bond restraints: 8792 Sorted by residual: bond pdb=" N LEU B 669 " pdb=" CA LEU B 669 " ideal model delta sigma weight residual 1.463 1.491 -0.027 6.90e-03 2.10e+04 1.58e+01 bond pdb=" N LEU A 669 " pdb=" CA LEU A 669 " ideal model delta sigma weight residual 1.463 1.491 -0.027 6.90e-03 2.10e+04 1.57e+01 bond pdb=" N LEU B 874 " pdb=" CA LEU B 874 " ideal model delta sigma weight residual 1.462 1.495 -0.033 8.50e-03 1.38e+04 1.53e+01 bond pdb=" N THR A 431 " pdb=" CA THR A 431 " ideal model delta sigma weight residual 1.457 1.502 -0.045 1.16e-02 7.43e+03 1.49e+01 bond pdb=" N THR B 431 " pdb=" CA THR B 431 " ideal model delta sigma weight residual 1.457 1.502 -0.045 1.16e-02 7.43e+03 1.49e+01 ... (remaining 8787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 9035 2.13 - 4.26: 2548 4.26 - 6.39: 383 6.39 - 8.53: 6 8.53 - 10.66: 2 Bond angle restraints: 11974 Sorted by residual: angle pdb=" N VAL A 825 " pdb=" CA VAL A 825 " pdb=" C VAL A 825 " ideal model delta sigma weight residual 111.00 105.19 5.81 1.09e+00 8.42e-01 2.84e+01 angle pdb=" C PRO B 598 " pdb=" N GLY B 599 " pdb=" CA GLY B 599 " ideal model delta sigma weight residual 120.03 125.79 -5.76 1.12e+00 7.97e-01 2.65e+01 angle pdb=" C PRO A 598 " pdb=" N GLY A 599 " pdb=" CA GLY A 599 " ideal model delta sigma weight residual 120.03 125.76 -5.73 1.12e+00 7.97e-01 2.62e+01 angle pdb=" N TYR B 596 " pdb=" CA TYR B 596 " pdb=" C TYR B 596 " ideal model delta sigma weight residual 108.41 116.71 -8.30 1.63e+00 3.76e-01 2.59e+01 angle pdb=" N GLU A 429 " pdb=" CA GLU A 429 " pdb=" C GLU A 429 " ideal model delta sigma weight residual 111.82 106.03 5.79 1.16e+00 7.43e-01 2.49e+01 ... (remaining 11969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.46: 4676 19.46 - 38.93: 317 38.93 - 58.39: 77 58.39 - 77.85: 17 77.85 - 97.32: 5 Dihedral angle restraints: 5092 sinusoidal: 2122 harmonic: 2970 Sorted by residual: dihedral pdb=" CA TYR A 596 " pdb=" C TYR A 596 " pdb=" N PHE A 597 " pdb=" CA PHE A 597 " ideal model delta harmonic sigma weight residual 180.00 159.14 20.86 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA TYR B 555 " pdb=" C TYR B 555 " pdb=" N ASN B 556 " pdb=" CA ASN B 556 " ideal model delta harmonic sigma weight residual 180.00 160.45 19.55 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA TYR A 555 " pdb=" C TYR A 555 " pdb=" N ASN A 556 " pdb=" CA ASN A 556 " ideal model delta harmonic sigma weight residual 180.00 160.86 19.14 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 775 0.077 - 0.154: 596 0.154 - 0.232: 61 0.232 - 0.309: 0 0.309 - 0.386: 2 Chirality restraints: 1434 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.67e+01 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.29e+01 chirality pdb=" CA VAL A 825 " pdb=" N VAL A 825 " pdb=" C VAL A 825 " pdb=" CB VAL A 825 " both_signs ideal model delta sigma weight residual False 2.44 2.83 -0.39 2.00e-01 2.50e+01 3.72e+00 ... (remaining 1431 not shown) Planarity restraints: 1410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " 0.326 2.00e-02 2.50e+03 2.77e-01 9.58e+02 pdb=" C7 NAG C 1 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.182 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " -0.483 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.291 2.00e-02 2.50e+03 2.44e-01 7.44e+02 pdb=" C7 NAG D 1 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.187 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.415 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " -0.221 2.00e-02 2.50e+03 1.83e-01 4.17e+02 pdb=" C7 NAG C 2 " 0.059 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " -0.157 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " 0.299 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " 0.019 2.00e-02 2.50e+03 ... (remaining 1407 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 401 2.75 - 3.29: 9297 3.29 - 3.83: 13893 3.83 - 4.36: 18726 4.36 - 4.90: 30644 Nonbonded interactions: 72961 Sorted by model distance: nonbonded pdb=" OH TYR A 555 " pdb=" OH TYR B 555 " model vdw 2.215 3.040 nonbonded pdb=" O ASP B 607 " pdb=" O HOH B2301 " model vdw 2.222 3.040 nonbonded pdb=" OE1 GLN A 447 " pdb=" O HOH A2301 " model vdw 2.422 3.040 nonbonded pdb=" OE1 GLN B 447 " pdb=" O HOH B2302 " model vdw 2.423 3.040 nonbonded pdb=" NH2 ARG A 490 " pdb=" O MET A 721 " model vdw 2.450 3.120 ... (remaining 72956 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.290 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.600 Find NCS groups from input model: 0.120 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:7.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 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 : 0.013 0.051 8796 Z= 0.998 Angle : 1.798 10.657 11986 Z= 1.370 Chirality : 0.087 0.386 1434 Planarity : 0.012 0.277 1408 Dihedral : 14.675 97.319 3176 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.87 % Favored : 94.03 % Rotamer: Outliers : 0.45 % Allowed : 5.47 % Favored : 94.08 % 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: -2.69 (0.22), residues: 1022 helix: -1.56 (0.16), residues: 670 sheet: None (None), residues: 0 loop : -1.93 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 730 TYR 0.013 0.002 TYR B 628 PHE 0.016 0.002 PHE B 451 TRP 0.018 0.002 TRP A 492 HIS 0.005 0.002 HIS A 819 Details of bonding type rmsd/Z covalent geometry : bond 0.01305 / 1.00 ( 8792) covalent geometry : angle 1.79787 / 1.37 (11974) hydrogen bonds : bond 0.23428 / 15.90 ( 524) hydrogen bonds : angle 8.20359 / 5.95 ( 1518) link_BETA1-4 : bond 0.00201 / 0.10 ( 2) link_BETA1-4 : angle 0.66710 / 0.32 ( 6) link_NAG-ASN : bond 0.00180 / 0.09 ( 2) link_NAG-ASN : angle 2.55403 / 1.35 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 482 ASN cc_start: 0.8611 (m-40) cc_final: 0.8260 (m110) REVERT: A 498 ILE cc_start: 0.9632 (mt) cc_final: 0.9415 (mp) REVERT: A 681 GLU cc_start: 0.8803 (tt0) cc_final: 0.8347 (tt0) REVERT: A 741 MET cc_start: 0.9316 (mmm) cc_final: 0.8973 (mmm) REVERT: A 880 ASN cc_start: 0.9250 (p0) cc_final: 0.9047 (t0) REVERT: B 433 ASN cc_start: 0.9395 (m-40) cc_final: 0.9174 (m-40) REVERT: B 482 ASN cc_start: 0.8615 (m-40) cc_final: 0.8244 (m110) REVERT: B 498 ILE cc_start: 0.9630 (mt) cc_final: 0.9424 (mp) REVERT: B 681 GLU cc_start: 0.8808 (tt0) cc_final: 0.8352 (tt0) REVERT: B 741 MET cc_start: 0.9318 (mmm) cc_final: 0.8975 (mmm) REVERT: B 880 ASN cc_start: 0.9252 (p0) cc_final: 0.9038 (t0) outliers start: 4 outliers final: 2 residues processed: 130 average time/residue: 0.4603 time to fit residues: 64.7228 Evaluate side-chains 73 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain B residue 511 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 433 ASN A 457 GLN A 545 GLN A 564 GLN A 683 GLN B 457 GLN B 545 GLN B 564 GLN B 834 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.058906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.049553 restraints weight = 29020.115| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 3.30 r_work: 0.2646 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8796 Z= 0.168 Angle : 0.676 9.458 11986 Z= 0.321 Chirality : 0.040 0.147 1434 Planarity : 0.005 0.043 1408 Dihedral : 10.106 76.106 1278 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.34 % Allowed : 10.60 % Favored : 87.05 % 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: 0.69 (0.25), residues: 1022 helix: 1.30 (0.19), residues: 688 sheet: None (None), residues: 0 loop : -1.31 (0.30), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 603 TYR 0.006 0.001 TYR A 824 PHE 0.019 0.002 PHE A 411 TRP 0.029 0.003 TRP A 662 HIS 0.002 0.001 HIS A 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 8792) covalent geometry : angle 0.67407 / 0.32 (11974) hydrogen bonds : bond 0.05079 / 3.45 ( 524) hydrogen bonds : angle 4.66067 / 3.35 ( 1518) link_BETA1-4 : bond 0.00171 / 0.09 ( 2) link_BETA1-4 : angle 1.69408 / 1.09 ( 6) link_NAG-ASN : bond 0.00319 / 0.17 ( 2) link_NAG-ASN : angle 1.46764 / 0.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8812 (pp) REVERT: A 554 ASN cc_start: 0.8478 (t0) cc_final: 0.8166 (t0) REVERT: A 681 GLU cc_start: 0.8954 (tt0) cc_final: 0.8183 (tm-30) REVERT: A 696 MET cc_start: 0.8581 (mmm) cc_final: 0.8263 (mmm) REVERT: A 721 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8809 (mtm) REVERT: A 759 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8366 (pm20) REVERT: B 386 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8792 (pp) REVERT: B 554 ASN cc_start: 0.8374 (t0) cc_final: 0.7954 (t0) REVERT: B 681 GLU cc_start: 0.8957 (tt0) cc_final: 0.8186 (tm-30) REVERT: B 721 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8492 (mtp) REVERT: B 759 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8464 (pm20) outliers start: 21 outliers final: 1 residues processed: 93 average time/residue: 0.3720 time to fit residues: 37.9947 Evaluate side-chains 74 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 759 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 24 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 683 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.057453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.048552 restraints weight = 29712.695| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 3.25 r_work: 0.2629 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8796 Z= 0.162 Angle : 0.604 7.476 11986 Z= 0.287 Chirality : 0.040 0.141 1434 Planarity : 0.005 0.047 1408 Dihedral : 9.302 60.946 1276 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.35 % Allowed : 10.38 % Favored : 86.27 % 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: 1.50 (0.26), residues: 1022 helix: 1.91 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.99 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 656 TYR 0.013 0.001 TYR A 824 PHE 0.014 0.001 PHE B 411 TRP 0.025 0.002 TRP A 662 HIS 0.003 0.001 HIS A 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 8792) covalent geometry : angle 0.60141 / 0.29 (11974) hydrogen bonds : bond 0.04126 / 2.82 ( 524) hydrogen bonds : angle 4.42742 / 3.17 ( 1518) link_BETA1-4 : bond 0.00204 / 0.11 ( 2) link_BETA1-4 : angle 1.01647 / 0.52 ( 6) link_NAG-ASN : bond 0.00420 / 0.20 ( 2) link_NAG-ASN : angle 2.24972 / 1.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 75 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 554 ASN cc_start: 0.8822 (t0) cc_final: 0.8409 (t0) REVERT: A 681 GLU cc_start: 0.8919 (tt0) cc_final: 0.8172 (tm-30) REVERT: A 696 MET cc_start: 0.8727 (mmm) cc_final: 0.8141 (mmm) REVERT: A 721 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8420 (mpp) REVERT: B 554 ASN cc_start: 0.8903 (t0) cc_final: 0.8447 (t0) REVERT: B 681 GLU cc_start: 0.8927 (tt0) cc_final: 0.8177 (tm-30) REVERT: B 721 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8733 (mmm) outliers start: 30 outliers final: 5 residues processed: 91 average time/residue: 0.3268 time to fit residues: 32.8097 Evaluate side-chains 69 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 864 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 53 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.055771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.046995 restraints weight = 30788.928| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 3.26 r_work: 0.2591 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8796 Z= 0.205 Angle : 0.624 8.339 11986 Z= 0.294 Chirality : 0.040 0.136 1434 Planarity : 0.005 0.047 1408 Dihedral : 9.105 59.518 1276 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.24 % Allowed : 11.27 % Favored : 85.49 % 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: 1.76 (0.26), residues: 1022 helix: 2.07 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -0.80 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 656 TYR 0.014 0.001 TYR B 824 PHE 0.014 0.001 PHE A 471 TRP 0.019 0.002 TRP A 662 HIS 0.002 0.001 HIS B 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 ( 8792) covalent geometry : angle 0.62216 / 0.29 (11974) hydrogen bonds : bond 0.04097 / 2.81 ( 524) hydrogen bonds : angle 4.35030 / 3.11 ( 1518) link_BETA1-4 : bond 0.00235 / 0.12 ( 2) link_BETA1-4 : angle 0.93967 / 0.45 ( 6) link_NAG-ASN : bond 0.00429 / 0.21 ( 2) link_NAG-ASN : angle 1.92758 / 1.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 63 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 498 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.8982 (mp) REVERT: A 554 ASN cc_start: 0.8950 (t0) cc_final: 0.8526 (t0) REVERT: A 696 MET cc_start: 0.8835 (mmm) cc_final: 0.8243 (mmm) REVERT: A 721 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8754 (mtm) REVERT: A 759 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8400 (pm20) REVERT: B 433 ASN cc_start: 0.9558 (m110) cc_final: 0.9311 (m110) REVERT: B 554 ASN cc_start: 0.8995 (t0) cc_final: 0.8532 (t0) REVERT: B 681 GLU cc_start: 0.8951 (tt0) cc_final: 0.8382 (tm-30) REVERT: B 705 ASP cc_start: 0.9369 (m-30) cc_final: 0.9068 (m-30) REVERT: B 721 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8275 (mtp) REVERT: B 759 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8506 (pm20) outliers start: 29 outliers final: 8 residues processed: 84 average time/residue: 0.3255 time to fit residues: 30.5797 Evaluate side-chains 75 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 759 GLN Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 864 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 29 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 62 optimal weight: 0.0070 chunk 35 optimal weight: 1.9990 chunk 42 optimal weight: 0.0040 chunk 66 optimal weight: 0.6980 chunk 100 optimal weight: 0.0980 chunk 53 optimal weight: 0.0980 chunk 39 optimal weight: 0.0010 overall best weight: 0.0416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.058572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.049815 restraints weight = 29429.823| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 3.29 r_work: 0.2672 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8796 Z= 0.111 Angle : 0.592 8.770 11986 Z= 0.274 Chirality : 0.038 0.132 1434 Planarity : 0.005 0.048 1408 Dihedral : 8.620 59.875 1276 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.01 % Allowed : 13.17 % Favored : 84.82 % 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: 1.88 (0.27), residues: 1022 helix: 2.14 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -0.66 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 656 TYR 0.014 0.001 TYR A 824 PHE 0.014 0.001 PHE A 471 TRP 0.015 0.001 TRP A 492 HIS 0.002 0.001 HIS B 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 8792) covalent geometry : angle 0.59044 / 0.27 (11974) hydrogen bonds : bond 0.03523 / 2.43 ( 524) hydrogen bonds : angle 4.20382 / 2.99 ( 1518) link_BETA1-4 : bond 0.00178 / 0.09 ( 2) link_BETA1-4 : angle 0.85854 / 0.46 ( 6) link_NAG-ASN : bond 0.00013 / 0.01 ( 2) link_NAG-ASN : angle 1.85443 / 1.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ASN cc_start: 0.9515 (m110) cc_final: 0.9297 (m-40) REVERT: A 554 ASN cc_start: 0.8905 (t0) cc_final: 0.8426 (t0) REVERT: A 559 MET cc_start: 0.8876 (mtm) cc_final: 0.8314 (mtt) REVERT: A 681 GLU cc_start: 0.8895 (tt0) cc_final: 0.8343 (tm-30) REVERT: A 759 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8151 (pm20) REVERT: B 433 ASN cc_start: 0.9548 (m110) cc_final: 0.9177 (m110) REVERT: B 554 ASN cc_start: 0.8975 (t0) cc_final: 0.8482 (t0) REVERT: B 681 GLU cc_start: 0.8916 (tt0) cc_final: 0.8201 (tt0) REVERT: B 705 ASP cc_start: 0.9338 (m-30) cc_final: 0.9137 (m-30) REVERT: B 721 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8237 (mmm) REVERT: B 759 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8410 (pm20) outliers start: 18 outliers final: 10 residues processed: 93 average time/residue: 0.3353 time to fit residues: 34.3374 Evaluate side-chains 78 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 759 GLN Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 864 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 67 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 93 optimal weight: 0.0570 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.056031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.047353 restraints weight = 30444.802| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 3.27 r_work: 0.2610 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8796 Z= 0.192 Angle : 0.627 9.011 11986 Z= 0.289 Chirality : 0.040 0.158 1434 Planarity : 0.005 0.047 1408 Dihedral : 8.511 58.804 1276 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.23 % Allowed : 13.39 % Favored : 84.38 % 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: 1.87 (0.27), residues: 1022 helix: 2.09 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -0.69 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 656 TYR 0.013 0.001 TYR B 824 PHE 0.012 0.001 PHE A 471 TRP 0.013 0.001 TRP B 662 HIS 0.002 0.001 HIS B 819 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 ( 8792) covalent geometry : angle 0.62577 / 0.29 (11974) hydrogen bonds : bond 0.03801 / 2.62 ( 524) hydrogen bonds : angle 4.28367 / 3.06 ( 1518) link_BETA1-4 : bond 0.00367 / 0.19 ( 2) link_BETA1-4 : angle 0.94430 / 0.51 ( 6) link_NAG-ASN : bond 0.00356 / 0.18 ( 2) link_NAG-ASN : angle 1.87773 / 1.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ASN cc_start: 0.9558 (m110) cc_final: 0.9151 (m-40) REVERT: A 554 ASN cc_start: 0.9015 (t0) cc_final: 0.8550 (t0) REVERT: A 559 MET cc_start: 0.8819 (mtm) cc_final: 0.8326 (mtt) REVERT: A 705 ASP cc_start: 0.9360 (m-30) cc_final: 0.9077 (m-30) REVERT: A 721 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8219 (mtp) REVERT: A 759 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8336 (pm20) REVERT: B 433 ASN cc_start: 0.9595 (m110) cc_final: 0.9127 (m110) REVERT: B 554 ASN cc_start: 0.9051 (t0) cc_final: 0.8604 (t0) REVERT: B 681 GLU cc_start: 0.8932 (tt0) cc_final: 0.8414 (tm-30) REVERT: B 705 ASP cc_start: 0.9357 (m-30) cc_final: 0.9097 (m-30) REVERT: B 721 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8703 (mmm) REVERT: B 759 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8605 (pm20) outliers start: 20 outliers final: 9 residues processed: 84 average time/residue: 0.3565 time to fit residues: 32.9618 Evaluate side-chains 77 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 759 GLN Chi-restraints excluded: chain B residue 864 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 63 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 94 optimal weight: 0.0670 chunk 53 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 521 GLN A 819 HIS B 819 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.057159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.048511 restraints weight = 30581.621| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 3.30 r_work: 0.2637 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8796 Z= 0.129 Angle : 0.610 9.507 11986 Z= 0.281 Chirality : 0.039 0.153 1434 Planarity : 0.005 0.047 1408 Dihedral : 8.369 58.502 1276 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.90 % Allowed : 14.29 % Favored : 83.82 % 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: 1.84 (0.27), residues: 1022 helix: 2.05 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -0.66 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 656 TYR 0.013 0.001 TYR A 824 PHE 0.013 0.001 PHE A 471 TRP 0.015 0.001 TRP A 492 HIS 0.002 0.001 HIS A 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 8792) covalent geometry : angle 0.60826 / 0.28 (11974) hydrogen bonds : bond 0.03646 / 2.52 ( 524) hydrogen bonds : angle 4.23936 / 3.03 ( 1518) link_BETA1-4 : bond 0.00208 / 0.11 ( 2) link_BETA1-4 : angle 0.87222 / 0.46 ( 6) link_NAG-ASN : bond 0.00251 / 0.12 ( 2) link_NAG-ASN : angle 1.85856 / 1.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ASN cc_start: 0.9531 (m110) cc_final: 0.9282 (m-40) REVERT: A 554 ASN cc_start: 0.9014 (t0) cc_final: 0.8524 (t0) REVERT: A 559 MET cc_start: 0.8846 (mtm) cc_final: 0.8346 (mtt) REVERT: A 721 MET cc_start: 0.8788 (mmm) cc_final: 0.8189 (mtp) REVERT: A 759 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8305 (pm20) REVERT: B 433 ASN cc_start: 0.9538 (m110) cc_final: 0.9177 (m110) REVERT: B 554 ASN cc_start: 0.9055 (t0) cc_final: 0.8561 (t0) REVERT: B 681 GLU cc_start: 0.8911 (tt0) cc_final: 0.8167 (tt0) REVERT: B 705 ASP cc_start: 0.9372 (m-30) cc_final: 0.9121 (m-30) REVERT: B 759 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8563 (pm20) outliers start: 17 outliers final: 10 residues processed: 81 average time/residue: 0.3393 time to fit residues: 30.5751 Evaluate side-chains 77 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 759 GLN Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 864 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 2 optimal weight: 0.1980 chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.057359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.048881 restraints weight = 30130.369| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 3.30 r_work: 0.2649 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8796 Z= 0.125 Angle : 0.614 10.935 11986 Z= 0.282 Chirality : 0.039 0.165 1434 Planarity : 0.005 0.047 1408 Dihedral : 8.222 58.567 1276 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.12 % Allowed : 14.29 % Favored : 83.59 % 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: 1.90 (0.27), residues: 1022 helix: 2.08 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -0.59 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 656 TYR 0.013 0.001 TYR A 824 PHE 0.013 0.001 PHE A 471 TRP 0.014 0.001 TRP B 662 HIS 0.002 0.001 HIS B 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 ( 8792) covalent geometry : angle 0.61306 / 0.28 (11974) hydrogen bonds : bond 0.03578 / 2.47 ( 524) hydrogen bonds : angle 4.22879 / 3.03 ( 1518) link_BETA1-4 : bond 0.00236 / 0.12 ( 2) link_BETA1-4 : angle 0.86726 / 0.47 ( 6) link_NAG-ASN : bond 0.00208 / 0.10 ( 2) link_NAG-ASN : angle 1.83984 / 1.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ASN cc_start: 0.9509 (m110) cc_final: 0.9235 (m-40) REVERT: A 554 ASN cc_start: 0.9040 (t0) cc_final: 0.8543 (t0) REVERT: A 559 MET cc_start: 0.8828 (mtm) cc_final: 0.8351 (mtt) REVERT: A 759 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8380 (pm20) REVERT: B 433 ASN cc_start: 0.9527 (m110) cc_final: 0.9140 (m110) REVERT: B 554 ASN cc_start: 0.9051 (t0) cc_final: 0.8543 (t0) REVERT: B 559 MET cc_start: 0.8837 (mtm) cc_final: 0.8289 (mtt) REVERT: B 681 GLU cc_start: 0.8907 (tt0) cc_final: 0.8168 (tt0) REVERT: B 705 ASP cc_start: 0.9373 (m-30) cc_final: 0.9115 (m-30) REVERT: B 759 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8572 (pm20) outliers start: 19 outliers final: 10 residues processed: 85 average time/residue: 0.3408 time to fit residues: 32.0994 Evaluate side-chains 76 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 759 GLN Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 864 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 0 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.056117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.047615 restraints weight = 30548.359| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 3.25 r_work: 0.2617 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8796 Z= 0.173 Angle : 0.653 12.545 11986 Z= 0.302 Chirality : 0.040 0.170 1434 Planarity : 0.005 0.047 1408 Dihedral : 8.229 59.796 1276 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.79 % Allowed : 14.84 % Favored : 83.37 % 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: 1.89 (0.27), residues: 1022 helix: 2.03 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -0.59 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 656 TYR 0.012 0.001 TYR A 824 PHE 0.012 0.001 PHE B 471 TRP 0.015 0.001 TRP A 662 HIS 0.002 0.001 HIS A 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 8792) covalent geometry : angle 0.65194 / 0.30 (11974) hydrogen bonds : bond 0.03786 / 2.61 ( 524) hydrogen bonds : angle 4.34044 / 3.11 ( 1518) link_BETA1-4 : bond 0.00246 / 0.12 ( 2) link_BETA1-4 : angle 0.87826 / 0.47 ( 6) link_NAG-ASN : bond 0.00316 / 0.16 ( 2) link_NAG-ASN : angle 1.87946 / 1.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ASN cc_start: 0.9541 (m110) cc_final: 0.9295 (m-40) REVERT: A 554 ASN cc_start: 0.9060 (t0) cc_final: 0.8506 (t0) REVERT: A 559 MET cc_start: 0.8825 (mtm) cc_final: 0.8324 (mtt) REVERT: A 721 MET cc_start: 0.8945 (mmm) cc_final: 0.8255 (mtp) REVERT: A 757 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8076 (mmtp) REVERT: A 759 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8487 (pm20) REVERT: B 433 ASN cc_start: 0.9532 (m110) cc_final: 0.9173 (m110) REVERT: B 554 ASN cc_start: 0.9056 (t0) cc_final: 0.8532 (t0) REVERT: B 559 MET cc_start: 0.8827 (mtm) cc_final: 0.8300 (mtt) REVERT: B 681 GLU cc_start: 0.8913 (tt0) cc_final: 0.8347 (tm-30) REVERT: B 705 ASP cc_start: 0.9372 (m-30) cc_final: 0.9106 (m-30) REVERT: B 721 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8430 (mmm) outliers start: 16 outliers final: 9 residues processed: 79 average time/residue: 0.4391 time to fit residues: 37.9977 Evaluate side-chains 75 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 757 LYS Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 864 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 24 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.056901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.048456 restraints weight = 30414.999| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 3.29 r_work: 0.2640 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8796 Z= 0.144 Angle : 0.677 13.270 11986 Z= 0.309 Chirality : 0.041 0.265 1434 Planarity : 0.005 0.047 1408 Dihedral : 8.118 59.163 1276 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.56 % Allowed : 14.84 % Favored : 83.59 % 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: 1.91 (0.27), residues: 1022 helix: 2.05 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -0.56 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 490 TYR 0.014 0.001 TYR A 824 PHE 0.012 0.001 PHE A 471 TRP 0.013 0.001 TRP A 492 HIS 0.002 0.001 HIS B 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 8792) covalent geometry : angle 0.67578 / 0.31 (11974) hydrogen bonds : bond 0.03685 / 2.55 ( 524) hydrogen bonds : angle 4.37237 / 3.13 ( 1518) link_BETA1-4 : bond 0.00297 / 0.15 ( 2) link_BETA1-4 : angle 0.88091 / 0.49 ( 6) link_NAG-ASN : bond 0.00286 / 0.14 ( 2) link_NAG-ASN : angle 1.90222 / 1.13 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ASN cc_start: 0.9490 (m110) cc_final: 0.9237 (m-40) REVERT: A 554 ASN cc_start: 0.9038 (t0) cc_final: 0.8495 (t0) REVERT: A 559 MET cc_start: 0.8858 (mtm) cc_final: 0.8396 (mtt) REVERT: A 721 MET cc_start: 0.8842 (mmm) cc_final: 0.8127 (mtp) REVERT: A 757 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8225 (mmmm) REVERT: A 759 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8523 (pm20) REVERT: B 433 ASN cc_start: 0.9526 (m110) cc_final: 0.9151 (m110) REVERT: B 554 ASN cc_start: 0.9070 (t0) cc_final: 0.8553 (t0) REVERT: B 559 MET cc_start: 0.8841 (mtm) cc_final: 0.8345 (mtt) REVERT: B 681 GLU cc_start: 0.8911 (tt0) cc_final: 0.8354 (tm-30) REVERT: B 705 ASP cc_start: 0.9357 (m-30) cc_final: 0.9102 (m-30) REVERT: B 721 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8392 (mmm) outliers start: 14 outliers final: 8 residues processed: 78 average time/residue: 0.4176 time to fit residues: 35.9277 Evaluate side-chains 75 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 757 LYS Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 864 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 3 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 85 optimal weight: 0.0870 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 55 optimal weight: 0.3980 chunk 88 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 521 GLN B 880 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.057562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.049050 restraints weight = 30797.705| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 3.32 r_work: 0.2673 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8796 Z= 0.126 Angle : 0.667 15.536 11986 Z= 0.304 Chirality : 0.041 0.295 1434 Planarity : 0.005 0.047 1408 Dihedral : 7.906 59.165 1276 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.56 % Allowed : 15.07 % Favored : 83.37 % 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: 1.89 (0.27), residues: 1022 helix: 2.02 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -0.51 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 656 TYR 0.013 0.001 TYR A 824 PHE 0.012 0.001 PHE B 471 TRP 0.012 0.001 TRP A 492 HIS 0.002 0.001 HIS B 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 8792) covalent geometry : angle 0.66549 / 0.30 (11974) hydrogen bonds : bond 0.03543 / 2.44 ( 524) hydrogen bonds : angle 4.33551 / 3.10 ( 1518) link_BETA1-4 : bond 0.00290 / 0.15 ( 2) link_BETA1-4 : angle 0.85646 / 0.50 ( 6) link_NAG-ASN : bond 0.00161 / 0.08 ( 2) link_NAG-ASN : angle 1.85240 / 1.08 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1975.29 seconds wall clock time: 34 minutes 43.18 seconds (2083.18 seconds total)