Starting phenix.real_space_refine on Sat Jul 4 06:32:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uz3_26874/07_2026/7uz3_26874_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uz3_26874/07_2026/7uz3_26874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uz3_26874/07_2026/7uz3_26874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uz3_26874/07_2026/7uz3_26874.map" model { file = "/net/cci-nas-00/data/ceres_data/7uz3_26874/07_2026/7uz3_26874_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uz3_26874/07_2026/7uz3_26874_trim.cif" } resolution = 2.35 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= 0.184 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 38 5.16 5 C 6134 2.51 5 N 1410 2.21 5 O 1725 1.98 5 H 9100 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18415 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 600 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 600 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 8315 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 517, 8314 Classifications: {'peptide': 517} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 488} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 517, 8314 Classifications: {'peptide': 517} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 488} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 8416 Chain: "E" Number of atoms: 8315 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 517, 8314 Classifications: {'peptide': 517} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 488} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 517, 8314 Classifications: {'peptide': 517} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 488} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 8416 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 192 Unusual residues: {'CLR': 2, 'PIO': 2, 'PLC': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 98 Unusual residues: {'CLR': 2, 'PLC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "E" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Time building chain proxies: 5.51, per 1000 atoms: 0.30 Number of scatterers: 18415 At special positions: 0 Unit cell: (84.245, 144.005, 87.565, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 38 16.00 P 8 15.00 O 1725 8.00 N 1410 7.00 C 6134 6.00 H 9100 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA A 3 " - " MAN A 4 " " BMA F 3 " - " MAN F 4 " ALPHA1-4 " BMA A 3 " - " MAN A 5 " " BMA F 3 " - " MAN F 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " BETA1-6 " NAG A 1 " - " FUC A 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG F 1 " - " FUC F 6 " NAG-ASN " NAG A 1 " - " ASN C 642 " " NAG F 1 " - " ASN E 642 " Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 906.9 milliseconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 4 sheets defined 75.6% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'B' and resid 88 through 114 Processing helix chain 'D' and resid 88 through 114 Processing helix chain 'C' and resid 379 through 390 Processing helix chain 'C' and resid 391 through 393 No H-bonds generated for 'chain 'C' and resid 391 through 393' Processing helix chain 'C' and resid 394 through 399 Processing helix chain 'C' and resid 402 through 432 removed outlier: 3.508A pdb=" N PHE C 414 " --> pdb=" O ILE C 410 " (cutoff:3.500A) Proline residue: C 419 - end of helix Processing helix chain 'C' and resid 436 through 455 Processing helix chain 'C' and resid 465 through 482 Processing helix chain 'C' and resid 485 through 507 Processing helix chain 'C' and resid 508 through 516 Processing helix chain 'C' and resid 517 through 547 removed outlier: 3.524A pdb=" N LEU C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 594 removed outlier: 3.581A pdb=" N ASN C 593 " --> pdb=" O ARG C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 608 Processing helix chain 'C' and resid 608 through 623 Processing helix chain 'C' and resid 660 through 667 removed outlier: 3.587A pdb=" N MET C 664 " --> pdb=" O PRO C 660 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE C 665 " --> pdb=" O ILE C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 690 Processing helix chain 'C' and resid 691 through 695 Processing helix chain 'C' and resid 701 through 719 removed outlier: 3.858A pdb=" N LEU C 718 " --> pdb=" O GLY C 714 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE C 719 " --> pdb=" O VAL C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 738 Processing helix chain 'C' and resid 760 through 773 Processing helix chain 'C' and resid 776 through 781 Processing helix chain 'C' and resid 784 through 799 removed outlier: 3.623A pdb=" N LEU C 788 " --> pdb=" O PRO C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 812 Processing helix chain 'C' and resid 813 through 814 No H-bonds generated for 'chain 'C' and resid 813 through 814' Processing helix chain 'C' and resid 815 through 819 Processing helix chain 'C' and resid 822 through 827 Processing helix chain 'C' and resid 829 through 852 Processing helix chain 'C' and resid 853 through 857 removed outlier: 4.537A pdb=" N LEU C 857 " --> pdb=" O PRO C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 865 Processing helix chain 'C' and resid 865 through 873 Processing helix chain 'C' and resid 873 through 878 removed outlier: 3.684A pdb=" N ILE C 877 " --> pdb=" O LEU C 873 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 887 Processing helix chain 'E' and resid 379 through 390 Processing helix chain 'E' and resid 391 through 393 No H-bonds generated for 'chain 'E' and resid 391 through 393' Processing helix chain 'E' and resid 394 through 399 Processing helix chain 'E' and resid 402 through 432 removed outlier: 3.507A pdb=" N PHE E 414 " --> pdb=" O ILE E 410 " (cutoff:3.500A) Proline residue: E 419 - end of helix Processing helix chain 'E' and resid 436 through 455 Processing helix chain 'E' and resid 465 through 482 Processing helix chain 'E' and resid 485 through 507 Processing helix chain 'E' and resid 508 through 516 Processing helix chain 'E' and resid 517 through 547 removed outlier: 3.524A pdb=" N LEU E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 594 removed outlier: 3.581A pdb=" N ASN E 593 " --> pdb=" O ARG E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 608 Processing helix chain 'E' and resid 608 through 623 Processing helix chain 'E' and resid 660 through 667 removed outlier: 3.587A pdb=" N MET E 664 " --> pdb=" O PRO E 660 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE E 665 " --> pdb=" O ILE E 661 " (cutoff:3.500A) Processing helix chain 'E' and resid 667 through 690 Processing helix chain 'E' and resid 691 through 695 Processing helix chain 'E' and resid 701 through 719 removed outlier: 3.858A pdb=" N LEU E 718 " --> pdb=" O GLY E 714 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE E 719 " --> pdb=" O VAL E 715 " (cutoff:3.500A) Processing helix chain 'E' and resid 727 through 738 Processing helix chain 'E' and resid 760 through 773 Processing helix chain 'E' and resid 776 through 781 Processing helix chain 'E' and resid 784 through 799 removed outlier: 3.624A pdb=" N LEU E 788 " --> pdb=" O PRO E 784 " (cutoff:3.500A) Processing helix chain 'E' and resid 803 through 812 Processing helix chain 'E' and resid 813 through 814 No H-bonds generated for 'chain 'E' and resid 813 through 814' Processing helix chain 'E' and resid 815 through 819 Processing helix chain 'E' and resid 822 through 827 Processing helix chain 'E' and resid 829 through 852 Processing helix chain 'E' and resid 853 through 857 removed outlier: 4.537A pdb=" N LEU E 857 " --> pdb=" O PRO E 854 " (cutoff:3.500A) Processing helix chain 'E' and resid 858 through 865 Processing helix chain 'E' and resid 865 through 873 Processing helix chain 'E' and resid 873 through 878 removed outlier: 3.684A pdb=" N ILE E 877 " --> pdb=" O LEU E 873 " (cutoff:3.500A) Processing helix chain 'E' and resid 879 through 887 Processing sheet with id=AA1, first strand: chain 'C' and resid 462 through 463 Processing sheet with id=AA2, first strand: chain 'C' and resid 739 through 741 Processing sheet with id=AA3, first strand: chain 'E' and resid 462 through 463 Processing sheet with id=AA4, first strand: chain 'E' and resid 739 through 741 590 hydrogen bonds defined for protein. 1698 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: 4.35 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9094 1.03 - 1.23: 89 1.23 - 1.42: 3635 1.42 - 1.62: 5588 1.62 - 1.82: 82 Bond restraints: 18488 Sorted by residual: bond pdb=" C PRO E 403 " pdb=" O PRO E 403 " ideal model delta sigma weight residual 1.238 1.189 0.048 1.24e-02 6.50e+03 1.53e+01 bond pdb=" C PRO C 403 " pdb=" O PRO C 403 " ideal model delta sigma weight residual 1.238 1.190 0.048 1.24e-02 6.50e+03 1.47e+01 bond pdb=" O4 PIO C1005 " pdb=" P4 PIO C1005 " ideal model delta sigma weight residual 1.710 1.640 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" O4 PIO C1004 " pdb=" P4 PIO C1004 " ideal model delta sigma weight residual 1.710 1.641 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C1B PIO C1004 " pdb=" O3C PIO C1004 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 18483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 33062 2.75 - 5.51: 305 5.51 - 8.26: 31 8.26 - 11.02: 10 11.02 - 13.77: 4 Bond angle restraints: 33412 Sorted by residual: angle pdb=" N SER E 594 " pdb=" CA SER E 594 " pdb=" C SER E 594 " ideal model delta sigma weight residual 110.41 118.35 -7.94 1.23e+00 6.61e-01 4.17e+01 angle pdb=" N SER C 594 " pdb=" CA SER C 594 " pdb=" C SER C 594 " ideal model delta sigma weight residual 110.41 118.31 -7.90 1.23e+00 6.61e-01 4.12e+01 angle pdb=" C3 PIO C1005 " pdb=" C4 PIO C1005 " pdb=" C5 PIO C1005 " ideal model delta sigma weight residual 109.16 122.93 -13.77 3.00e+00 1.11e-01 2.11e+01 angle pdb=" CA GLY C 742 " pdb=" C GLY C 742 " pdb=" O GLY C 742 " ideal model delta sigma weight residual 122.76 117.71 5.05 1.12e+00 7.97e-01 2.04e+01 angle pdb=" CA GLY E 742 " pdb=" C GLY E 742 " pdb=" O GLY E 742 " ideal model delta sigma weight residual 122.76 117.75 5.01 1.12e+00 7.97e-01 2.00e+01 ... (remaining 33407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.79: 8258 23.79 - 47.58: 508 47.58 - 71.37: 205 71.37 - 95.16: 59 95.16 - 118.95: 22 Dihedral angle restraints: 9052 sinusoidal: 5158 harmonic: 3894 Sorted by residual: dihedral pdb=" CA PRO E 722 " pdb=" C PRO E 722 " pdb=" N TRP E 723 " pdb=" CA TRP E 723 " ideal model delta harmonic sigma weight residual 180.00 158.64 21.36 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA PRO C 722 " pdb=" C PRO C 722 " pdb=" N TRP C 723 " pdb=" CA TRP C 723 " ideal model delta harmonic sigma weight residual 180.00 158.64 21.36 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" O3 NAG F 2 " pdb=" C3 NAG F 2 " pdb=" C4 NAG F 2 " pdb=" O4 NAG F 2 " ideal model delta sinusoidal sigma weight residual 295.45 176.50 118.95 1 3.00e+01 1.11e-03 1.58e+01 ... (remaining 9049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.341: 1560 0.341 - 0.683: 0 0.683 - 1.024: 0 1.024 - 1.366: 0 1.366 - 1.707: 2 Chirality restraints: 1562 Sorted by residual: chirality pdb=" C4 PIO C1005 " pdb=" C3 PIO C1005 " pdb=" C5 PIO C1005 " pdb=" O4 PIO C1005 " both_signs ideal model delta sigma weight residual False 2.50 0.79 1.71 2.00e-01 2.50e+01 7.28e+01 chirality pdb=" C4 PIO C1004 " pdb=" C3 PIO C1004 " pdb=" C5 PIO C1004 " pdb=" O4 PIO C1004 " both_signs ideal model delta sigma weight residual False 2.50 0.81 1.69 2.00e-01 2.50e+01 7.17e+01 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 1559 not shown) Planarity restraints: 2546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 593 " 0.242 2.00e-02 2.50e+03 2.99e-01 1.34e+03 pdb=" CG ASN C 593 " -0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN C 593 " -0.238 2.00e-02 2.50e+03 pdb=" ND2 ASN C 593 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN C 593 " 0.460 2.00e-02 2.50e+03 pdb="HD22 ASN C 593 " -0.455 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 593 " -0.242 2.00e-02 2.50e+03 2.98e-01 1.34e+03 pdb=" CG ASN E 593 " 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN E 593 " 0.238 2.00e-02 2.50e+03 pdb=" ND2 ASN E 593 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN E 593 " -0.460 2.00e-02 2.50e+03 pdb="HD22 ASN E 593 " 0.455 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN E 404 " -0.138 2.00e-02 2.50e+03 1.50e-01 3.36e+02 pdb=" CD GLN E 404 " 0.007 2.00e-02 2.50e+03 pdb=" OE1 GLN E 404 " 0.134 2.00e-02 2.50e+03 pdb=" NE2 GLN E 404 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN E 404 " 0.220 2.00e-02 2.50e+03 pdb="HE22 GLN E 404 " -0.221 2.00e-02 2.50e+03 ... (remaining 2543 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1865 2.23 - 2.82: 40364 2.82 - 3.42: 52304 3.42 - 4.01: 71278 4.01 - 4.60: 107200 Nonbonded interactions: 273011 Sorted by model distance: nonbonded pdb=" O LYS E 562 " pdb="HE21 GLN E 564 " model vdw 1.639 2.450 nonbonded pdb=" O LYS C 562 " pdb="HE21 GLN C 564 " model vdw 1.639 2.450 nonbonded pdb=" O VAL C 729 " pdb=" HG1 THR C 733 " model vdw 1.678 2.450 nonbonded pdb=" O VAL E 729 " pdb=" HG1 THR E 733 " model vdw 1.678 2.450 nonbonded pdb=" H LEU D 83 " pdb=" O LEU E 655 " model vdw 1.707 2.450 ... (remaining 273006 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = (chain 'C' and (resid 371 through 613 or resid 615 through 1003)) selection = (chain 'E' and (resid 371 through 613 or resid 615 through 1003)) } 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=0.49 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: 4.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 0.570 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 21.920 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:8.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 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 : 0.006 0.070 9400 Z= 0.326 Angle : 0.947 13.772 12810 Z= 0.495 Chirality : 0.078 1.707 1562 Planarity : 0.005 0.046 1498 Dihedral : 20.502 118.953 3798 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.84 % Allowed : 14.74 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.25), residues: 1102 helix: 1.72 (0.18), residues: 752 sheet: None (None), residues: 0 loop : 0.01 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 514 TYR 0.014 0.002 TYR C 519 PHE 0.012 0.002 PHE C 414 TRP 0.015 0.002 TRP C 492 HIS 0.004 0.001 HIS E 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.33 ( 9388) covalent geometry : angle 0.93764 / 0.49 (12774) hydrogen bonds : bond 0.12961 / 9.25 ( 590) hydrogen bonds : angle 5.31401 / 3.91 ( 1698) link_ALPHA1-3 : bond 0.01691 / 1.00 ( 2) link_ALPHA1-3 : angle 3.54837 / 1.61 ( 6) link_ALPHA1-4 : bond 0.00707 / 0.42 ( 2) link_ALPHA1-4 : angle 1.77928 / 0.90 ( 6) link_BETA1-4 : bond 0.01657 / 1.12 ( 4) link_BETA1-4 : angle 3.58043 / 1.76 ( 12) link_BETA1-6 : bond 0.00888 / 0.53 ( 2) link_BETA1-6 : angle 1.00146 / 0.51 ( 6) link_NAG-ASN : bond 0.00119 / 0.07 ( 2) link_NAG-ASN : angle 1.43534 / 0.75 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 890 ASP cc_start: 0.6537 (p0) cc_final: 0.6331 (t0) REVERT: E 890 ASP cc_start: 0.6536 (p0) cc_final: 0.6325 (t0) outliers start: 8 outliers final: 6 residues processed: 151 average time/residue: 1.1718 time to fit residues: 191.0295 Evaluate side-chains 144 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 138 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain E residue 613 SER Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 646 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 482 ASN E 482 ASN E 564 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.129780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.105308 restraints weight = 24735.553| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.28 r_work: 0.2942 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.0582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9400 Z= 0.136 Angle : 0.597 8.148 12810 Z= 0.296 Chirality : 0.041 0.208 1562 Planarity : 0.005 0.043 1498 Dihedral : 18.485 107.182 1800 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.47 % Allowed : 14.21 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.25), residues: 1102 helix: 1.91 (0.19), residues: 746 sheet: None (None), residues: 0 loop : 0.08 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 514 TYR 0.011 0.001 TYR C 486 PHE 0.014 0.001 PHE C 836 TRP 0.012 0.001 TRP E 492 HIS 0.003 0.001 HIS E 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 9388) covalent geometry : angle 0.57603 / 0.29 (12774) hydrogen bonds : bond 0.05415 / 3.86 ( 590) hydrogen bonds : angle 4.62695 / 3.41 ( 1698) link_ALPHA1-3 : bond 0.01837 / 1.09 ( 2) link_ALPHA1-3 : angle 3.12518 / 1.67 ( 6) link_ALPHA1-4 : bond 0.01389 / 0.82 ( 2) link_ALPHA1-4 : angle 3.96902 / 1.82 ( 6) link_BETA1-4 : bond 0.01587 / 1.07 ( 4) link_BETA1-4 : angle 3.68277 / 1.81 ( 12) link_BETA1-6 : bond 0.00738 / 0.44 ( 2) link_BETA1-6 : angle 1.06290 / 0.56 ( 6) link_NAG-ASN : bond 0.00283 / 0.17 ( 2) link_NAG-ASN : angle 0.72168 / 0.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 718 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8320 (mt) REVERT: C 890 ASP cc_start: 0.6550 (p0) cc_final: 0.6213 (t0) REVERT: E 718 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8324 (mt) REVERT: E 890 ASP cc_start: 0.6553 (p0) cc_final: 0.6213 (t0) outliers start: 14 outliers final: 5 residues processed: 153 average time/residue: 1.2210 time to fit residues: 201.2547 Evaluate side-chains 145 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain E residue 613 SER Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 718 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 69 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 482 ASN E 482 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.126922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.102395 restraints weight = 24597.190| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.28 r_work: 0.2907 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.0695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9400 Z= 0.208 Angle : 0.649 7.639 12810 Z= 0.321 Chirality : 0.043 0.234 1562 Planarity : 0.005 0.043 1498 Dihedral : 17.773 111.116 1799 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.79 % Allowed : 13.68 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.24), residues: 1102 helix: 1.77 (0.18), residues: 742 sheet: None (None), residues: 0 loop : -0.15 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 389 TYR 0.011 0.002 TYR E 519 PHE 0.016 0.002 PHE C 471 TRP 0.014 0.002 TRP E 492 HIS 0.004 0.001 HIS E 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.21 ( 9388) covalent geometry : angle 0.63091 / 0.32 (12774) hydrogen bonds : bond 0.06051 / 4.29 ( 590) hydrogen bonds : angle 4.67599 / 3.43 ( 1698) link_ALPHA1-3 : bond 0.01806 / 1.06 ( 2) link_ALPHA1-3 : angle 3.35530 / 1.77 ( 6) link_ALPHA1-4 : bond 0.01422 / 0.84 ( 2) link_ALPHA1-4 : angle 3.76026 / 1.70 ( 6) link_BETA1-4 : bond 0.01629 / 1.10 ( 4) link_BETA1-4 : angle 3.48234 / 1.70 ( 12) link_BETA1-6 : bond 0.01068 / 0.63 ( 2) link_BETA1-6 : angle 0.88080 / 0.46 ( 6) link_NAG-ASN : bond 0.00228 / 0.13 ( 2) link_NAG-ASN : angle 0.73490 / 0.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 384 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7600 (mpt-90) REVERT: C 473 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8119 (mm-30) REVERT: C 681 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: C 718 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8405 (mt) REVERT: E 384 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7604 (mpt-90) REVERT: E 473 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8120 (mm-30) REVERT: E 681 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: E 718 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8408 (mt) REVERT: E 890 ASP cc_start: 0.6628 (p0) cc_final: 0.6284 (t0) outliers start: 17 outliers final: 7 residues processed: 147 average time/residue: 1.1460 time to fit residues: 181.6814 Evaluate side-chains 153 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 681 GLU Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain C residue 877 ILE Chi-restraints excluded: chain E residue 384 ARG Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 681 GLU Chi-restraints excluded: chain E residue 718 LEU Chi-restraints excluded: chain E residue 877 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 86 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 482 ASN E 482 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.127641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.103132 restraints weight = 24675.521| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.29 r_work: 0.2925 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9400 Z= 0.161 Angle : 0.612 7.710 12810 Z= 0.299 Chirality : 0.042 0.247 1562 Planarity : 0.005 0.042 1498 Dihedral : 16.757 115.473 1796 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.00 % Allowed : 13.26 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.25), residues: 1102 helix: 1.74 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -0.26 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 389 TYR 0.012 0.002 TYR E 486 PHE 0.014 0.001 PHE E 471 TRP 0.014 0.002 TRP C 492 HIS 0.003 0.001 HIS C 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 9388) covalent geometry : angle 0.59233 / 0.29 (12774) hydrogen bonds : bond 0.05359 / 3.81 ( 590) hydrogen bonds : angle 4.56143 / 3.35 ( 1698) link_ALPHA1-3 : bond 0.01754 / 1.04 ( 2) link_ALPHA1-3 : angle 3.03205 / 1.64 ( 6) link_ALPHA1-4 : bond 0.01298 / 0.77 ( 2) link_ALPHA1-4 : angle 4.18530 / 1.87 ( 6) link_BETA1-4 : bond 0.01618 / 1.10 ( 4) link_BETA1-4 : angle 3.58523 / 1.74 ( 12) link_BETA1-6 : bond 0.00903 / 0.53 ( 2) link_BETA1-6 : angle 0.79741 / 0.42 ( 6) link_NAG-ASN : bond 0.00184 / 0.11 ( 2) link_NAG-ASN : angle 0.76224 / 0.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 681 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: C 718 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8310 (mt) REVERT: E 681 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7782 (tt0) REVERT: E 718 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8314 (mt) REVERT: E 890 ASP cc_start: 0.6534 (p0) cc_final: 0.6238 (t0) outliers start: 19 outliers final: 11 residues processed: 151 average time/residue: 1.1790 time to fit residues: 191.3695 Evaluate side-chains 151 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 681 GLU Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain C residue 877 ILE Chi-restraints excluded: chain E residue 384 ARG Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 681 GLU Chi-restraints excluded: chain E residue 718 LEU Chi-restraints excluded: chain E residue 877 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 76 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 4 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 52 optimal weight: 0.1980 chunk 56 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 482 ASN E 482 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.128690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.104134 restraints weight = 24667.516| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.29 r_work: 0.2929 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9400 Z= 0.145 Angle : 0.603 7.653 12810 Z= 0.291 Chirality : 0.041 0.254 1562 Planarity : 0.005 0.041 1498 Dihedral : 15.795 115.851 1796 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.89 % Allowed : 13.37 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.25), residues: 1102 helix: 1.80 (0.18), residues: 758 sheet: None (None), residues: 0 loop : -0.13 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 603 TYR 0.012 0.001 TYR E 486 PHE 0.013 0.001 PHE C 471 TRP 0.013 0.001 TRP E 492 HIS 0.002 0.001 HIS E 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 9388) covalent geometry : angle 0.58200 / 0.29 (12774) hydrogen bonds : bond 0.05105 / 3.63 ( 590) hydrogen bonds : angle 4.48958 / 3.29 ( 1698) link_ALPHA1-3 : bond 0.01759 / 1.04 ( 2) link_ALPHA1-3 : angle 3.05913 / 1.66 ( 6) link_ALPHA1-4 : bond 0.01250 / 0.74 ( 2) link_ALPHA1-4 : angle 4.09455 / 1.84 ( 6) link_BETA1-4 : bond 0.01507 / 1.02 ( 4) link_BETA1-4 : angle 3.65989 / 1.77 ( 12) link_BETA1-6 : bond 0.00875 / 0.52 ( 2) link_BETA1-6 : angle 0.76959 / 0.41 ( 6) link_NAG-ASN : bond 0.00261 / 0.15 ( 2) link_NAG-ASN : angle 0.80121 / 0.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 681 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7769 (tt0) REVERT: C 718 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8261 (mt) REVERT: E 681 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7750 (tt0) REVERT: E 718 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8263 (mt) REVERT: E 890 ASP cc_start: 0.6533 (p0) cc_final: 0.6218 (t0) outliers start: 18 outliers final: 10 residues processed: 149 average time/residue: 1.1517 time to fit residues: 185.1199 Evaluate side-chains 150 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 681 GLU Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain C residue 877 ILE Chi-restraints excluded: chain E residue 384 ARG Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 681 GLU Chi-restraints excluded: chain E residue 718 LEU Chi-restraints excluded: chain E residue 877 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 434 GLN C 482 ASN E 434 GLN E 482 ASN E 564 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.127275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.102615 restraints weight = 24481.357| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.29 r_work: 0.2922 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9400 Z= 0.181 Angle : 0.647 8.374 12810 Z= 0.312 Chirality : 0.043 0.258 1562 Planarity : 0.005 0.042 1498 Dihedral : 14.920 114.849 1796 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.68 % Allowed : 13.89 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.24), residues: 1102 helix: 1.67 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -0.25 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 389 TYR 0.012 0.002 TYR E 486 PHE 0.016 0.001 PHE E 471 TRP 0.013 0.002 TRP E 492 HIS 0.003 0.001 HIS C 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 ( 9388) covalent geometry : angle 0.62732 / 0.31 (12774) hydrogen bonds : bond 0.05600 / 3.97 ( 590) hydrogen bonds : angle 4.57821 / 3.35 ( 1698) link_ALPHA1-3 : bond 0.02154 / 1.27 ( 2) link_ALPHA1-3 : angle 3.26257 / 1.74 ( 6) link_ALPHA1-4 : bond 0.01212 / 0.72 ( 2) link_ALPHA1-4 : angle 4.14990 / 1.87 ( 6) link_BETA1-4 : bond 0.01366 / 0.92 ( 4) link_BETA1-4 : angle 3.74617 / 1.80 ( 12) link_BETA1-6 : bond 0.01030 / 0.61 ( 2) link_BETA1-6 : angle 0.74237 / 0.38 ( 6) link_NAG-ASN : bond 0.00278 / 0.16 ( 2) link_NAG-ASN : angle 0.80027 / 0.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 681 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7808 (tt0) REVERT: C 718 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8328 (mt) REVERT: E 384 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7620 (mpt-90) REVERT: E 681 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: E 718 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8331 (mt) outliers start: 16 outliers final: 9 residues processed: 146 average time/residue: 1.2007 time to fit residues: 189.2350 Evaluate side-chains 149 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 681 GLU Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain C residue 877 ILE Chi-restraints excluded: chain E residue 384 ARG Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 681 GLU Chi-restraints excluded: chain E residue 718 LEU Chi-restraints excluded: chain E residue 877 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 13 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 482 ASN E 482 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.127362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.102728 restraints weight = 24710.916| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.29 r_work: 0.2923 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 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 0.038 9400 Z= 0.165 Angle : 0.627 8.624 12810 Z= 0.301 Chirality : 0.042 0.223 1562 Planarity : 0.005 0.042 1498 Dihedral : 13.886 115.002 1796 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.68 % Allowed : 13.68 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.24), residues: 1102 helix: 1.73 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -0.24 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 389 TYR 0.012 0.002 TYR E 486 PHE 0.014 0.001 PHE E 471 TRP 0.014 0.002 TRP C 492 HIS 0.003 0.001 HIS C 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 9388) covalent geometry : angle 0.60717 / 0.30 (12774) hydrogen bonds : bond 0.05327 / 3.79 ( 590) hydrogen bonds : angle 4.53039 / 3.32 ( 1698) link_ALPHA1-3 : bond 0.02276 / 1.34 ( 2) link_ALPHA1-3 : angle 2.99363 / 1.57 ( 6) link_ALPHA1-4 : bond 0.01198 / 0.71 ( 2) link_ALPHA1-4 : angle 3.96445 / 1.79 ( 6) link_BETA1-4 : bond 0.01035 / 0.69 ( 4) link_BETA1-4 : angle 3.68315 / 1.75 ( 12) link_BETA1-6 : bond 0.00930 / 0.55 ( 2) link_BETA1-6 : angle 0.77778 / 0.41 ( 6) link_NAG-ASN : bond 0.00299 / 0.18 ( 2) link_NAG-ASN : angle 0.86206 / 0.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 681 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7787 (tt0) REVERT: C 718 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8311 (mt) REVERT: C 827 ARG cc_start: 0.8331 (mtp85) cc_final: 0.8127 (mtp85) REVERT: E 384 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7622 (mpt-90) REVERT: E 681 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7762 (tt0) REVERT: E 718 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8314 (mt) outliers start: 16 outliers final: 9 residues processed: 144 average time/residue: 1.1919 time to fit residues: 184.6491 Evaluate side-chains 147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 681 GLU Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain C residue 877 ILE Chi-restraints excluded: chain E residue 384 ARG Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 681 GLU Chi-restraints excluded: chain E residue 718 LEU Chi-restraints excluded: chain E residue 877 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 83 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 434 GLN C 482 ASN E 434 GLN E 482 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.127590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.103085 restraints weight = 24486.023| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.28 r_work: 0.2913 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9400 Z= 0.162 Angle : 0.608 6.104 12810 Z= 0.297 Chirality : 0.041 0.188 1562 Planarity : 0.005 0.042 1498 Dihedral : 12.958 112.692 1796 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.68 % Allowed : 13.05 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.24), residues: 1102 helix: 1.71 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -0.23 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 389 TYR 0.012 0.002 TYR E 486 PHE 0.015 0.001 PHE E 471 TRP 0.013 0.002 TRP C 492 HIS 0.003 0.001 HIS C 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 9388) covalent geometry : angle 0.59218 / 0.29 (12774) hydrogen bonds : bond 0.05341 / 3.79 ( 590) hydrogen bonds : angle 4.53144 / 3.32 ( 1698) link_ALPHA1-3 : bond 0.01988 / 1.18 ( 2) link_ALPHA1-3 : angle 2.46887 / 1.22 ( 6) link_ALPHA1-4 : bond 0.01087 / 0.64 ( 2) link_ALPHA1-4 : angle 3.87993 / 1.77 ( 6) link_BETA1-4 : bond 0.00400 / 0.26 ( 4) link_BETA1-4 : angle 3.14820 / 1.46 ( 12) link_BETA1-6 : bond 0.00934 / 0.55 ( 2) link_BETA1-6 : angle 0.72703 / 0.38 ( 6) link_NAG-ASN : bond 0.00301 / 0.18 ( 2) link_NAG-ASN : angle 0.98256 / 0.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 681 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7809 (tt0) REVERT: C 718 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8293 (mt) REVERT: E 384 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7615 (mpt-90) REVERT: E 681 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7787 (tt0) REVERT: E 718 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8294 (mt) outliers start: 16 outliers final: 9 residues processed: 143 average time/residue: 1.1336 time to fit residues: 174.9306 Evaluate side-chains 145 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 681 GLU Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain C residue 877 ILE Chi-restraints excluded: chain E residue 384 ARG Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 681 GLU Chi-restraints excluded: chain E residue 718 LEU Chi-restraints excluded: chain E residue 877 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 33 optimal weight: 0.0770 chunk 26 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 482 ASN E 482 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.129698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.105462 restraints weight = 24677.047| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.28 r_work: 0.2955 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9400 Z= 0.119 Angle : 0.552 5.853 12810 Z= 0.270 Chirality : 0.039 0.180 1562 Planarity : 0.005 0.040 1498 Dihedral : 12.383 112.121 1796 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.42 % Allowed : 14.11 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.25), residues: 1102 helix: 1.83 (0.19), residues: 764 sheet: None (None), residues: 0 loop : 0.02 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 603 TYR 0.012 0.001 TYR E 486 PHE 0.011 0.001 PHE E 836 TRP 0.014 0.001 TRP C 492 HIS 0.002 0.001 HIS E 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 ( 9388) covalent geometry : angle 0.53641 / 0.27 (12774) hydrogen bonds : bond 0.04621 / 3.30 ( 590) hydrogen bonds : angle 4.39002 / 3.22 ( 1698) link_ALPHA1-3 : bond 0.01626 / 0.96 ( 2) link_ALPHA1-3 : angle 1.61562 / 0.87 ( 6) link_ALPHA1-4 : bond 0.00928 / 0.55 ( 2) link_ALPHA1-4 : angle 3.64172 / 1.70 ( 6) link_BETA1-4 : bond 0.00286 / 0.18 ( 4) link_BETA1-4 : angle 3.16947 / 1.45 ( 12) link_BETA1-6 : bond 0.00770 / 0.45 ( 2) link_BETA1-6 : angle 0.80850 / 0.43 ( 6) link_NAG-ASN : bond 0.00221 / 0.13 ( 2) link_NAG-ASN : angle 0.99799 / 0.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 146 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 387 ARG cc_start: 0.8275 (mtt90) cc_final: 0.8039 (mtt90) REVERT: C 718 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8224 (mt) REVERT: E 387 ARG cc_start: 0.8273 (mtt90) cc_final: 0.8047 (mtt90) REVERT: E 718 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8225 (mt) outliers start: 4 outliers final: 2 residues processed: 150 average time/residue: 1.1067 time to fit residues: 178.6704 Evaluate side-chains 145 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 718 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 10 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 1 optimal weight: 0.4980 chunk 52 optimal weight: 0.6980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 482 ASN E 482 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.128165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.103847 restraints weight = 24802.117| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.29 r_work: 0.2933 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9400 Z= 0.143 Angle : 0.575 5.768 12810 Z= 0.283 Chirality : 0.040 0.190 1562 Planarity : 0.005 0.041 1498 Dihedral : 12.275 110.679 1796 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.53 % Allowed : 14.11 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.25), residues: 1102 helix: 1.82 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -0.05 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 603 TYR 0.012 0.001 TYR E 486 PHE 0.014 0.001 PHE E 471 TRP 0.013 0.002 TRP C 492 HIS 0.002 0.001 HIS C 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 9388) covalent geometry : angle 0.56077 / 0.28 (12774) hydrogen bonds : bond 0.05024 / 3.58 ( 590) hydrogen bonds : angle 4.43127 / 3.24 ( 1698) link_ALPHA1-3 : bond 0.01549 / 0.91 ( 2) link_ALPHA1-3 : angle 1.69524 / 0.91 ( 6) link_ALPHA1-4 : bond 0.00956 / 0.57 ( 2) link_ALPHA1-4 : angle 3.65436 / 1.71 ( 6) link_BETA1-4 : bond 0.00379 / 0.25 ( 4) link_BETA1-4 : angle 3.12294 / 1.43 ( 12) link_BETA1-6 : bond 0.00904 / 0.54 ( 2) link_BETA1-6 : angle 0.76152 / 0.40 ( 6) link_NAG-ASN : bond 0.00176 / 0.10 ( 2) link_NAG-ASN : angle 0.98792 / 0.43 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 138 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 387 ARG cc_start: 0.8280 (mtt90) cc_final: 0.8036 (mtt90) REVERT: C 718 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8257 (mt) REVERT: E 387 ARG cc_start: 0.8283 (mtt90) cc_final: 0.8048 (mtt90) REVERT: E 718 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8256 (mt) outliers start: 5 outliers final: 3 residues processed: 143 average time/residue: 1.1078 time to fit residues: 170.2852 Evaluate side-chains 142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 718 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 78 optimal weight: 0.4980 chunk 95 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 58 optimal weight: 0.0770 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.0540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 482 ASN E 482 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.129421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.105154 restraints weight = 24885.284| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.30 r_work: 0.2965 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2823 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2823 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9400 Z= 0.120 Angle : 0.548 5.332 12810 Z= 0.270 Chirality : 0.039 0.177 1562 Planarity : 0.005 0.041 1498 Dihedral : 12.010 109.779 1796 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.74 % Allowed : 13.79 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.25), residues: 1102 helix: 1.88 (0.19), residues: 762 sheet: None (None), residues: 0 loop : 0.01 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 603 TYR 0.012 0.001 TYR E 486 PHE 0.011 0.001 PHE E 471 TRP 0.013 0.001 TRP C 492 HIS 0.002 0.001 HIS E 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 9388) covalent geometry : angle 0.53444 / 0.27 (12774) hydrogen bonds : bond 0.04631 / 3.31 ( 590) hydrogen bonds : angle 4.36774 / 3.20 ( 1698) link_ALPHA1-3 : bond 0.01495 / 0.88 ( 2) link_ALPHA1-3 : angle 1.52863 / 0.83 ( 6) link_ALPHA1-4 : bond 0.00983 / 0.58 ( 2) link_ALPHA1-4 : angle 3.40973 / 1.62 ( 6) link_BETA1-4 : bond 0.00459 / 0.30 ( 4) link_BETA1-4 : angle 2.93909 / 1.35 ( 12) link_BETA1-6 : bond 0.00785 / 0.46 ( 2) link_BETA1-6 : angle 0.78858 / 0.42 ( 6) link_NAG-ASN : bond 0.00136 / 0.08 ( 2) link_NAG-ASN : angle 0.91982 / 0.40 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8152.31 seconds wall clock time: 138 minutes 29.44 seconds (8309.44 seconds total)