Starting phenix.real_space_refine on Fri Jul 3 01:12:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wor_37696/07_2026/8wor_37696.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wor_37696/07_2026/8wor_37696.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/8wor_37696/07_2026/8wor_37696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wor_37696/07_2026/8wor_37696.map" model { file = "/net/cci-nas-00/data/ceres_data/8wor_37696/07_2026/8wor_37696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wor_37696/07_2026/8wor_37696.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= 0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 2 6.06 5 S 60 5.16 5 C 7539 2.51 5 N 1696 2.21 5 O 1919 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s 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: 11218 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5261 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 647, 5252 Classifications: {'peptide': 647} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 620} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 647, 5252 Classifications: {'peptide': 647} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 620} Chain breaks: 4 bond proxies already assigned to first conformer: 5384 Chain: "B" Number of atoms: 5261 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 647, 5252 Classifications: {'peptide': 647} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 620} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 647, 5252 Classifications: {'peptide': 647} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 620} Chain breaks: 4 bond proxies already assigned to first conformer: 5384 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 275 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1, 'CLR': 7, 'NAG': 2, 'OLA': 1, 'SPL': 1} Classifications: {'undetermined': 12} Link IDs: {None: 10} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 303 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1, 'CLR': 8, 'NAG': 2, 'OLA': 1, 'SPL': 1} Classifications: {'undetermined': 13} Link IDs: {None: 11} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 4.26, per 1000 atoms: 0.38 Number of scatterers: 11218 At special positions: 0 Unit cell: (93.61, 89.355, 135.309, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 Ca 2 19.99 S 60 16.00 O 1919 8.00 N 1696 7.00 C 7539 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 222 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 787 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 222 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 479 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 787 " 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 903 " - " ASN A 67 " " NAG A 904 " - " ASN A 136 " " NAG B 903 " - " ASN B 67 " " NAG B 904 " - " ASN B 136 " " NAG C 1 " - " ASN A 57 " " NAG D 1 " - " ASN A 83 " " NAG E 1 " - " ASN B 57 " " NAG F 1 " - " ASN B 83 " Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 835.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 563 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 796 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 800 " pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 563 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 796 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 800 " 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2492 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 49.9% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 38 through 43 removed outlier: 4.270A pdb=" N ALA A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 302 through 335 removed outlier: 3.841A pdb=" N TYR A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHE A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 474 removed outlier: 4.024A pdb=" N ILE A 448 " --> pdb=" O TYR A 444 " (cutoff:3.500A) Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 482 through 486 removed outlier: 3.948A pdb=" N ALA A 486 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 501 through 527 removed outlier: 3.842A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 563 Processing helix chain 'A' and resid 570 through 594 removed outlier: 4.204A pdb=" N ASP A 574 " --> pdb=" O ASN A 570 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET A 578 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 579 " --> pdb=" O THR A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 621 removed outlier: 3.741A pdb=" N ALA A 606 " --> pdb=" O TYR A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 650 Processing helix chain 'A' and resid 686 through 709 Processing helix chain 'A' and resid 713 through 738 Processing helix chain 'A' and resid 745 through 767 removed outlier: 3.581A pdb=" N LEU A 749 " --> pdb=" O LEU A 745 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A 765 " --> pdb=" O ALA A 761 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 782 Processing helix chain 'A' and resid 788 through 792 removed outlier: 3.643A pdb=" N ASP A 791 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 816 removed outlier: 3.520A pdb=" N ILE A 798 " --> pdb=" O ASP A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 824 Processing helix chain 'B' and resid 38 through 43 removed outlier: 4.202A pdb=" N ALA B 42 " --> pdb=" O ASP B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 302 through 335 removed outlier: 3.848A pdb=" N TYR B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 474 removed outlier: 4.014A pdb=" N ILE B 448 " --> pdb=" O TYR B 444 " (cutoff:3.500A) Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 482 through 486 removed outlier: 3.933A pdb=" N ALA B 486 " --> pdb=" O PHE B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 500 Processing helix chain 'B' and resid 501 through 527 removed outlier: 3.860A pdb=" N VAL B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 563 Processing helix chain 'B' and resid 570 through 594 removed outlier: 4.205A pdb=" N ASP B 574 " --> pdb=" O ASN B 570 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET B 578 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR B 579 " --> pdb=" O THR B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 621 removed outlier: 3.711A pdb=" N ALA B 606 " --> pdb=" O TYR B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 650 removed outlier: 3.547A pdb=" N PHE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TRP B 629 " --> pdb=" O ASP B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 709 Processing helix chain 'B' and resid 713 through 738 Processing helix chain 'B' and resid 745 through 767 removed outlier: 3.563A pdb=" N LEU B 749 " --> pdb=" O LEU B 745 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE B 765 " --> pdb=" O ALA B 761 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 782 Processing helix chain 'B' and resid 788 through 792 removed outlier: 3.635A pdb=" N ASP B 791 " --> pdb=" O ILE B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 816 removed outlier: 3.514A pdb=" N ILE B 798 " --> pdb=" O ASP B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 824 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 45 Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 56 removed outlier: 4.478A pdb=" N VAL A 78 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 113 Processing sheet with id=AA4, first strand: chain 'A' and resid 177 through 181 Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 192 Processing sheet with id=AA6, first strand: chain 'B' and resid 44 through 45 Processing sheet with id=AA7, first strand: chain 'B' and resid 51 through 56 removed outlier: 4.449A pdb=" N VAL B 78 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 113 Processing sheet with id=AA9, first strand: chain 'B' and resid 177 through 181 Processing sheet with id=AB1, first strand: chain 'B' and resid 187 through 192 630 hydrogen bonds defined for protein. 1795 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: 1.82 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3258 1.34 - 1.46: 2819 1.46 - 1.58: 5368 1.58 - 1.70: 2 1.70 - 1.82: 94 Bond restraints: 11541 Sorted by residual: bond pdb=" C10 OLA A 911 " pdb=" C9 OLA A 911 " ideal model delta sigma weight residual 1.332 1.468 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C10 OLA B 914 " pdb=" C9 OLA B 914 " ideal model delta sigma weight residual 1.332 1.468 -0.136 2.00e-02 2.50e+03 4.60e+01 bond pdb=" CB PRO B 748 " pdb=" CG PRO B 748 " ideal model delta sigma weight residual 1.492 1.589 -0.097 5.00e-02 4.00e+02 3.79e+00 bond pdb=" CB PRO A 748 " pdb=" CG PRO A 748 " ideal model delta sigma weight residual 1.492 1.585 -0.093 5.00e-02 4.00e+02 3.43e+00 bond pdb=" C1 OLA A 911 " pdb=" C2 OLA A 911 " ideal model delta sigma weight residual 1.542 1.510 0.032 2.00e-02 2.50e+03 2.60e+00 ... (remaining 11536 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.28: 15709 4.28 - 8.56: 37 8.56 - 12.85: 0 12.85 - 17.13: 0 17.13 - 21.41: 2 Bond angle restraints: 15748 Sorted by residual: angle pdb=" CA LEU B 728 " pdb=" CB LEU B 728 " pdb=" CG LEU B 728 " ideal model delta sigma weight residual 116.30 137.71 -21.41 3.50e+00 8.16e-02 3.74e+01 angle pdb=" CA PRO B 748 " pdb=" N PRO B 748 " pdb=" CD PRO B 748 " ideal model delta sigma weight residual 112.00 104.60 7.40 1.40e+00 5.10e-01 2.79e+01 angle pdb=" CA LEU A 728 " pdb=" CB LEU A 728 " pdb=" CG LEU A 728 " ideal model delta sigma weight residual 116.30 134.47 -18.17 3.50e+00 8.16e-02 2.70e+01 angle pdb=" CA PRO A 748 " pdb=" N PRO A 748 " pdb=" CD PRO A 748 " ideal model delta sigma weight residual 112.00 105.37 6.63 1.40e+00 5.10e-01 2.24e+01 angle pdb=" C ILE B 612 " pdb=" N MET B 613 " pdb=" CA MET B 613 " ideal model delta sigma weight residual 120.72 114.17 6.55 1.67e+00 3.59e-01 1.54e+01 ... (remaining 15743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 6563 17.36 - 34.73: 800 34.73 - 52.09: 223 52.09 - 69.45: 57 69.45 - 86.82: 8 Dihedral angle restraints: 7651 sinusoidal: 3791 harmonic: 3860 Sorted by residual: dihedral pdb=" CA TYR B 210 " pdb=" C TYR B 210 " pdb=" N PRO B 211 " pdb=" CA PRO B 211 " ideal model delta harmonic sigma weight residual 0.00 20.33 -20.33 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA TYR A 210 " pdb=" C TYR A 210 " pdb=" N PRO A 211 " pdb=" CA PRO A 211 " ideal model delta harmonic sigma weight residual 0.00 20.20 -20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA CYS A 787 " pdb=" C CYS A 787 " pdb=" N ILE A 788 " pdb=" CA ILE A 788 " ideal model delta harmonic sigma weight residual 180.00 -161.15 -18.85 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 7648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1583 0.057 - 0.115: 232 0.115 - 0.172: 21 0.172 - 0.229: 2 0.229 - 0.287: 2 Chirality restraints: 1840 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 57 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 57 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA MET A 613 " pdb=" N MET A 613 " pdb=" C MET A 613 " pdb=" CB MET A 613 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.66e-01 ... (remaining 1837 not shown) Planarity restraints: 1858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA A 911 " -0.185 2.00e-02 2.50e+03 1.44e-01 2.08e+02 pdb=" C11 OLA A 911 " 0.085 2.00e-02 2.50e+03 pdb=" C8 OLA A 911 " -0.085 2.00e-02 2.50e+03 pdb=" C9 OLA A 911 " 0.186 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLA B 914 " 0.185 2.00e-02 2.50e+03 1.44e-01 2.08e+02 pdb=" C11 OLA B 914 " -0.085 2.00e-02 2.50e+03 pdb=" C8 OLA B 914 " 0.085 2.00e-02 2.50e+03 pdb=" C9 OLA B 914 " -0.185 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 747 " 0.082 5.00e-02 4.00e+02 1.21e-01 2.34e+01 pdb=" N PRO A 748 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO A 748 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 748 " 0.065 5.00e-02 4.00e+02 ... (remaining 1855 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 61 2.52 - 3.12: 8574 3.12 - 3.71: 16133 3.71 - 4.31: 22955 4.31 - 4.90: 39543 Nonbonded interactions: 87266 Sorted by model distance: nonbonded pdb="ZN ZN A 901 " pdb=" O HOH A1001 " model vdw 1.928 2.230 nonbonded pdb="ZN ZN B 901 " pdb=" O HOH B1001 " model vdw 1.928 2.230 nonbonded pdb=" OH TYR A 64 " pdb=" OH TYR A 159 " model vdw 2.080 3.040 nonbonded pdb=" OH TYR B 64 " pdb=" OH TYR B 159 " model vdw 2.085 3.040 nonbonded pdb=" O ASN B 598 " pdb=" OH TYR B 602 " model vdw 2.193 3.040 ... (remaining 87261 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 35 through 80 or resid 82 through 906 or resid 908 through \ 910 or resid 913)) selection = (chain 'B' and (resid 35 through 80 or resid 82 through 906 or resid 908 through \ 910 or resid 913)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.21 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: 3.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.840 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 : 0.004 0.136 11567 Z= 0.174 Angle : 0.641 21.410 15800 Z= 0.308 Chirality : 0.041 0.287 1840 Planarity : 0.007 0.144 1850 Dihedral : 15.745 86.815 5135 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.45 % Favored : 96.39 % Rotamer: Outliers : 5.08 % Allowed : 27.19 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 1.60 (0.24), residues: 1276 helix: 2.90 (0.21), residues: 590 sheet: 1.34 (0.30), residues: 272 loop : -2.08 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 593 TYR 0.011 0.001 TYR B 188 PHE 0.038 0.001 PHE A 732 TRP 0.009 0.001 TRP A 446 HIS 0.004 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (11541) covalent geometry : angle 0.63574 / 0.31 (15748) SS BOND : bond 0.00123 / 0.07 ( 8) SS BOND : angle 0.93078 / 0.49 ( 16) hydrogen bonds : bond 0.08913 / 5.64 ( 630) hydrogen bonds : angle 4.39253 / 3.12 ( 1795) metal coordination : bond 0.00167 / 0.10 ( 6) link_BETA1-4 : bond 0.00281 / 0.17 ( 4) link_BETA1-4 : angle 1.21617 / 0.74 ( 12) link_NAG-ASN : bond 0.00327 / 0.17 ( 8) link_NAG-ASN : angle 2.07644 / 1.61 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 116 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 117 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8744 (mp10) REVERT: A 158 GLN cc_start: 0.8522 (mt0) cc_final: 0.8296 (mt0) REVERT: A 554 MET cc_start: 0.7669 (tpp) cc_final: 0.7331 (mmm) REVERT: B 117 GLN cc_start: 0.9001 (mm-40) cc_final: 0.8797 (mp10) REVERT: B 554 MET cc_start: 0.7676 (tpp) cc_final: 0.7338 (mmm) REVERT: B 650 MET cc_start: 0.2997 (tpt) cc_final: 0.2770 (tpt) REVERT: B 686 MET cc_start: 0.5258 (mmt) cc_final: 0.4300 (pmm) REVERT: B 718 MET cc_start: 0.8145 (ttp) cc_final: 0.7940 (ttm) outliers start: 59 outliers final: 47 residues processed: 170 average time/residue: 0.3887 time to fit residues: 73.9829 Evaluate side-chains 160 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 113 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 541 HIS Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 541 HIS Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 813 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.3980 chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN A 142 GLN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 71 GLN B 90 ASN B 142 GLN B 286 ASN ** B 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.165417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.101524 restraints weight = 19252.228| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.97 r_work: 0.3114 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11567 Z= 0.161 Angle : 0.737 18.331 15800 Z= 0.347 Chirality : 0.045 0.303 1840 Planarity : 0.005 0.077 1850 Dihedral : 9.460 59.779 2800 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.40 % Favored : 95.45 % Rotamer: Outliers : 5.16 % Allowed : 25.56 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 1.35 (0.23), residues: 1276 helix: 2.46 (0.21), residues: 590 sheet: 1.35 (0.29), residues: 274 loop : -1.93 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 781 TYR 0.015 0.001 TYR A 188 PHE 0.016 0.001 PHE A 722 TRP 0.009 0.001 TRP A 627 HIS 0.007 0.001 HIS B 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (11541) covalent geometry : angle 0.72799 / 0.34 (15748) SS BOND : bond 0.00102 / 0.05 ( 8) SS BOND : angle 1.26624 / 0.69 ( 16) hydrogen bonds : bond 0.05482 / 3.60 ( 630) hydrogen bonds : angle 4.00110 / 2.78 ( 1795) metal coordination : bond 0.00349 / 0.21 ( 6) link_BETA1-4 : bond 0.00520 / 0.32 ( 4) link_BETA1-4 : angle 1.55210 / 0.88 ( 12) link_NAG-ASN : bond 0.00470 / 0.23 ( 8) link_NAG-ASN : angle 2.78106 / 2.21 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 117 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 554 MET cc_start: 0.8338 (tpp) cc_final: 0.8024 (mmm) REVERT: A 594 HIS cc_start: 0.6647 (OUTLIER) cc_final: 0.6090 (m90) REVERT: A 605 TYR cc_start: 0.3887 (OUTLIER) cc_final: 0.3631 (p90) REVERT: A 686 MET cc_start: 0.5295 (mmt) cc_final: 0.4505 (mpt) REVERT: B 289 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8823 (mtp-110) REVERT: B 554 MET cc_start: 0.8354 (tpp) cc_final: 0.8014 (mmm) REVERT: B 605 TYR cc_start: 0.3972 (OUTLIER) cc_final: 0.3650 (p90) REVERT: B 650 MET cc_start: 0.3132 (OUTLIER) cc_final: 0.2896 (tpt) REVERT: B 686 MET cc_start: 0.5370 (mmt) cc_final: 0.4427 (pmm) REVERT: B 710 ARG cc_start: 0.8256 (mmm-85) cc_final: 0.7870 (mmt-90) REVERT: B 712 ARG cc_start: 0.5497 (mpt180) cc_final: 0.4661 (mpp80) outliers start: 60 outliers final: 26 residues processed: 167 average time/residue: 0.4308 time to fit residues: 79.6604 Evaluate side-chains 143 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 594 HIS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 763 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 97 optimal weight: 0.6980 chunk 123 optimal weight: 0.0020 chunk 106 optimal weight: 2.9990 chunk 83 optimal weight: 0.2980 chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 90 ASN B 142 GLN B 286 ASN ** B 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.165436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.100344 restraints weight = 22732.611| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.12 r_work: 0.3097 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11567 Z= 0.168 Angle : 0.703 18.289 15800 Z= 0.334 Chirality : 0.045 0.276 1840 Planarity : 0.005 0.067 1850 Dihedral : 8.554 59.606 2760 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.00 % Favored : 95.92 % Rotamer: Outliers : 5.16 % Allowed : 25.82 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 1.25 (0.23), residues: 1276 helix: 2.32 (0.21), residues: 590 sheet: 1.42 (0.29), residues: 274 loop : -1.97 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 781 TYR 0.015 0.001 TYR B 188 PHE 0.013 0.001 PHE A 722 TRP 0.009 0.001 TRP A 627 HIS 0.006 0.001 HIS B 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (11541) covalent geometry : angle 0.69474 / 0.33 (15748) SS BOND : bond 0.00083 / 0.05 ( 8) SS BOND : angle 1.32199 / 0.70 ( 16) hydrogen bonds : bond 0.05486 / 3.60 ( 630) hydrogen bonds : angle 3.93691 / 2.73 ( 1795) metal coordination : bond 0.00372 / 0.22 ( 6) link_BETA1-4 : bond 0.00547 / 0.32 ( 4) link_BETA1-4 : angle 1.41753 / 0.78 ( 12) link_NAG-ASN : bond 0.00411 / 0.20 ( 8) link_NAG-ASN : angle 2.57370 / 2.05 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 110 time to evaluate : 0.516 Fit side-chains REVERT: A 554 MET cc_start: 0.8349 (tpp) cc_final: 0.8073 (mmm) REVERT: A 590 TYR cc_start: 0.6465 (OUTLIER) cc_final: 0.5995 (t80) REVERT: A 594 HIS cc_start: 0.6631 (OUTLIER) cc_final: 0.6090 (m90) REVERT: A 605 TYR cc_start: 0.4105 (OUTLIER) cc_final: 0.3813 (p90) REVERT: A 781 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8308 (ttm110) REVERT: B 289 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8783 (mtm180) REVERT: B 461 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8248 (mt0) REVERT: B 554 MET cc_start: 0.8386 (tpp) cc_final: 0.8101 (mmm) REVERT: B 686 MET cc_start: 0.5294 (mmt) cc_final: 0.4395 (pmm) REVERT: B 710 ARG cc_start: 0.8173 (mmm-85) cc_final: 0.7932 (mmt-90) REVERT: B 781 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8297 (ttm110) outliers start: 60 outliers final: 36 residues processed: 161 average time/residue: 0.4613 time to fit residues: 82.0642 Evaluate side-chains 152 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 109 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 594 HIS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 725 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 725 ASN Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 781 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 87 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 GLN A 90 ASN A 123 GLN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 71 GLN B 90 ASN B 286 ASN ** B 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.165101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.099826 restraints weight = 23047.899| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.15 r_work: 0.3083 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11567 Z= 0.192 Angle : 0.717 18.426 15800 Z= 0.342 Chirality : 0.046 0.282 1840 Planarity : 0.005 0.065 1850 Dihedral : 8.362 59.272 2756 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 5.42 % Allowed : 25.30 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 1.17 (0.23), residues: 1276 helix: 2.25 (0.21), residues: 590 sheet: 1.43 (0.29), residues: 274 loop : -2.06 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 781 TYR 0.016 0.001 TYR B 188 PHE 0.012 0.001 PHE A 722 TRP 0.009 0.001 TRP A 627 HIS 0.005 0.001 HIS B 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.19 (11541) covalent geometry : angle 0.70853 / 0.34 (15748) SS BOND : bond 0.00084 / 0.05 ( 8) SS BOND : angle 1.43383 / 0.77 ( 16) hydrogen bonds : bond 0.05745 / 3.77 ( 630) hydrogen bonds : angle 3.95014 / 2.73 ( 1795) metal coordination : bond 0.00458 / 0.28 ( 6) link_BETA1-4 : bond 0.00557 / 0.34 ( 4) link_BETA1-4 : angle 1.44309 / 0.79 ( 12) link_NAG-ASN : bond 0.00439 / 0.21 ( 8) link_NAG-ASN : angle 2.62545 / 2.09 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 109 time to evaluate : 0.336 Fit side-chains REVERT: A 461 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8236 (mt0) REVERT: A 554 MET cc_start: 0.8338 (tpp) cc_final: 0.8065 (mmm) REVERT: A 590 TYR cc_start: 0.6450 (OUTLIER) cc_final: 0.6024 (t80) REVERT: A 613 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8430 (pmm) REVERT: A 781 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8279 (ttm110) REVERT: B 289 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.8815 (mtm180) REVERT: B 461 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8235 (mt0) REVERT: B 554 MET cc_start: 0.8368 (tpp) cc_final: 0.8087 (mmm) REVERT: B 587 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7960 (mp) REVERT: B 650 MET cc_start: 0.2980 (tpt) cc_final: 0.2741 (tpt) REVERT: B 686 MET cc_start: 0.5222 (mmt) cc_final: 0.4324 (pmm) REVERT: B 710 ARG cc_start: 0.8089 (mmm-85) cc_final: 0.7879 (mmt-90) REVERT: B 781 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8273 (ttm110) outliers start: 63 outliers final: 35 residues processed: 158 average time/residue: 0.4551 time to fit residues: 79.2029 Evaluate side-chains 151 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 108 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 725 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 781 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 127 optimal weight: 0.9990 chunk 47 optimal weight: 0.2980 chunk 78 optimal weight: 0.6980 chunk 91 optimal weight: 0.3980 chunk 24 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN A 142 GLN A 288 GLN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 90 ASN B 286 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.167207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.102523 restraints weight = 25338.766| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.39 r_work: 0.3106 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11567 Z= 0.135 Angle : 0.675 17.805 15800 Z= 0.320 Chirality : 0.043 0.286 1840 Planarity : 0.004 0.060 1850 Dihedral : 8.019 59.403 2756 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.30 % Allowed : 26.42 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 1.27 (0.23), residues: 1276 helix: 2.47 (0.21), residues: 578 sheet: 1.50 (0.29), residues: 274 loop : -2.12 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 593 TYR 0.013 0.001 TYR B 188 PHE 0.012 0.001 PHE B 732 TRP 0.009 0.001 TRP A 627 HIS 0.004 0.001 HIS B 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (11541) covalent geometry : angle 0.66578 / 0.32 (15748) SS BOND : bond 0.00072 / 0.04 ( 8) SS BOND : angle 1.01501 / 0.54 ( 16) hydrogen bonds : bond 0.04921 / 3.23 ( 630) hydrogen bonds : angle 3.83497 / 2.65 ( 1795) metal coordination : bond 0.00216 / 0.13 ( 6) link_BETA1-4 : bond 0.00520 / 0.31 ( 4) link_BETA1-4 : angle 1.38662 / 0.77 ( 12) link_NAG-ASN : bond 0.00465 / 0.24 ( 8) link_NAG-ASN : angle 2.68514 / 2.13 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 112 time to evaluate : 0.342 Fit side-chains REVERT: A 554 MET cc_start: 0.8301 (tpp) cc_final: 0.8014 (mmm) REVERT: A 590 TYR cc_start: 0.6489 (OUTLIER) cc_final: 0.6054 (t80) REVERT: A 613 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8455 (pmm) REVERT: A 781 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8274 (ttm110) REVERT: B 554 MET cc_start: 0.8322 (tpp) cc_final: 0.8040 (mmm) REVERT: B 559 SER cc_start: 0.8808 (OUTLIER) cc_final: 0.8523 (p) REVERT: B 587 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7919 (mp) REVERT: B 590 TYR cc_start: 0.6624 (OUTLIER) cc_final: 0.6264 (t80) REVERT: B 650 MET cc_start: 0.3359 (tpt) cc_final: 0.3153 (tpt) REVERT: B 686 MET cc_start: 0.5270 (mmt) cc_final: 0.4337 (pmm) REVERT: B 710 ARG cc_start: 0.8018 (mmm-85) cc_final: 0.7809 (mmt-90) outliers start: 50 outliers final: 28 residues processed: 152 average time/residue: 0.4258 time to fit residues: 71.4866 Evaluate side-chains 141 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 725 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 87 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 GLN A 90 ASN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 71 GLN B 74 GLN B 90 ASN B 142 GLN B 286 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.165089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.099741 restraints weight = 22977.114| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.13 r_work: 0.3080 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11567 Z= 0.194 Angle : 0.715 18.660 15800 Z= 0.342 Chirality : 0.045 0.280 1840 Planarity : 0.005 0.061 1850 Dihedral : 7.935 58.975 2750 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.99 % Allowed : 25.56 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 1.14 (0.23), residues: 1276 helix: 2.36 (0.21), residues: 578 sheet: 1.47 (0.29), residues: 274 loop : -2.20 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 781 TYR 0.017 0.001 TYR B 188 PHE 0.015 0.002 PHE B 732 TRP 0.008 0.001 TRP A 627 HIS 0.004 0.001 HIS B 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.19 (11541) covalent geometry : angle 0.70619 / 0.34 (15748) SS BOND : bond 0.00080 / 0.05 ( 8) SS BOND : angle 1.42599 / 0.77 ( 16) hydrogen bonds : bond 0.05685 / 3.73 ( 630) hydrogen bonds : angle 3.90260 / 2.70 ( 1795) metal coordination : bond 0.00478 / 0.29 ( 6) link_BETA1-4 : bond 0.00508 / 0.30 ( 4) link_BETA1-4 : angle 1.42728 / 0.78 ( 12) link_NAG-ASN : bond 0.00449 / 0.22 ( 8) link_NAG-ASN : angle 2.61735 / 2.08 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 106 time to evaluate : 0.419 Fit side-chains REVERT: A 554 MET cc_start: 0.8329 (tpp) cc_final: 0.8087 (mmm) REVERT: A 590 TYR cc_start: 0.6512 (OUTLIER) cc_final: 0.6056 (t80) REVERT: A 613 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8431 (pmm) REVERT: A 781 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8374 (ttm110) REVERT: B 117 GLN cc_start: 0.8884 (mp10) cc_final: 0.8684 (mp10) REVERT: B 461 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8246 (mt0) REVERT: B 554 MET cc_start: 0.8388 (tpp) cc_final: 0.8139 (mmm) REVERT: B 559 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8468 (p) REVERT: B 587 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7883 (mp) REVERT: B 686 MET cc_start: 0.5259 (mmt) cc_final: 0.4383 (pmm) REVERT: B 710 ARG cc_start: 0.7960 (mmm-85) cc_final: 0.7749 (mmt-90) REVERT: B 781 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8345 (ttm110) outliers start: 58 outliers final: 41 residues processed: 151 average time/residue: 0.4338 time to fit residues: 72.1020 Evaluate side-chains 154 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 106 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 725 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 10 optimal weight: 0.0770 chunk 23 optimal weight: 1.9990 chunk 86 optimal weight: 0.0070 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 GLN A 90 ASN A 142 GLN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 71 GLN B 74 GLN B 90 ASN B 142 GLN B 286 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.167618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.102316 restraints weight = 25324.568| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.27 r_work: 0.3117 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11567 Z= 0.126 Angle : 0.672 17.254 15800 Z= 0.316 Chirality : 0.043 0.285 1840 Planarity : 0.004 0.059 1850 Dihedral : 7.698 59.336 2750 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.04 % Allowed : 26.42 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 1.22 (0.23), residues: 1276 helix: 2.41 (0.21), residues: 578 sheet: 1.53 (0.28), residues: 274 loop : -2.15 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 781 TYR 0.012 0.001 TYR A 188 PHE 0.014 0.001 PHE B 732 TRP 0.008 0.001 TRP A 627 HIS 0.004 0.001 HIS B 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (11541) covalent geometry : angle 0.66251 / 0.31 (15748) SS BOND : bond 0.00093 / 0.05 ( 8) SS BOND : angle 1.08493 / 0.54 ( 16) hydrogen bonds : bond 0.04812 / 3.16 ( 630) hydrogen bonds : angle 3.81936 / 2.65 ( 1795) metal coordination : bond 0.00178 / 0.11 ( 6) link_BETA1-4 : bond 0.00459 / 0.27 ( 4) link_BETA1-4 : angle 1.38474 / 0.76 ( 12) link_NAG-ASN : bond 0.00466 / 0.24 ( 8) link_NAG-ASN : angle 2.68424 / 2.13 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 110 time to evaluate : 0.310 Fit side-chains REVERT: A 554 MET cc_start: 0.8334 (tpp) cc_final: 0.8080 (mmm) REVERT: A 590 TYR cc_start: 0.6573 (OUTLIER) cc_final: 0.6068 (t80) REVERT: A 613 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8408 (pmm) REVERT: A 781 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8350 (mtm-85) REVERT: B 117 GLN cc_start: 0.8873 (mp10) cc_final: 0.8667 (mp10) REVERT: B 461 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8215 (mt0) REVERT: B 554 MET cc_start: 0.8367 (tpp) cc_final: 0.8102 (mmm) REVERT: B 559 SER cc_start: 0.8821 (OUTLIER) cc_final: 0.8554 (p) REVERT: B 590 TYR cc_start: 0.6617 (OUTLIER) cc_final: 0.6226 (t80) REVERT: B 686 MET cc_start: 0.5278 (mmt) cc_final: 0.4403 (pmm) REVERT: B 781 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8318 (mtm-85) outliers start: 47 outliers final: 31 residues processed: 148 average time/residue: 0.3994 time to fit residues: 64.9890 Evaluate side-chains 142 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 104 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 28 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 74 GLN B 90 ASN B 286 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.163067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.098809 restraints weight = 17358.219| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.82 r_work: 0.3068 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 11567 Z= 0.311 Angle : 0.790 18.096 15800 Z= 0.386 Chirality : 0.050 0.278 1840 Planarity : 0.005 0.063 1850 Dihedral : 7.962 58.717 2746 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.73 % Allowed : 26.16 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.23), residues: 1276 helix: 2.17 (0.21), residues: 578 sheet: 1.40 (0.29), residues: 274 loop : -2.36 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 710 TYR 0.021 0.002 TYR A 188 PHE 0.034 0.002 PHE B 628 TRP 0.025 0.002 TRP B 629 HIS 0.005 0.002 HIS B 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00769 / 0.31 (11541) covalent geometry : angle 0.78171 / 0.38 (15748) SS BOND : bond 0.00100 / 0.06 ( 8) SS BOND : angle 1.86882 / 1.07 ( 16) hydrogen bonds : bond 0.06746 / 4.42 ( 630) hydrogen bonds : angle 4.04161 / 2.79 ( 1795) metal coordination : bond 0.00841 / 0.51 ( 6) link_BETA1-4 : bond 0.00553 / 0.33 ( 4) link_BETA1-4 : angle 1.55534 / 0.87 ( 12) link_NAG-ASN : bond 0.00445 / 0.20 ( 8) link_NAG-ASN : angle 2.62157 / 2.10 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 110 time to evaluate : 0.385 Fit side-chains REVERT: A 554 MET cc_start: 0.8337 (tpp) cc_final: 0.8079 (mmm) REVERT: A 590 TYR cc_start: 0.6441 (OUTLIER) cc_final: 0.6046 (t80) REVERT: A 613 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8404 (pmm) REVERT: A 781 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8429 (ttm110) REVERT: B 117 GLN cc_start: 0.8913 (mp10) cc_final: 0.8689 (mp10) REVERT: B 461 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8253 (mt0) REVERT: B 554 MET cc_start: 0.8401 (tpp) cc_final: 0.8135 (mmm) REVERT: B 559 SER cc_start: 0.8737 (OUTLIER) cc_final: 0.8534 (t) REVERT: B 686 MET cc_start: 0.5299 (mmt) cc_final: 0.4452 (pmm) REVERT: B 736 MET cc_start: 0.8038 (tpp) cc_final: 0.7330 (mpp) REVERT: B 781 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8433 (mtm-85) outliers start: 55 outliers final: 34 residues processed: 153 average time/residue: 0.4414 time to fit residues: 74.7264 Evaluate side-chains 148 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 71 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 101 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 GLN A 74 GLN A 90 ASN A 142 GLN A 769 ASN B 71 GLN B 74 GLN B 90 ASN B 142 GLN B 286 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.166984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.102282 restraints weight = 20001.373| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.99 r_work: 0.3131 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11567 Z= 0.138 Angle : 0.689 17.356 15800 Z= 0.327 Chirality : 0.044 0.280 1840 Planarity : 0.004 0.059 1850 Dihedral : 7.528 59.856 2744 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.53 % Allowed : 27.11 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.23), residues: 1276 helix: 2.34 (0.21), residues: 578 sheet: 1.46 (0.29), residues: 274 loop : -2.25 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 710 TYR 0.011 0.001 TYR A 188 PHE 0.025 0.001 PHE B 628 TRP 0.017 0.001 TRP B 629 HIS 0.004 0.001 HIS B 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (11541) covalent geometry : angle 0.67993 / 0.32 (15748) SS BOND : bond 0.00099 / 0.06 ( 8) SS BOND : angle 1.21777 / 0.63 ( 16) hydrogen bonds : bond 0.05070 / 3.32 ( 630) hydrogen bonds : angle 3.87885 / 2.69 ( 1795) metal coordination : bond 0.00137 / 0.08 ( 6) link_BETA1-4 : bond 0.00501 / 0.30 ( 4) link_BETA1-4 : angle 1.41418 / 0.79 ( 12) link_NAG-ASN : bond 0.00498 / 0.25 ( 8) link_NAG-ASN : angle 2.71117 / 2.15 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 0.431 Fit side-chains REVERT: A 554 MET cc_start: 0.8337 (tpp) cc_final: 0.8070 (mmm) REVERT: A 590 TYR cc_start: 0.6538 (OUTLIER) cc_final: 0.6054 (t80) REVERT: A 613 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8426 (pmm) REVERT: A 781 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8328 (ttm110) REVERT: B 461 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8174 (mt0) REVERT: B 554 MET cc_start: 0.8331 (tpp) cc_final: 0.8066 (mmm) REVERT: B 559 SER cc_start: 0.8778 (OUTLIER) cc_final: 0.8494 (p) REVERT: B 686 MET cc_start: 0.5249 (mmt) cc_final: 0.4388 (pmm) REVERT: B 781 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8323 (ttm110) outliers start: 41 outliers final: 29 residues processed: 145 average time/residue: 0.4733 time to fit residues: 75.4854 Evaluate side-chains 141 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 109 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN A 90 ASN A 769 ASN B 74 GLN B 90 ASN B 142 GLN B 286 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.166810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.101544 restraints weight = 23145.223| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 3.16 r_work: 0.3116 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 11567 Z= 0.162 Angle : 0.956 59.191 15800 Z= 0.508 Chirality : 0.051 1.135 1840 Planarity : 0.004 0.059 1850 Dihedral : 7.525 59.813 2744 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.70 % Allowed : 27.11 % Favored : 69.19 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.23), residues: 1276 helix: 2.34 (0.21), residues: 578 sheet: 1.46 (0.29), residues: 274 loop : -2.25 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 710 TYR 0.012 0.001 TYR A 188 PHE 0.023 0.001 PHE B 628 TRP 0.016 0.001 TRP B 629 HIS 0.004 0.001 HIS B 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (11541) covalent geometry : angle 0.94962 / 0.51 (15748) SS BOND : bond 0.00081 / 0.04 ( 8) SS BOND : angle 1.21480 / 0.63 ( 16) hydrogen bonds : bond 0.05076 / 3.33 ( 630) hydrogen bonds : angle 3.87966 / 2.69 ( 1795) metal coordination : bond 0.00147 / 0.09 ( 6) link_BETA1-4 : bond 0.00274 / 0.17 ( 4) link_BETA1-4 : angle 1.44548 / 0.81 ( 12) link_NAG-ASN : bond 0.00497 / 0.25 ( 8) link_NAG-ASN : angle 2.71061 / 2.14 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 108 time to evaluate : 0.424 Fit side-chains REVERT: A 554 MET cc_start: 0.8356 (tpp) cc_final: 0.8091 (mmm) REVERT: A 590 TYR cc_start: 0.6545 (OUTLIER) cc_final: 0.6059 (t80) REVERT: A 613 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8425 (pmm) REVERT: A 781 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8341 (ttm110) REVERT: B 87 GLU cc_start: 0.5926 (OUTLIER) cc_final: 0.4780 (pm20) REVERT: B 461 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8200 (mt0) REVERT: B 554 MET cc_start: 0.8356 (tpp) cc_final: 0.8094 (mmm) REVERT: B 559 SER cc_start: 0.8794 (OUTLIER) cc_final: 0.8517 (p) REVERT: B 686 MET cc_start: 0.5253 (mmt) cc_final: 0.4386 (pmm) REVERT: B 781 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8319 (ttm110) outliers start: 43 outliers final: 31 residues processed: 140 average time/residue: 0.4900 time to fit residues: 75.4840 Evaluate side-chains 146 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.0040 chunk 3 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.0670 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 122 optimal weight: 0.0060 chunk 70 optimal weight: 0.9980 overall best weight: 0.3946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN A 90 ASN A 142 GLN A 769 ASN B 74 GLN B 90 ASN B 142 GLN B 286 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.166926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.104288 restraints weight = 13130.633| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.56 r_work: 0.3164 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 11567 Z= 0.162 Angle : 0.956 59.191 15800 Z= 0.508 Chirality : 0.051 1.135 1840 Planarity : 0.004 0.059 1850 Dihedral : 7.525 59.813 2744 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.53 % Allowed : 27.28 % Favored : 69.19 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.23), residues: 1276 helix: 2.34 (0.21), residues: 578 sheet: 1.46 (0.29), residues: 274 loop : -2.25 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 710 TYR 0.012 0.001 TYR A 188 PHE 0.023 0.001 PHE B 628 TRP 0.016 0.001 TRP B 629 HIS 0.004 0.001 HIS B 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (11541) covalent geometry : angle 0.94962 / 0.51 (15748) SS BOND : bond 0.00081 / 0.04 ( 8) SS BOND : angle 1.21480 / 0.63 ( 16) hydrogen bonds : bond 0.05076 / 3.33 ( 630) hydrogen bonds : angle 3.87966 / 2.69 ( 1795) metal coordination : bond 0.00147 / 0.09 ( 6) link_BETA1-4 : bond 0.00274 / 0.17 ( 4) link_BETA1-4 : angle 1.44548 / 0.81 ( 12) link_NAG-ASN : bond 0.00497 / 0.25 ( 8) link_NAG-ASN : angle 2.71061 / 2.14 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4547.30 seconds wall clock time: 78 minutes 13.07 seconds (4693.07 seconds total)