Starting phenix.real_space_refine on Sun Jul 5 21:25:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mbs_23745/07_2026/7mbs_23745.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mbs_23745/07_2026/7mbs_23745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mbs_23745/07_2026/7mbs_23745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mbs_23745/07_2026/7mbs_23745.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mbs_23745/07_2026/7mbs_23745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mbs_23745/07_2026/7mbs_23745.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 176 5.16 5 C 20116 2.51 5 N 5160 2.21 5 O 5156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.03s 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: 30616 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7545 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 952} Chain breaks: 4 Unresolved non-hydrogen bonds: 500 Unresolved non-hydrogen angles: 620 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ASP:plan': 31, 'ARG:plan': 9, 'GLU:plan': 32, 'GLN:plan1': 14, 'HIS:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 355 Chain: "B" Number of atoms: 7545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7545 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 952} Chain breaks: 4 Unresolved non-hydrogen bonds: 500 Unresolved non-hydrogen angles: 620 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ASP:plan': 31, 'ARG:plan': 9, 'GLU:plan': 32, 'GLN:plan1': 14, 'HIS:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 355 Chain: "C" Number of atoms: 7545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7545 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 952} Chain breaks: 4 Unresolved non-hydrogen bonds: 500 Unresolved non-hydrogen angles: 620 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ASP:plan': 31, 'ARG:plan': 9, 'GLU:plan': 32, 'GLN:plan1': 14, 'HIS:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 355 Chain: "D" Number of atoms: 7545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7545 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 952} Chain breaks: 4 Unresolved non-hydrogen bonds: 500 Unresolved non-hydrogen angles: 620 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ASP:plan': 31, 'ARG:plan': 9, 'GLU:plan': 32, 'GLN:plan1': 14, 'HIS:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 355 Chain: "A" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 103 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 103 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 103 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 103 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 6.97, per 1000 atoms: 0.23 Number of scatterers: 30616 At special positions: 0 Unit cell: (146.922, 147.964, 155.258, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 176 16.00 O 5156 8.00 N 5160 7.00 C 20116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1501 " - " ASN A 921 " " NAG B1501 " - " ASN B 921 " " NAG C1501 " - " ASN C 921 " " NAG D3002 " - " ASN D 921 " Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 1.4 seconds 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7600 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 8 sheets defined 70.8% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 40 through 50 removed outlier: 3.565A pdb=" N ILE A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 90 removed outlier: 4.066A pdb=" N SER A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 119 removed outlier: 3.664A pdb=" N ASN A 107 " --> pdb=" O GLY A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 139 through 144 removed outlier: 3.589A pdb=" N LEU A 143 " --> pdb=" O ASN A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 200 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 226 through 236 Processing helix chain 'A' and resid 248 through 260 Processing helix chain 'A' and resid 263 through 275 Processing helix chain 'A' and resid 280 through 298 Processing helix chain 'A' and resid 311 through 328 Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 334 through 345 Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 366 through 376 Processing helix chain 'A' and resid 378 through 388 Processing helix chain 'A' and resid 391 through 396 Processing helix chain 'A' and resid 397 through 407 Processing helix chain 'A' and resid 412 through 429 removed outlier: 3.671A pdb=" N THR A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 460 Processing helix chain 'A' and resid 499 through 511 removed outlier: 3.813A pdb=" N GLN A 511 " --> pdb=" O TRP A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 523 removed outlier: 3.508A pdb=" N ALA A 517 " --> pdb=" O ARG A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 545 Processing helix chain 'A' and resid 548 through 556 removed outlier: 3.534A pdb=" N ASN A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 574 Processing helix chain 'A' and resid 576 through 584 removed outlier: 3.510A pdb=" N SER A 580 " --> pdb=" O ASP A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 602 Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 609 through 622 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 699 through 714 Processing helix chain 'A' and resid 715 through 740 Processing helix chain 'A' and resid 751 through 774 Processing helix chain 'A' and resid 780 through 791 removed outlier: 3.961A pdb=" N ASP A 791 " --> pdb=" O LEU A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 812 Processing helix chain 'A' and resid 813 through 815 No H-bonds generated for 'chain 'A' and resid 813 through 815' Processing helix chain 'A' and resid 816 through 835 Processing helix chain 'A' and resid 836 through 842 Processing helix chain 'A' and resid 845 through 882 removed outlier: 3.849A pdb=" N ILE A 849 " --> pdb=" O LEU A 845 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A 850 " --> pdb=" O GLY A 846 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE A 864 " --> pdb=" O PHE A 860 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N PHE A 865 " --> pdb=" O PHE A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 903 removed outlier: 4.776A pdb=" N ARG A 898 " --> pdb=" O ARG A 894 " (cutoff:3.500A) Proline residue: A 899 - end of helix removed outlier: 3.672A pdb=" N ILE A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 912 Processing helix chain 'A' and resid 913 through 917 Processing helix chain 'A' and resid 925 through 932 Processing helix chain 'A' and resid 942 through 959 removed outlier: 3.550A pdb=" N VAL A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 979 removed outlier: 3.866A pdb=" N ASN A 979 " --> pdb=" O VAL A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 997 Processing helix chain 'A' and resid 1005 through 1020 removed outlier: 3.934A pdb=" N SER A1009 " --> pdb=" O PHE A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1062 Processing helix chain 'A' and resid 1063 through 1092 removed outlier: 3.524A pdb=" N MET A1092 " --> pdb=" O GLN A1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 50 removed outlier: 3.565A pdb=" N ILE B 44 " --> pdb=" O ASP B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 90 removed outlier: 4.066A pdb=" N SER B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 119 removed outlier: 3.664A pdb=" N ASN B 107 " --> pdb=" O GLY B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 139 through 144 removed outlier: 3.589A pdb=" N LEU B 143 " --> pdb=" O ASN B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 200 Processing helix chain 'B' and resid 223 through 225 No H-bonds generated for 'chain 'B' and resid 223 through 225' Processing helix chain 'B' and resid 226 through 236 Processing helix chain 'B' and resid 248 through 260 Processing helix chain 'B' and resid 263 through 275 Processing helix chain 'B' and resid 280 through 298 Processing helix chain 'B' and resid 311 through 328 Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 334 through 345 Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 366 through 376 Processing helix chain 'B' and resid 378 through 388 Processing helix chain 'B' and resid 391 through 396 Processing helix chain 'B' and resid 397 through 407 Processing helix chain 'B' and resid 412 through 429 removed outlier: 3.670A pdb=" N THR B 416 " --> pdb=" O ASN B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 460 Processing helix chain 'B' and resid 499 through 511 removed outlier: 3.813A pdb=" N GLN B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 523 removed outlier: 3.507A pdb=" N ALA B 517 " --> pdb=" O ARG B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 545 Processing helix chain 'B' and resid 548 through 556 removed outlier: 3.533A pdb=" N ASN B 556 " --> pdb=" O ARG B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 574 Processing helix chain 'B' and resid 576 through 584 removed outlier: 3.509A pdb=" N SER B 580 " --> pdb=" O ASP B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 602 Processing helix chain 'B' and resid 603 through 608 Processing helix chain 'B' and resid 609 through 622 Processing helix chain 'B' and resid 629 through 639 Processing helix chain 'B' and resid 640 through 645 Processing helix chain 'B' and resid 699 through 714 Processing helix chain 'B' and resid 715 through 740 Processing helix chain 'B' and resid 751 through 774 Processing helix chain 'B' and resid 780 through 791 removed outlier: 3.960A pdb=" N ASP B 791 " --> pdb=" O LEU B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 812 Processing helix chain 'B' and resid 813 through 815 No H-bonds generated for 'chain 'B' and resid 813 through 815' Processing helix chain 'B' and resid 816 through 835 Processing helix chain 'B' and resid 836 through 842 Processing helix chain 'B' and resid 845 through 882 removed outlier: 3.849A pdb=" N ILE B 849 " --> pdb=" O LEU B 845 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE B 850 " --> pdb=" O GLY B 846 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE B 864 " --> pdb=" O PHE B 860 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N PHE B 865 " --> pdb=" O PHE B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 903 removed outlier: 4.778A pdb=" N ARG B 898 " --> pdb=" O ARG B 894 " (cutoff:3.500A) Proline residue: B 899 - end of helix removed outlier: 3.671A pdb=" N ILE B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 912 Processing helix chain 'B' and resid 913 through 917 Processing helix chain 'B' and resid 925 through 932 Processing helix chain 'B' and resid 942 through 959 removed outlier: 3.551A pdb=" N VAL B 946 " --> pdb=" O ALA B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 979 removed outlier: 3.864A pdb=" N ASN B 979 " --> pdb=" O VAL B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 997 Processing helix chain 'B' and resid 1005 through 1020 removed outlier: 3.934A pdb=" N SER B1009 " --> pdb=" O PHE B1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1062 Processing helix chain 'B' and resid 1063 through 1092 removed outlier: 3.525A pdb=" N MET B1092 " --> pdb=" O GLN B1088 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 50 removed outlier: 3.565A pdb=" N ILE C 44 " --> pdb=" O ASP C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 90 removed outlier: 4.064A pdb=" N SER C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 119 removed outlier: 3.663A pdb=" N ASN C 107 " --> pdb=" O GLY C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 139 through 144 removed outlier: 3.588A pdb=" N LEU C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 200 Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 226 through 236 Processing helix chain 'C' and resid 248 through 260 Processing helix chain 'C' and resid 263 through 275 Processing helix chain 'C' and resid 280 through 298 Processing helix chain 'C' and resid 311 through 328 Processing helix chain 'C' and resid 331 through 333 No H-bonds generated for 'chain 'C' and resid 331 through 333' Processing helix chain 'C' and resid 334 through 345 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 366 through 376 Processing helix chain 'C' and resid 378 through 388 Processing helix chain 'C' and resid 391 through 396 Processing helix chain 'C' and resid 397 through 407 Processing helix chain 'C' and resid 412 through 429 removed outlier: 3.670A pdb=" N THR C 416 " --> pdb=" O ASN C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 460 Processing helix chain 'C' and resid 499 through 511 removed outlier: 3.813A pdb=" N GLN C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 523 removed outlier: 3.508A pdb=" N ALA C 517 " --> pdb=" O ARG C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 545 Processing helix chain 'C' and resid 548 through 556 removed outlier: 3.533A pdb=" N ASN C 556 " --> pdb=" O ARG C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 574 Processing helix chain 'C' and resid 576 through 584 removed outlier: 3.510A pdb=" N SER C 580 " --> pdb=" O ASP C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 602 Processing helix chain 'C' and resid 603 through 608 Processing helix chain 'C' and resid 609 through 622 Processing helix chain 'C' and resid 629 through 639 Processing helix chain 'C' and resid 640 through 645 Processing helix chain 'C' and resid 699 through 714 Processing helix chain 'C' and resid 715 through 740 Processing helix chain 'C' and resid 751 through 774 Processing helix chain 'C' and resid 780 through 791 removed outlier: 3.961A pdb=" N ASP C 791 " --> pdb=" O LEU C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 791 through 812 Processing helix chain 'C' and resid 813 through 815 No H-bonds generated for 'chain 'C' and resid 813 through 815' Processing helix chain 'C' and resid 816 through 835 Processing helix chain 'C' and resid 836 through 842 Processing helix chain 'C' and resid 845 through 882 removed outlier: 3.847A pdb=" N ILE C 849 " --> pdb=" O LEU C 845 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE C 850 " --> pdb=" O GLY C 846 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE C 864 " --> pdb=" O PHE C 860 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE C 865 " --> pdb=" O PHE C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 903 removed outlier: 4.777A pdb=" N ARG C 898 " --> pdb=" O ARG C 894 " (cutoff:3.500A) Proline residue: C 899 - end of helix removed outlier: 3.672A pdb=" N ILE C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 912 Processing helix chain 'C' and resid 913 through 917 Processing helix chain 'C' and resid 925 through 932 Processing helix chain 'C' and resid 942 through 959 removed outlier: 3.551A pdb=" N VAL C 946 " --> pdb=" O ALA C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 979 removed outlier: 3.868A pdb=" N ASN C 979 " --> pdb=" O VAL C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 997 Processing helix chain 'C' and resid 1005 through 1020 removed outlier: 3.935A pdb=" N SER C1009 " --> pdb=" O PHE C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1034 through 1062 Processing helix chain 'C' and resid 1063 through 1092 removed outlier: 3.524A pdb=" N MET C1092 " --> pdb=" O GLN C1088 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 50 removed outlier: 3.565A pdb=" N ILE D 44 " --> pdb=" O ASP D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 90 removed outlier: 4.066A pdb=" N SER D 90 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 119 removed outlier: 3.664A pdb=" N ASN D 107 " --> pdb=" O GLY D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 137 No H-bonds generated for 'chain 'D' and resid 135 through 137' Processing helix chain 'D' and resid 139 through 144 removed outlier: 3.587A pdb=" N LEU D 143 " --> pdb=" O ASN D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 200 Processing helix chain 'D' and resid 223 through 225 No H-bonds generated for 'chain 'D' and resid 223 through 225' Processing helix chain 'D' and resid 226 through 236 Processing helix chain 'D' and resid 248 through 260 Processing helix chain 'D' and resid 263 through 275 Processing helix chain 'D' and resid 280 through 298 Processing helix chain 'D' and resid 311 through 328 Processing helix chain 'D' and resid 331 through 333 No H-bonds generated for 'chain 'D' and resid 331 through 333' Processing helix chain 'D' and resid 334 through 345 Processing helix chain 'D' and resid 346 through 353 Processing helix chain 'D' and resid 363 through 365 No H-bonds generated for 'chain 'D' and resid 363 through 365' Processing helix chain 'D' and resid 366 through 376 Processing helix chain 'D' and resid 378 through 388 Processing helix chain 'D' and resid 391 through 396 Processing helix chain 'D' and resid 397 through 407 Processing helix chain 'D' and resid 412 through 429 removed outlier: 3.671A pdb=" N THR D 416 " --> pdb=" O ASN D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 460 Processing helix chain 'D' and resid 499 through 511 removed outlier: 3.814A pdb=" N GLN D 511 " --> pdb=" O TRP D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 523 removed outlier: 3.507A pdb=" N ALA D 517 " --> pdb=" O ARG D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 545 Processing helix chain 'D' and resid 548 through 556 removed outlier: 3.533A pdb=" N ASN D 556 " --> pdb=" O ARG D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 574 Processing helix chain 'D' and resid 576 through 584 removed outlier: 3.510A pdb=" N SER D 580 " --> pdb=" O ASP D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 602 Processing helix chain 'D' and resid 603 through 608 Processing helix chain 'D' and resid 609 through 622 Processing helix chain 'D' and resid 629 through 639 Processing helix chain 'D' and resid 640 through 645 Processing helix chain 'D' and resid 699 through 714 Processing helix chain 'D' and resid 715 through 740 Processing helix chain 'D' and resid 751 through 774 Processing helix chain 'D' and resid 780 through 791 removed outlier: 3.960A pdb=" N ASP D 791 " --> pdb=" O LEU D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 791 through 812 Processing helix chain 'D' and resid 813 through 815 No H-bonds generated for 'chain 'D' and resid 813 through 815' Processing helix chain 'D' and resid 816 through 835 Processing helix chain 'D' and resid 836 through 842 Processing helix chain 'D' and resid 845 through 882 removed outlier: 3.848A pdb=" N ILE D 849 " --> pdb=" O LEU D 845 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE D 850 " --> pdb=" O GLY D 846 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE D 864 " --> pdb=" O PHE D 860 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE D 865 " --> pdb=" O PHE D 861 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 903 removed outlier: 4.778A pdb=" N ARG D 898 " --> pdb=" O ARG D 894 " (cutoff:3.500A) Proline residue: D 899 - end of helix removed outlier: 3.671A pdb=" N ILE D 903 " --> pdb=" O PRO D 899 " (cutoff:3.500A) Processing helix chain 'D' and resid 908 through 912 Processing helix chain 'D' and resid 913 through 917 Processing helix chain 'D' and resid 925 through 932 Processing helix chain 'D' and resid 942 through 959 removed outlier: 3.550A pdb=" N VAL D 946 " --> pdb=" O ALA D 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 959 through 979 removed outlier: 3.865A pdb=" N ASN D 979 " --> pdb=" O VAL D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 979 through 997 Processing helix chain 'D' and resid 1005 through 1020 removed outlier: 3.934A pdb=" N SER D1009 " --> pdb=" O PHE D1005 " (cutoff:3.500A) Processing helix chain 'D' and resid 1034 through 1062 Processing helix chain 'D' and resid 1063 through 1092 removed outlier: 3.523A pdb=" N MET D1092 " --> pdb=" O GLN D1088 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 155 removed outlier: 3.637A pdb=" N THR A 28 " --> pdb=" O PHE A 22 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS A 173 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N LEU A 241 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N CYS A 217 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU A 243 " --> pdb=" O CYS A 217 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LEU A 219 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP A 240 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N HIS A 304 " --> pdb=" O TRP A 240 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE A 242 " --> pdb=" O HIS A 304 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 205 Processing sheet with id=AA3, first strand: chain 'B' and resid 152 through 155 removed outlier: 3.637A pdb=" N THR B 28 " --> pdb=" O PHE B 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS B 173 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LEU B 241 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N CYS B 217 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU B 243 " --> pdb=" O CYS B 217 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU B 219 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TRP B 240 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N HIS B 304 " --> pdb=" O TRP B 240 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE B 242 " --> pdb=" O HIS B 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 202 through 205 Processing sheet with id=AA5, first strand: chain 'C' and resid 152 through 155 removed outlier: 3.637A pdb=" N THR C 28 " --> pdb=" O PHE C 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS C 173 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LEU C 241 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N CYS C 217 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU C 243 " --> pdb=" O CYS C 217 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LEU C 219 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP C 240 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N HIS C 304 " --> pdb=" O TRP C 240 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE C 242 " --> pdb=" O HIS C 304 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 202 through 205 Processing sheet with id=AA7, first strand: chain 'D' and resid 152 through 155 removed outlier: 3.636A pdb=" N THR D 28 " --> pdb=" O PHE D 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS D 173 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LEU D 241 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N CYS D 217 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU D 243 " --> pdb=" O CYS D 217 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LEU D 219 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TRP D 240 " --> pdb=" O THR D 302 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N HIS D 304 " --> pdb=" O TRP D 240 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE D 242 " --> pdb=" O HIS D 304 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 202 through 205 2072 hydrogen bonds defined for protein. 6060 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: 6.74 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9423 1.34 - 1.46: 5229 1.46 - 1.58: 16452 1.58 - 1.69: 0 1.69 - 1.81: 292 Bond restraints: 31396 Sorted by residual: bond pdb=" C3 NAG C1501 " pdb=" O3 NAG C1501 " ideal model delta sigma weight residual 1.403 1.432 -0.029 2.00e-02 2.50e+03 2.06e+00 bond pdb=" C3 NAG B1501 " pdb=" O3 NAG B1501 " ideal model delta sigma weight residual 1.403 1.432 -0.029 2.00e-02 2.50e+03 2.06e+00 bond pdb=" C3 NAG D3002 " pdb=" O3 NAG D3002 " ideal model delta sigma weight residual 1.403 1.432 -0.029 2.00e-02 2.50e+03 2.06e+00 bond pdb=" C3 NAG A1501 " pdb=" O3 NAG A1501 " ideal model delta sigma weight residual 1.403 1.431 -0.028 2.00e-02 2.50e+03 1.95e+00 bond pdb=" C1 NAG D3002 " pdb=" O5 NAG D3002 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 ... (remaining 31391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 41887 1.60 - 3.20: 851 3.20 - 4.80: 139 4.80 - 6.40: 38 6.40 - 8.00: 13 Bond angle restraints: 42928 Sorted by residual: angle pdb=" N GLN D 511 " pdb=" CA GLN D 511 " pdb=" C GLN D 511 " ideal model delta sigma weight residual 112.59 118.41 -5.82 1.22e+00 6.72e-01 2.27e+01 angle pdb=" N GLN A 511 " pdb=" CA GLN A 511 " pdb=" C GLN A 511 " ideal model delta sigma weight residual 112.59 118.39 -5.80 1.22e+00 6.72e-01 2.26e+01 angle pdb=" N GLN C 511 " pdb=" CA GLN C 511 " pdb=" C GLN C 511 " ideal model delta sigma weight residual 112.59 118.38 -5.79 1.22e+00 6.72e-01 2.25e+01 angle pdb=" N GLN B 511 " pdb=" CA GLN B 511 " pdb=" C GLN B 511 " ideal model delta sigma weight residual 112.59 118.34 -5.75 1.22e+00 6.72e-01 2.22e+01 angle pdb=" N ARG D 513 " pdb=" CA ARG D 513 " pdb=" C ARG D 513 " ideal model delta sigma weight residual 108.41 101.10 7.31 1.61e+00 3.86e-01 2.06e+01 ... (remaining 42923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 17105 17.59 - 35.18: 1587 35.18 - 52.77: 367 52.77 - 70.35: 105 70.35 - 87.94: 20 Dihedral angle restraints: 19184 sinusoidal: 7504 harmonic: 11680 Sorted by residual: dihedral pdb=" CA LEU D 544 " pdb=" C LEU D 544 " pdb=" N ALA D 545 " pdb=" CA ALA D 545 " ideal model delta harmonic sigma weight residual 180.00 159.26 20.74 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA LEU A 544 " pdb=" C LEU A 544 " pdb=" N ALA A 545 " pdb=" CA ALA A 545 " ideal model delta harmonic sigma weight residual 180.00 159.28 20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA LEU B 544 " pdb=" C LEU B 544 " pdb=" N ALA B 545 " pdb=" CA ALA B 545 " ideal model delta harmonic sigma weight residual 180.00 159.28 20.72 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 19181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 4377 0.057 - 0.113: 697 0.113 - 0.170: 34 0.170 - 0.227: 8 0.227 - 0.283: 16 Chirality restraints: 5132 Sorted by residual: chirality pdb=" CA ASN C 512 " pdb=" N ASN C 512 " pdb=" C ASN C 512 " pdb=" CB ASN C 512 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C41 YUY B1505 " pdb=" C40 YUY B1505 " pdb=" C42 YUY B1505 " pdb=" O7 YUY B1505 " both_signs ideal model delta sigma weight residual False -2.21 -2.50 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA ASN B 512 " pdb=" N ASN B 512 " pdb=" C ASN B 512 " pdb=" CB ASN B 512 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 5129 not shown) Planarity restraints: 5240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D3002 " -0.038 2.00e-02 2.50e+03 3.09e-02 1.19e+01 pdb=" C7 NAG D3002 " 0.011 2.00e-02 2.50e+03 pdb=" C8 NAG D3002 " -0.029 2.00e-02 2.50e+03 pdb=" N2 NAG D3002 " 0.048 2.00e-02 2.50e+03 pdb=" O7 NAG D3002 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1501 " -0.037 2.00e-02 2.50e+03 3.07e-02 1.18e+01 pdb=" C7 NAG C1501 " 0.011 2.00e-02 2.50e+03 pdb=" C8 NAG C1501 " -0.029 2.00e-02 2.50e+03 pdb=" N2 NAG C1501 " 0.048 2.00e-02 2.50e+03 pdb=" O7 NAG C1501 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1501 " -0.037 2.00e-02 2.50e+03 3.06e-02 1.17e+01 pdb=" C7 NAG B1501 " 0.011 2.00e-02 2.50e+03 pdb=" C8 NAG B1501 " -0.029 2.00e-02 2.50e+03 pdb=" N2 NAG B1501 " 0.048 2.00e-02 2.50e+03 pdb=" O7 NAG B1501 " 0.007 2.00e-02 2.50e+03 ... (remaining 5237 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6267 2.78 - 3.31: 30003 3.31 - 3.84: 54250 3.84 - 4.37: 61811 4.37 - 4.90: 105295 Nonbonded interactions: 257626 Sorted by model distance: nonbonded pdb=" O GLN C 771 " pdb=" OG1 THR C 775 " model vdw 2.246 3.040 nonbonded pdb=" O GLN B 771 " pdb=" OG1 THR B 775 " model vdw 2.246 3.040 nonbonded pdb=" O GLN A 771 " pdb=" OG1 THR A 775 " model vdw 2.247 3.040 nonbonded pdb=" O GLN D 771 " pdb=" OG1 THR D 775 " model vdw 2.248 3.040 nonbonded pdb=" NE2 GLN C 906 " pdb=" O HOH C1601 " model vdw 2.266 3.120 ... (remaining 257621 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: 0.09 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 1092 or resid 1503)) selection = (chain 'B' and (resid 16 through 1092 or resid 1503)) selection = (chain 'C' and (resid 16 through 1092 or resid 1503)) selection = (chain 'D' and (resid 16 through 1092 or resid 3003)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 29.020 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31400 Z= 0.170 Angle : 0.591 7.998 42940 Z= 0.337 Chirality : 0.042 0.283 5132 Planarity : 0.005 0.078 5236 Dihedral : 14.965 87.942 11584 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.93 % Favored : 95.97 % Rotamer: Outliers : 0.58 % Allowed : 17.01 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.80 (0.14), residues: 3944 helix: 2.03 (0.10), residues: 2576 sheet: 0.43 (0.32), residues: 308 loop : -0.67 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1069 TYR 0.012 0.001 TYR D 995 PHE 0.029 0.002 PHE A 32 TRP 0.017 0.001 TRP A 984 HIS 0.004 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.17 (31396) covalent geometry : angle 0.58998 / 0.34 (42928) hydrogen bonds : bond 0.12397 / 8.64 ( 2072) hydrogen bonds : angle 5.08622 / 3.71 ( 6060) link_NAG-ASN : bond 0.00052 / 0.03 ( 4) link_NAG-ASN : angle 2.05282 / 1.54 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 239 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 4 residues processed: 252 average time/residue: 0.2033 time to fit residues: 83.2711 Evaluate side-chains 147 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 143 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain C residue 1068 LEU Chi-restraints excluded: chain D residue 1068 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 0.6980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.0060 overall best weight: 3.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 HIS A 906 GLN B 304 HIS B 906 GLN C 304 HIS C 906 GLN D 233 ASN D 304 HIS D 906 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.051451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.038421 restraints weight = 158747.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.039817 restraints weight = 75531.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.040740 restraints weight = 47655.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.041297 restraints weight = 35557.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.041736 restraints weight = 29616.790| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31400 Z= 0.199 Angle : 0.578 11.400 42940 Z= 0.295 Chirality : 0.039 0.213 5132 Planarity : 0.005 0.058 5236 Dihedral : 5.509 55.933 5260 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.05 % Allowed : 15.37 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.14), residues: 3944 helix: 2.30 (0.10), residues: 2628 sheet: 0.47 (0.32), residues: 268 loop : -0.52 (0.20), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1069 TYR 0.012 0.001 TYR C 995 PHE 0.010 0.001 PHE C 567 TRP 0.013 0.001 TRP B 134 HIS 0.003 0.001 HIS D1060 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (31396) covalent geometry : angle 0.57797 / 0.29 (42928) hydrogen bonds : bond 0.04014 / 2.80 ( 2072) hydrogen bonds : angle 4.32651 / 3.13 ( 6060) link_NAG-ASN : bond 0.00222 / 0.11 ( 4) link_NAG-ASN : angle 1.49064 / 1.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 1.214 Fit side-chains REVERT: A 785 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8319 (tmt) REVERT: A 829 MET cc_start: 0.9134 (ttm) cc_final: 0.8915 (ttm) REVERT: B 829 MET cc_start: 0.9143 (ttm) cc_final: 0.8932 (ttm) REVERT: C 829 MET cc_start: 0.9139 (ttm) cc_final: 0.8918 (ttm) REVERT: D 785 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8332 (tmt) REVERT: D 829 MET cc_start: 0.9146 (ttm) cc_final: 0.8938 (ttm) outliers start: 31 outliers final: 7 residues processed: 174 average time/residue: 0.1923 time to fit residues: 56.2163 Evaluate side-chains 145 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 785 MET Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 785 MET Chi-restraints excluded: chain D residue 803 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 89 optimal weight: 0.9990 chunk 12 optimal weight: 20.0000 chunk 332 optimal weight: 20.0000 chunk 266 optimal weight: 9.9990 chunk 295 optimal weight: 8.9990 chunk 201 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 205 optimal weight: 10.0000 chunk 290 optimal weight: 7.9990 chunk 257 optimal weight: 0.0170 chunk 113 optimal weight: 30.0000 overall best weight: 5.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN A 556 ASN B 71 GLN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN B 556 ASN C 71 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN C 556 ASN D 71 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 ASN D 556 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.048927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.035923 restraints weight = 161900.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.037240 restraints weight = 77947.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.038115 restraints weight = 49571.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.038632 restraints weight = 37188.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.039010 restraints weight = 31225.199| |-----------------------------------------------------------------------------| r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 31400 Z= 0.254 Angle : 0.607 8.481 42940 Z= 0.305 Chirality : 0.039 0.142 5132 Planarity : 0.005 0.060 5236 Dihedral : 5.246 56.304 5252 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.80 % Allowed : 15.54 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.14), residues: 3944 helix: 2.47 (0.10), residues: 2608 sheet: 0.20 (0.30), residues: 276 loop : -0.46 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1080 TYR 0.015 0.001 TYR D 995 PHE 0.011 0.001 PHE B 381 TRP 0.045 0.002 TRP A 240 HIS 0.004 0.001 HIS D 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.25 (31396) covalent geometry : angle 0.60620 / 0.31 (42928) hydrogen bonds : bond 0.04072 / 2.84 ( 2072) hydrogen bonds : angle 4.21988 / 3.07 ( 6060) link_NAG-ASN : bond 0.00306 / 0.15 ( 4) link_NAG-ASN : angle 1.72299 / 1.29 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 143 time to evaluate : 1.214 Fit side-chains REVERT: A 136 MET cc_start: 0.9272 (ptp) cc_final: 0.9021 (ptp) REVERT: B 136 MET cc_start: 0.9273 (ptp) cc_final: 0.9027 (ptp) REVERT: B 230 MET cc_start: 0.9411 (tpt) cc_final: 0.9069 (tpt) REVERT: C 136 MET cc_start: 0.9274 (ptp) cc_final: 0.9021 (ptp) REVERT: D 136 MET cc_start: 0.9272 (ptp) cc_final: 0.9026 (ptp) outliers start: 53 outliers final: 20 residues processed: 194 average time/residue: 0.1889 time to fit residues: 61.3936 Evaluate side-chains 155 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 1075 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 1075 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 181 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 126 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 356 optimal weight: 4.9990 chunk 308 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 185 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 163 optimal weight: 0.9990 chunk 1 optimal weight: 30.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.049257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.036307 restraints weight = 160348.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.037653 restraints weight = 76775.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.038538 restraints weight = 48658.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.039051 restraints weight = 36360.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.039460 restraints weight = 30536.709| |-----------------------------------------------------------------------------| r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31400 Z= 0.155 Angle : 0.518 7.429 42940 Z= 0.263 Chirality : 0.037 0.139 5132 Planarity : 0.004 0.062 5236 Dihedral : 4.995 53.640 5252 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.85 % Allowed : 16.63 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.14), residues: 3944 helix: 2.68 (0.10), residues: 2580 sheet: 0.26 (0.29), residues: 276 loop : -0.49 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 552 TYR 0.012 0.001 TYR C 559 PHE 0.008 0.001 PHE D 804 TRP 0.013 0.001 TRP A 984 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (31396) covalent geometry : angle 0.51775 / 0.26 (42928) hydrogen bonds : bond 0.03561 / 2.48 ( 2072) hydrogen bonds : angle 4.00834 / 2.91 ( 6060) link_NAG-ASN : bond 0.00095 / 0.05 ( 4) link_NAG-ASN : angle 1.31637 / 0.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 1.214 Fit side-chains REVERT: A 136 MET cc_start: 0.9247 (ptp) cc_final: 0.8955 (ptp) REVERT: B 136 MET cc_start: 0.9243 (ptp) cc_final: 0.8954 (ptp) REVERT: C 136 MET cc_start: 0.9258 (ptp) cc_final: 0.8957 (ptp) REVERT: C 194 MET cc_start: 0.9485 (mmm) cc_final: 0.9225 (mmm) REVERT: D 136 MET cc_start: 0.9243 (ptp) cc_final: 0.8951 (ptp) REVERT: D 143 LEU cc_start: 0.9445 (pt) cc_final: 0.9191 (mt) outliers start: 25 outliers final: 16 residues processed: 164 average time/residue: 0.1742 time to fit residues: 50.3457 Evaluate side-chains 152 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 951 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 71 optimal weight: 7.9990 chunk 235 optimal weight: 9.9990 chunk 371 optimal weight: 0.7980 chunk 375 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 165 optimal weight: 9.9990 chunk 219 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 277 optimal weight: 0.8980 chunk 202 optimal weight: 5.9990 overall best weight: 4.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.048095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.035168 restraints weight = 163323.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.036466 restraints weight = 78584.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.037318 restraints weight = 50146.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.037819 restraints weight = 37786.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.038203 restraints weight = 31812.286| |-----------------------------------------------------------------------------| r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 31400 Z= 0.231 Angle : 0.563 7.204 42940 Z= 0.284 Chirality : 0.038 0.133 5132 Planarity : 0.005 0.061 5236 Dihedral : 4.959 54.716 5252 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.05 % Allowed : 17.59 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.14), residues: 3944 helix: 2.73 (0.10), residues: 2580 sheet: 0.25 (0.29), residues: 276 loop : -0.54 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 552 TYR 0.016 0.001 TYR B 995 PHE 0.011 0.001 PHE A 773 TRP 0.012 0.001 TRP C 713 HIS 0.004 0.001 HIS C 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.23 (31396) covalent geometry : angle 0.56289 / 0.28 (42928) hydrogen bonds : bond 0.03716 / 2.59 ( 2072) hydrogen bonds : angle 4.05390 / 2.95 ( 6060) link_NAG-ASN : bond 0.00305 / 0.15 ( 4) link_NAG-ASN : angle 1.58136 / 1.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 1.226 Fit side-chains REVERT: A 136 MET cc_start: 0.9253 (ptp) cc_final: 0.8985 (ptp) REVERT: A 212 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7562 (pm20) REVERT: A 981 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8405 (p0) REVERT: B 136 MET cc_start: 0.9253 (ptp) cc_final: 0.8989 (ptp) REVERT: B 212 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7566 (pm20) REVERT: B 981 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8399 (p0) REVERT: C 64 MET cc_start: 0.9050 (mmm) cc_final: 0.8837 (mmm) REVERT: C 136 MET cc_start: 0.9259 (ptp) cc_final: 0.8986 (ptp) REVERT: C 212 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7557 (pm20) REVERT: C 981 ASP cc_start: 0.8688 (OUTLIER) cc_final: 0.8401 (p0) REVERT: D 136 MET cc_start: 0.9249 (ptp) cc_final: 0.8984 (ptp) REVERT: D 212 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7665 (pm20) REVERT: D 981 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8399 (p0) outliers start: 31 outliers final: 14 residues processed: 170 average time/residue: 0.1721 time to fit residues: 51.4605 Evaluate side-chains 158 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 1075 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 981 ASP Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain D residue 212 GLU Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 981 ASP Chi-restraints excluded: chain D residue 1075 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 108 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 271 optimal weight: 4.9990 chunk 352 optimal weight: 10.0000 chunk 304 optimal weight: 9.9990 chunk 188 optimal weight: 0.7980 chunk 276 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 282 optimal weight: 1.9990 chunk 393 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 882 HIS C 882 HIS D 882 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.048514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.035733 restraints weight = 161112.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.037053 restraints weight = 76600.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.037922 restraints weight = 48531.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.038428 restraints weight = 36244.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.038818 restraints weight = 30417.254| |-----------------------------------------------------------------------------| r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 31400 Z= 0.159 Angle : 0.518 9.171 42940 Z= 0.262 Chirality : 0.037 0.137 5132 Planarity : 0.004 0.061 5236 Dihedral : 4.791 51.376 5252 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.12 % Allowed : 18.10 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.14), residues: 3944 helix: 2.81 (0.10), residues: 2580 sheet: 0.09 (0.28), residues: 300 loop : -0.50 (0.20), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 552 TYR 0.011 0.001 TYR D 995 PHE 0.008 0.001 PHE C 862 TRP 0.012 0.001 TRP A 984 HIS 0.006 0.001 HIS D 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (31396) covalent geometry : angle 0.51785 / 0.26 (42928) hydrogen bonds : bond 0.03516 / 2.45 ( 2072) hydrogen bonds : angle 3.90128 / 2.84 ( 6060) link_NAG-ASN : bond 0.00122 / 0.06 ( 4) link_NAG-ASN : angle 1.27898 / 0.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 1.288 Fit side-chains REVERT: A 136 MET cc_start: 0.9241 (ptp) cc_final: 0.8977 (ptp) REVERT: A 143 LEU cc_start: 0.9464 (pt) cc_final: 0.9155 (mt) REVERT: A 212 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7614 (pm20) REVERT: A 981 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8428 (p0) REVERT: B 136 MET cc_start: 0.9253 (ptp) cc_final: 0.8991 (ptp) REVERT: B 143 LEU cc_start: 0.9479 (pt) cc_final: 0.9164 (mt) REVERT: B 917 MET cc_start: 0.9372 (mtm) cc_final: 0.8762 (mtm) REVERT: B 981 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8423 (p0) REVERT: C 64 MET cc_start: 0.9143 (mmm) cc_final: 0.8932 (mmm) REVERT: C 136 MET cc_start: 0.9266 (ptp) cc_final: 0.8999 (ptp) REVERT: C 143 LEU cc_start: 0.9477 (pt) cc_final: 0.9160 (mt) REVERT: C 212 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7607 (pm20) REVERT: C 981 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8426 (p0) REVERT: D 136 MET cc_start: 0.9238 (ptp) cc_final: 0.8976 (ptp) REVERT: D 981 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8422 (p0) outliers start: 33 outliers final: 20 residues processed: 171 average time/residue: 0.1682 time to fit residues: 50.8238 Evaluate side-chains 161 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 1075 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 981 ASP Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 981 ASP Chi-restraints excluded: chain D residue 1075 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 170 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 277 optimal weight: 7.9990 chunk 288 optimal weight: 6.9990 chunk 202 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 329 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 514 GLN D 514 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.047585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.034762 restraints weight = 163754.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.036053 restraints weight = 78600.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.036899 restraints weight = 50065.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.037446 restraints weight = 37545.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.037734 restraints weight = 31390.867| |-----------------------------------------------------------------------------| r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 31400 Z= 0.246 Angle : 0.574 9.851 42940 Z= 0.289 Chirality : 0.038 0.130 5132 Planarity : 0.004 0.060 5236 Dihedral : 4.862 52.931 5252 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.43 % Allowed : 18.61 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.14), residues: 3944 helix: 2.77 (0.10), residues: 2572 sheet: 0.10 (0.28), residues: 300 loop : -0.63 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 552 TYR 0.016 0.001 TYR B 995 PHE 0.011 0.001 PHE B 567 TRP 0.012 0.001 TRP B 713 HIS 0.006 0.001 HIS D 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.25 (31396) covalent geometry : angle 0.57330 / 0.29 (42928) hydrogen bonds : bond 0.03713 / 2.59 ( 2072) hydrogen bonds : angle 4.01441 / 2.92 ( 6060) link_NAG-ASN : bond 0.00340 / 0.17 ( 4) link_NAG-ASN : angle 1.55857 / 1.09 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 0.957 Fit side-chains REVERT: A 136 MET cc_start: 0.9209 (ptp) cc_final: 0.8968 (ptp) REVERT: A 190 MET cc_start: 0.9495 (tpp) cc_final: 0.9286 (tpp) REVERT: A 194 MET cc_start: 0.9472 (mmm) cc_final: 0.9223 (mmm) REVERT: A 212 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7669 (pm20) REVERT: A 257 MET cc_start: 0.8686 (mmm) cc_final: 0.8408 (mmm) REVERT: A 917 MET cc_start: 0.9408 (mtm) cc_final: 0.8799 (mtm) REVERT: A 981 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8405 (p0) REVERT: B 136 MET cc_start: 0.9227 (ptp) cc_final: 0.8989 (ptp) REVERT: B 190 MET cc_start: 0.9479 (tpp) cc_final: 0.9266 (tpp) REVERT: B 194 MET cc_start: 0.9473 (mmm) cc_final: 0.9217 (mmm) REVERT: B 212 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7667 (pm20) REVERT: B 257 MET cc_start: 0.8671 (mmm) cc_final: 0.8345 (mmm) REVERT: B 779 MET cc_start: 0.8106 (mpp) cc_final: 0.7734 (mpp) REVERT: B 917 MET cc_start: 0.9413 (OUTLIER) cc_final: 0.8834 (mtm) REVERT: B 981 ASP cc_start: 0.8673 (OUTLIER) cc_final: 0.8402 (p0) REVERT: C 136 MET cc_start: 0.9235 (ptp) cc_final: 0.8989 (ptp) REVERT: C 212 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7666 (pm20) REVERT: C 257 MET cc_start: 0.8727 (mmm) cc_final: 0.8383 (mmm) REVERT: C 917 MET cc_start: 0.9409 (mtm) cc_final: 0.8797 (mtm) REVERT: C 981 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8399 (p0) REVERT: D 136 MET cc_start: 0.9210 (ptp) cc_final: 0.8968 (ptp) REVERT: D 212 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7660 (pm20) REVERT: D 257 MET cc_start: 0.8685 (mmm) cc_final: 0.8391 (mmm) REVERT: D 917 MET cc_start: 0.9405 (mtm) cc_final: 0.8792 (mtm) REVERT: D 981 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8396 (p0) outliers start: 42 outliers final: 26 residues processed: 167 average time/residue: 0.1463 time to fit residues: 42.7665 Evaluate side-chains 165 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 917 MET Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 1075 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 981 ASP Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain D residue 212 GLU Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 981 ASP Chi-restraints excluded: chain D residue 1075 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 132 optimal weight: 5.9990 chunk 367 optimal weight: 4.9990 chunk 350 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 228 optimal weight: 10.0000 chunk 216 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 267 optimal weight: 9.9990 chunk 29 optimal weight: 0.2980 chunk 269 optimal weight: 1.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.048007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.035292 restraints weight = 161856.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.036587 restraints weight = 76856.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.037449 restraints weight = 48755.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.037957 restraints weight = 36548.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.038352 restraints weight = 30653.700| |-----------------------------------------------------------------------------| r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 31400 Z= 0.171 Angle : 0.525 10.907 42940 Z= 0.266 Chirality : 0.037 0.133 5132 Planarity : 0.004 0.060 5236 Dihedral : 4.720 49.218 5252 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.29 % Allowed : 18.44 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.14), residues: 3944 helix: 2.82 (0.10), residues: 2572 sheet: 0.09 (0.28), residues: 300 loop : -0.58 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 552 TYR 0.011 0.001 TYR B 995 PHE 0.009 0.001 PHE C 862 TRP 0.012 0.001 TRP D 984 HIS 0.006 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (31396) covalent geometry : angle 0.52495 / 0.27 (42928) hydrogen bonds : bond 0.03522 / 2.45 ( 2072) hydrogen bonds : angle 3.85236 / 2.81 ( 6060) link_NAG-ASN : bond 0.00127 / 0.06 ( 4) link_NAG-ASN : angle 1.25257 / 0.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 1.352 Fit side-chains REVERT: A 136 MET cc_start: 0.9231 (ptp) cc_final: 0.8990 (ptp) REVERT: A 190 MET cc_start: 0.9438 (tpp) cc_final: 0.9163 (tpp) REVERT: A 194 MET cc_start: 0.9505 (mmm) cc_final: 0.9215 (mmm) REVERT: A 212 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7566 (pm20) REVERT: A 257 MET cc_start: 0.8783 (mmm) cc_final: 0.8451 (mmm) REVERT: A 538 MET cc_start: 0.8406 (mtt) cc_final: 0.8186 (mtp) REVERT: A 917 MET cc_start: 0.9433 (mtm) cc_final: 0.8776 (mtm) REVERT: A 981 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8462 (p0) REVERT: B 136 MET cc_start: 0.9237 (ptp) cc_final: 0.8996 (ptp) REVERT: B 212 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7562 (pm20) REVERT: B 257 MET cc_start: 0.8750 (mmm) cc_final: 0.8361 (mmm) REVERT: B 779 MET cc_start: 0.8073 (mpp) cc_final: 0.7684 (mpp) REVERT: B 917 MET cc_start: 0.9434 (OUTLIER) cc_final: 0.8810 (mtm) REVERT: B 981 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8460 (p0) REVERT: C 136 MET cc_start: 0.9244 (ptp) cc_final: 0.8996 (ptp) REVERT: C 212 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7566 (pm20) REVERT: C 257 MET cc_start: 0.8766 (mmm) cc_final: 0.8353 (mmm) REVERT: C 917 MET cc_start: 0.9436 (mtm) cc_final: 0.8775 (mtm) REVERT: C 981 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8455 (p0) REVERT: D 136 MET cc_start: 0.9231 (ptp) cc_final: 0.8992 (ptp) REVERT: D 212 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7676 (pm20) REVERT: D 257 MET cc_start: 0.8766 (mmm) cc_final: 0.8387 (mmm) REVERT: D 538 MET cc_start: 0.8400 (mtt) cc_final: 0.8187 (mtp) REVERT: D 917 MET cc_start: 0.9427 (mtm) cc_final: 0.8769 (mtm) REVERT: D 981 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8456 (p0) outliers start: 38 outliers final: 22 residues processed: 167 average time/residue: 0.1772 time to fit residues: 52.0473 Evaluate side-chains 164 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 917 MET Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 1075 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 981 ASP Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain D residue 212 GLU Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 981 ASP Chi-restraints excluded: chain D residue 1075 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 218 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 189 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 195 optimal weight: 0.0670 chunk 80 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 chunk 329 optimal weight: 6.9990 chunk 248 optimal weight: 0.3980 overall best weight: 2.0924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.048433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.035718 restraints weight = 160532.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.037039 restraints weight = 76138.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.037853 restraints weight = 48237.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.038449 restraints weight = 36329.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.038783 restraints weight = 30138.864| |-----------------------------------------------------------------------------| r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31400 Z= 0.126 Angle : 0.524 11.415 42940 Z= 0.260 Chirality : 0.037 0.135 5132 Planarity : 0.004 0.060 5236 Dihedral : 4.611 47.409 5252 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.19 % Allowed : 18.88 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.67 (0.14), residues: 3944 helix: 2.87 (0.10), residues: 2572 sheet: 0.13 (0.27), residues: 300 loop : -0.56 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 552 TYR 0.009 0.001 TYR D 995 PHE 0.009 0.001 PHE B1005 TRP 0.013 0.001 TRP A 984 HIS 0.006 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (31396) covalent geometry : angle 0.52331 / 0.26 (42928) hydrogen bonds : bond 0.03385 / 2.37 ( 2072) hydrogen bonds : angle 3.74880 / 2.73 ( 6060) link_NAG-ASN : bond 0.00008 / 0.00 ( 4) link_NAG-ASN : angle 1.04195 / 0.73 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 1.252 Fit side-chains REVERT: A 136 MET cc_start: 0.9223 (ptp) cc_final: 0.8985 (ptp) REVERT: A 190 MET cc_start: 0.9428 (tpp) cc_final: 0.9171 (tpp) REVERT: A 194 MET cc_start: 0.9517 (mmm) cc_final: 0.9230 (mmm) REVERT: A 212 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7416 (pm20) REVERT: A 257 MET cc_start: 0.8859 (mmm) cc_final: 0.8483 (mmm) REVERT: A 538 MET cc_start: 0.8402 (mtt) cc_final: 0.8162 (mtp) REVERT: A 829 MET cc_start: 0.9099 (ttm) cc_final: 0.8803 (ttt) REVERT: A 917 MET cc_start: 0.9425 (mtm) cc_final: 0.8833 (mtm) REVERT: A 981 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8420 (p0) REVERT: B 136 MET cc_start: 0.9220 (ptp) cc_final: 0.9004 (ptp) REVERT: B 212 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7419 (pm20) REVERT: B 257 MET cc_start: 0.8852 (mmm) cc_final: 0.8463 (mmm) REVERT: B 779 MET cc_start: 0.8020 (mpp) cc_final: 0.7603 (mpp) REVERT: B 829 MET cc_start: 0.9101 (ttm) cc_final: 0.8814 (ttt) REVERT: B 917 MET cc_start: 0.9422 (OUTLIER) cc_final: 0.8806 (mtm) REVERT: B 981 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8414 (p0) REVERT: C 136 MET cc_start: 0.9226 (ptp) cc_final: 0.9004 (ptp) REVERT: C 212 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7424 (pm20) REVERT: C 257 MET cc_start: 0.8847 (mmm) cc_final: 0.8450 (mmm) REVERT: C 829 MET cc_start: 0.9101 (ttm) cc_final: 0.8801 (ttt) REVERT: C 917 MET cc_start: 0.9433 (mtm) cc_final: 0.8856 (mtm) REVERT: C 981 ASP cc_start: 0.8673 (OUTLIER) cc_final: 0.8414 (p0) REVERT: D 136 MET cc_start: 0.9221 (ptp) cc_final: 0.8983 (ptp) REVERT: D 212 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7560 (pm20) REVERT: D 257 MET cc_start: 0.8844 (mmm) cc_final: 0.8455 (mmm) REVERT: D 538 MET cc_start: 0.8408 (mtt) cc_final: 0.8167 (mtp) REVERT: D 829 MET cc_start: 0.9107 (ttm) cc_final: 0.8809 (ttt) REVERT: D 917 MET cc_start: 0.9424 (mtm) cc_final: 0.8855 (mtm) REVERT: D 981 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8418 (p0) outliers start: 35 outliers final: 22 residues processed: 168 average time/residue: 0.1728 time to fit residues: 51.0922 Evaluate side-chains 166 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 917 MET Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 1075 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 981 ASP Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain D residue 212 GLU Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 981 ASP Chi-restraints excluded: chain D residue 1075 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 47 optimal weight: 2.9990 chunk 389 optimal weight: 9.9990 chunk 219 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 367 optimal weight: 3.9990 chunk 190 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 293 optimal weight: 5.9990 chunk 317 optimal weight: 9.9990 chunk 174 optimal weight: 4.9990 chunk 127 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.047320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.034500 restraints weight = 162315.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.035771 restraints weight = 77722.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.036609 restraints weight = 49717.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.037069 restraints weight = 37651.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.037461 restraints weight = 32051.947| |-----------------------------------------------------------------------------| r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 31400 Z= 0.239 Angle : 0.587 11.991 42940 Z= 0.293 Chirality : 0.038 0.159 5132 Planarity : 0.004 0.060 5236 Dihedral : 4.706 49.198 5252 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.05 % Allowed : 18.95 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.60 (0.14), residues: 3944 helix: 2.80 (0.10), residues: 2580 sheet: 0.12 (0.28), residues: 296 loop : -0.59 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 552 TYR 0.015 0.001 TYR D 995 PHE 0.010 0.001 PHE C 862 TRP 0.014 0.001 TRP D 240 HIS 0.006 0.001 HIS D 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.24 (31396) covalent geometry : angle 0.58634 / 0.29 (42928) hydrogen bonds : bond 0.03634 / 2.53 ( 2072) hydrogen bonds : angle 3.89287 / 2.83 ( 6060) link_NAG-ASN : bond 0.00306 / 0.15 ( 4) link_NAG-ASN : angle 1.42892 / 0.99 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 1.240 Fit side-chains REVERT: A 136 MET cc_start: 0.9214 (ptp) cc_final: 0.8983 (ptp) REVERT: A 194 MET cc_start: 0.9529 (mmm) cc_final: 0.9312 (mmm) REVERT: A 212 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7489 (pm20) REVERT: A 257 MET cc_start: 0.8924 (mmm) cc_final: 0.8562 (mmm) REVERT: A 917 MET cc_start: 0.9448 (mtm) cc_final: 0.8811 (mtm) REVERT: A 981 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.8455 (p0) REVERT: B 136 MET cc_start: 0.9220 (ptp) cc_final: 0.8990 (ptp) REVERT: B 212 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7501 (pm20) REVERT: B 257 MET cc_start: 0.8938 (mmm) cc_final: 0.8569 (mmm) REVERT: B 917 MET cc_start: 0.9442 (OUTLIER) cc_final: 0.8829 (mtm) REVERT: B 981 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.8452 (p0) REVERT: C 136 MET cc_start: 0.9227 (ptp) cc_final: 0.8984 (ptp) REVERT: C 212 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7511 (pm20) REVERT: C 257 MET cc_start: 0.8950 (mmm) cc_final: 0.8597 (mmm) REVERT: C 917 MET cc_start: 0.9455 (mtm) cc_final: 0.8836 (mtm) REVERT: C 981 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.8451 (p0) REVERT: D 136 MET cc_start: 0.9217 (ptp) cc_final: 0.8984 (ptp) REVERT: D 212 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7499 (pm20) REVERT: D 257 MET cc_start: 0.8929 (mmm) cc_final: 0.8568 (mmm) REVERT: D 554 MET cc_start: 0.8781 (ptp) cc_final: 0.8540 (ptp) REVERT: D 917 MET cc_start: 0.9443 (mtm) cc_final: 0.8814 (mtm) REVERT: D 981 ASP cc_start: 0.8715 (OUTLIER) cc_final: 0.8449 (p0) outliers start: 31 outliers final: 22 residues processed: 159 average time/residue: 0.1732 time to fit residues: 48.4273 Evaluate side-chains 163 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 917 MET Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 1075 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 981 ASP Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain D residue 212 GLU Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 859 VAL Chi-restraints excluded: chain D residue 981 ASP Chi-restraints excluded: chain D residue 1075 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 346 optimal weight: 10.0000 chunk 292 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 276 optimal weight: 3.9990 chunk 232 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.048477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.035810 restraints weight = 160316.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.037122 restraints weight = 75423.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.037991 restraints weight = 47529.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.038464 restraints weight = 35539.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.038847 restraints weight = 30079.106| |-----------------------------------------------------------------------------| r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31400 Z= 0.118 Angle : 0.529 12.605 42940 Z= 0.262 Chirality : 0.037 0.139 5132 Planarity : 0.004 0.059 5236 Dihedral : 4.563 44.471 5252 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.02 % Allowed : 19.08 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.67 (0.14), residues: 3944 helix: 2.86 (0.10), residues: 2572 sheet: 0.18 (0.28), residues: 296 loop : -0.56 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 552 TYR 0.008 0.001 TYR D 995 PHE 0.008 0.001 PHE D 862 TRP 0.013 0.001 TRP A 984 HIS 0.006 0.001 HIS D 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (31396) covalent geometry : angle 0.52878 / 0.26 (42928) hydrogen bonds : bond 0.03362 / 2.35 ( 2072) hydrogen bonds : angle 3.72668 / 2.71 ( 6060) link_NAG-ASN : bond 0.00049 / 0.02 ( 4) link_NAG-ASN : angle 0.97709 / 0.69 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4265.77 seconds wall clock time: 75 minutes 24.40 seconds (4524.40 seconds total)