Starting phenix.real_space_refine on Fri Mar 6 11:17:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mbs_23745/03_2026/7mbs_23745.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mbs_23745/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7mbs_23745/03_2026/7mbs_23745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mbs_23745/03_2026/7mbs_23745.map" model { file = "/net/cci-nas-00/data/ceres_data/7mbs_23745/03_2026/7mbs_23745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mbs_23745/03_2026/7mbs_23745.cif" } 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-5986/lib/python3.9/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, 105 Unusual residues: {' CA': 2, 'NAG': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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, 105 Unusual residues: {' CA': 2, 'NAG': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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, 105 Unusual residues: {' CA': 2, 'NAG': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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, 105 Unusual residues: {' CA': 2, 'NAG': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 7.52, per 1000 atoms: 0.25 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: 2.37 Conformation dependent library (CDL) restraints added in 1.1 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: 1.04 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: 6.18 Time building geometry restraints manager: 3.04 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: 0.07 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 26.900 Find NCS groups from input model: 0.820 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 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 covalent geometry : bond 0.00332 (31396) covalent geometry : angle 0.58998 (42928) hydrogen bonds : bond 0.12397 ( 2072) hydrogen bonds : angle 5.08622 ( 6060) link_NAG-ASN : bond 0.00052 ( 4) link_NAG-ASN : angle 2.05282 ( 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 : 1.390 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: 0.1891 time to fit residues: 77.5124 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 : 1.174 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 GLN B 304 HIS ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 906 GLN C 304 HIS ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3155 r_free = 0.3155 target = 0.051640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.038498 restraints weight = 158881.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.039902 restraints weight = 76306.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.040833 restraints weight = 48499.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.041382 restraints weight = 36204.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.041801 restraints weight = 30275.389| |-----------------------------------------------------------------------------| r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 31400 Z= 0.198 Angle : 0.582 11.866 42940 Z= 0.295 Chirality : 0.039 0.195 5132 Planarity : 0.005 0.058 5236 Dihedral : 5.496 56.209 5260 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.12 % Allowed : 15.27 % Favored : 83.61 % 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: 2.20 (0.14), residues: 3944 helix: 2.33 (0.10), residues: 2624 sheet: 0.48 (0.32), residues: 268 loop : -0.54 (0.20), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1069 TYR 0.012 0.001 TYR A 995 PHE 0.010 0.001 PHE C 567 TRP 0.013 0.001 TRP C 620 HIS 0.004 0.001 HIS C1060 Details of bonding type rmsd covalent geometry : bond 0.00443 (31396) covalent geometry : angle 0.58121 (42928) hydrogen bonds : bond 0.03955 ( 2072) hydrogen bonds : angle 4.32305 ( 6060) link_NAG-ASN : bond 0.00129 ( 4) link_NAG-ASN : angle 1.50812 ( 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 180 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 1.192 Fit side-chains REVERT: A 829 MET cc_start: 0.9147 (ttm) cc_final: 0.8946 (ttm) REVERT: C 829 MET cc_start: 0.9148 (ttm) cc_final: 0.8948 (ttm) outliers start: 33 outliers final: 11 residues processed: 180 average time/residue: 0.1701 time to fit residues: 51.7182 Evaluate side-chains 147 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain C residue 324 CYS Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain D residue 324 CYS Chi-restraints excluded: chain D residue 633 LEU 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: 0.9980 chunk 12 optimal weight: 20.0000 chunk 332 optimal weight: 20.0000 chunk 266 optimal weight: 8.9990 chunk 295 optimal weight: 8.9990 chunk 201 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 chunk 205 optimal weight: 9.9990 chunk 290 optimal weight: 5.9990 chunk 257 optimal weight: 0.0980 chunk 113 optimal weight: 30.0000 overall best weight: 3.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.050670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.037505 restraints weight = 160235.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.038891 restraints weight = 77058.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.039805 restraints weight = 49097.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.040346 restraints weight = 36794.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.040755 restraints weight = 30895.793| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31400 Z= 0.174 Angle : 0.535 7.327 42940 Z= 0.271 Chirality : 0.037 0.145 5132 Planarity : 0.005 0.060 5236 Dihedral : 5.161 54.803 5252 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.04 % Allowed : 15.31 % 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: 2.53 (0.14), residues: 3944 helix: 2.60 (0.10), residues: 2612 sheet: 0.34 (0.30), residues: 276 loop : -0.35 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1080 TYR 0.012 0.001 TYR C 559 PHE 0.009 0.001 PHE D 567 TRP 0.041 0.001 TRP A 240 HIS 0.004 0.001 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00391 (31396) covalent geometry : angle 0.53412 (42928) hydrogen bonds : bond 0.03741 ( 2072) hydrogen bonds : angle 4.08017 ( 6060) link_NAG-ASN : bond 0.00099 ( 4) link_NAG-ASN : angle 1.34998 ( 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 203 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 143 time to evaluate : 1.110 Fit side-chains REVERT: A 136 MET cc_start: 0.9276 (OUTLIER) cc_final: 0.8961 (ptp) REVERT: B 136 MET cc_start: 0.9287 (OUTLIER) cc_final: 0.8981 (ptp) REVERT: C 136 MET cc_start: 0.9286 (OUTLIER) cc_final: 0.8977 (ptp) REVERT: C 230 MET cc_start: 0.9372 (tpp) cc_final: 0.9107 (tpp) REVERT: D 136 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.8972 (ptp) REVERT: D 194 MET cc_start: 0.9436 (mmm) cc_final: 0.9223 (tpt) outliers start: 60 outliers final: 21 residues processed: 197 average time/residue: 0.1664 time to fit residues: 55.3257 Evaluate side-chains 162 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 633 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 136 MET Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 633 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 136 MET Chi-restraints excluded: chain C residue 324 CYS 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 136 MET Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 785 MET 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: 9.9990 chunk 14 optimal weight: 20.0000 chunk 126 optimal weight: 6.9990 chunk 186 optimal weight: 6.9990 chunk 356 optimal weight: 0.3980 chunk 308 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 163 optimal weight: 3.9990 chunk 1 optimal weight: 30.0000 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 556 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.049319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.036256 restraints weight = 160793.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.037592 restraints weight = 77781.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.038476 restraints weight = 49755.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.038959 restraints weight = 37320.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.039351 restraints weight = 31659.898| |-----------------------------------------------------------------------------| r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2684 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= 0.218 Angle : 0.557 7.163 42940 Z= 0.283 Chirality : 0.038 0.143 5132 Planarity : 0.005 0.061 5236 Dihedral : 5.059 55.766 5252 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.50 % Allowed : 16.36 % Favored : 82.14 % 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: 2.50 (0.14), residues: 3944 helix: 2.65 (0.10), residues: 2584 sheet: 0.21 (0.29), residues: 276 loop : -0.46 (0.20), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 552 TYR 0.014 0.001 TYR D 995 PHE 0.010 0.001 PHE D 567 TRP 0.011 0.001 TRP B 620 HIS 0.003 0.001 HIS C 115 Details of bonding type rmsd covalent geometry : bond 0.00488 (31396) covalent geometry : angle 0.55629 (42928) hydrogen bonds : bond 0.03757 ( 2072) hydrogen bonds : angle 4.07187 ( 6060) link_NAG-ASN : bond 0.00268 ( 4) link_NAG-ASN : angle 1.51199 ( 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 183 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 139 time to evaluate : 1.069 Fit side-chains REVERT: A 136 MET cc_start: 0.9254 (ptp) cc_final: 0.9017 (ptp) REVERT: A 143 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9119 (mt) REVERT: A 194 MET cc_start: 0.9490 (mmm) cc_final: 0.9233 (mmm) REVERT: B 136 MET cc_start: 0.9261 (ptp) cc_final: 0.9027 (ptp) REVERT: B 143 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9126 (mt) REVERT: B 194 MET cc_start: 0.9504 (mmm) cc_final: 0.9271 (mmm) REVERT: C 136 MET cc_start: 0.9260 (ptp) cc_final: 0.9022 (ptp) REVERT: C 143 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9097 (mt) REVERT: C 194 MET cc_start: 0.9502 (mmm) cc_final: 0.9241 (mmm) REVERT: C 230 MET cc_start: 0.9375 (tpp) cc_final: 0.9110 (tpp) REVERT: D 136 MET cc_start: 0.9251 (ptp) cc_final: 0.9013 (ptp) REVERT: D 143 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9122 (mt) outliers start: 44 outliers final: 21 residues processed: 174 average time/residue: 0.1641 time to fit residues: 48.8355 Evaluate side-chains 160 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 324 CYS 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 1075 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 1075 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 324 CYS 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 1075 VAL Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 324 CYS 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=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: 0.9980 chunk 375 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 chunk 219 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 277 optimal weight: 0.6980 chunk 202 optimal weight: 7.9990 overall best weight: 4.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3078 r_free = 0.3078 target = 0.048542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.035541 restraints weight = 162761.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.036866 restraints weight = 78517.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.037722 restraints weight = 50313.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.038288 restraints weight = 37943.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.038589 restraints weight = 31651.665| |-----------------------------------------------------------------------------| r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3125 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= 0.226 Angle : 0.560 7.178 42940 Z= 0.283 Chirality : 0.038 0.133 5132 Planarity : 0.005 0.060 5236 Dihedral : 4.952 53.878 5252 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.33 % Allowed : 17.62 % Favored : 81.05 % 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: 2.75 (0.10), residues: 2572 sheet: 0.28 (0.29), residues: 276 loop : -0.57 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 552 TYR 0.014 0.001 TYR C 995 PHE 0.010 0.001 PHE D 773 TRP 0.012 0.001 TRP C 620 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00506 (31396) covalent geometry : angle 0.55902 (42928) hydrogen bonds : bond 0.03684 ( 2072) hydrogen bonds : angle 4.02195 ( 6060) link_NAG-ASN : bond 0.00219 ( 4) link_NAG-ASN : angle 1.54974 ( 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 178 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 0.988 Fit side-chains REVERT: A 143 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9104 (mt) REVERT: A 212 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7275 (pm20) REVERT: A 981 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8415 (p0) REVERT: B 143 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9113 (mt) REVERT: B 212 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7396 (pm20) REVERT: B 981 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8392 (p0) REVERT: C 143 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9110 (mt) REVERT: C 212 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7394 (pm20) REVERT: C 981 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8393 (p0) REVERT: D 143 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9113 (mt) REVERT: D 212 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7318 (pm20) REVERT: D 981 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8411 (p0) outliers start: 39 outliers final: 24 residues processed: 171 average time/residue: 0.1591 time to fit residues: 48.0168 Evaluate side-chains 168 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 324 CYS 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 143 LEU Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 721 MET 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 143 LEU Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 324 CYS 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 143 LEU Chi-restraints excluded: chain D residue 212 GLU Chi-restraints excluded: chain D residue 324 CYS 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 951 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: 8.9990 chunk 129 optimal weight: 4.9990 chunk 271 optimal weight: 4.9990 chunk 352 optimal weight: 6.9990 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: 0.0770 chunk 393 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 overall best weight: 2.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 882 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.049038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.036167 restraints weight = 160852.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.037502 restraints weight = 76915.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.038388 restraints weight = 48865.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.038908 restraints weight = 36582.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.039296 restraints weight = 30665.317| |-----------------------------------------------------------------------------| r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31400 Z= 0.140 Angle : 0.507 9.028 42940 Z= 0.256 Chirality : 0.037 0.138 5132 Planarity : 0.004 0.060 5236 Dihedral : 4.774 50.950 5252 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.36 % Allowed : 18.03 % Favored : 80.61 % 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: 2.85 (0.10), residues: 2572 sheet: 0.09 (0.27), residues: 300 loop : -0.49 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 552 TYR 0.012 0.001 TYR C 559 PHE 0.008 0.001 PHE A 862 TRP 0.012 0.001 TRP D 984 HIS 0.004 0.001 HIS C 115 Details of bonding type rmsd covalent geometry : bond 0.00316 (31396) covalent geometry : angle 0.50681 (42928) hydrogen bonds : bond 0.03448 ( 2072) hydrogen bonds : angle 3.87428 ( 6060) link_NAG-ASN : bond 0.00043 ( 4) link_NAG-ASN : angle 1.20802 ( 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 179 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 1.092 Fit side-chains REVERT: A 143 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9096 (mt) REVERT: A 981 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8451 (p0) REVERT: B 143 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9106 (mt) REVERT: B 981 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8450 (p0) REVERT: C 143 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9099 (mt) REVERT: C 981 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8450 (p0) REVERT: D 143 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9105 (mt) REVERT: D 981 ASP cc_start: 0.8696 (OUTLIER) cc_final: 0.8449 (p0) outliers start: 40 outliers final: 19 residues processed: 178 average time/residue: 0.1555 time to fit residues: 48.4626 Evaluate side-chains 163 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 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 951 VAL Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 633 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 143 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 951 VAL Chi-restraints excluded: chain C residue 981 ASP Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 324 CYS 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: 0.0020 chunk 63 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 277 optimal weight: 6.9990 chunk 288 optimal weight: 9.9990 chunk 202 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 329 optimal weight: 2.9990 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 GLN A 882 HIS C 882 HIS D 233 ASN D 514 GLN D 882 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.048881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.036080 restraints weight = 161102.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.037402 restraints weight = 77111.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.038285 restraints weight = 48999.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.038853 restraints weight = 36722.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.039201 restraints weight = 30509.359| |-----------------------------------------------------------------------------| r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31400 Z= 0.151 Angle : 0.524 10.011 42940 Z= 0.263 Chirality : 0.037 0.136 5132 Planarity : 0.004 0.061 5236 Dihedral : 4.721 51.073 5252 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.29 % Allowed : 17.72 % Favored : 80.99 % 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: 2.69 (0.14), residues: 3944 helix: 2.85 (0.10), residues: 2580 sheet: 0.13 (0.27), residues: 300 loop : -0.46 (0.20), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 552 TYR 0.011 0.001 TYR A 995 PHE 0.009 0.001 PHE A 862 TRP 0.011 0.001 TRP D 984 HIS 0.006 0.001 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00343 (31396) covalent geometry : angle 0.52417 (42928) hydrogen bonds : bond 0.03427 ( 2072) hydrogen bonds : angle 3.83251 ( 6060) link_NAG-ASN : bond 0.00086 ( 4) link_NAG-ASN : angle 1.20540 ( 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: 38 poor density : 136 time to evaluate : 0.918 Fit side-chains REVERT: A 143 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9085 (mt) REVERT: A 212 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7333 (pm20) REVERT: A 917 MET cc_start: 0.9347 (mtm) cc_final: 0.8712 (mtm) REVERT: A 981 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8445 (p0) REVERT: B 143 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9077 (mt) REVERT: B 212 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7334 (pm20) REVERT: B 917 MET cc_start: 0.9428 (mtm) cc_final: 0.8658 (mtm) REVERT: B 981 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8441 (p0) REVERT: C 212 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7333 (pm20) REVERT: C 257 MET cc_start: 0.8683 (mmm) cc_final: 0.8444 (mmm) REVERT: C 917 MET cc_start: 0.9351 (mtm) cc_final: 0.8706 (mtm) REVERT: C 981 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8443 (p0) REVERT: D 143 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9091 (mt) REVERT: D 190 MET cc_start: 0.9461 (tpp) cc_final: 0.9245 (tpp) REVERT: D 212 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7320 (pm20) REVERT: D 779 MET cc_start: 0.7953 (mpp) cc_final: 0.7599 (mpp) REVERT: D 917 MET cc_start: 0.9342 (mtm) cc_final: 0.8699 (mtm) REVERT: D 981 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8441 (p0) outliers start: 38 outliers final: 20 residues processed: 171 average time/residue: 0.1477 time to fit residues: 44.7027 Evaluate side-chains 168 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU 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 143 LEU Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 633 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 324 CYS 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 143 LEU Chi-restraints excluded: chain D residue 212 GLU Chi-restraints excluded: chain D residue 324 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 132 optimal weight: 8.9990 chunk 367 optimal weight: 6.9990 chunk 350 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 228 optimal weight: 9.9990 chunk 216 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 142 optimal weight: 4.9990 chunk 267 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 269 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.047176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.034341 restraints weight = 164527.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.035616 restraints weight = 79773.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.036457 restraints weight = 51370.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.036978 restraints weight = 38769.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.037270 restraints weight = 32577.353| |-----------------------------------------------------------------------------| r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 31400 Z= 0.300 Angle : 0.631 10.442 42940 Z= 0.317 Chirality : 0.040 0.132 5132 Planarity : 0.005 0.061 5236 Dihedral : 4.915 53.050 5252 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.36 % Allowed : 17.96 % Favored : 80.68 % 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: 2.44 (0.14), residues: 3944 helix: 2.66 (0.10), residues: 2584 sheet: 0.18 (0.28), residues: 292 loop : -0.65 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 400 TYR 0.020 0.002 TYR B 995 PHE 0.013 0.001 PHE A 567 TRP 0.014 0.001 TRP A 713 HIS 0.006 0.001 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00664 (31396) covalent geometry : angle 0.63085 (42928) hydrogen bonds : bond 0.03930 ( 2072) hydrogen bonds : angle 4.07431 ( 6060) link_NAG-ASN : bond 0.00469 ( 4) link_NAG-ASN : angle 1.72365 ( 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: 40 poor density : 131 time to evaluate : 1.052 Fit side-chains REVERT: A 212 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7541 (pm20) REVERT: A 257 MET cc_start: 0.8775 (mmm) cc_final: 0.8388 (mmm) REVERT: A 917 MET cc_start: 0.9408 (OUTLIER) cc_final: 0.8823 (mtm) REVERT: B 212 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7562 (pm20) REVERT: B 917 MET cc_start: 0.9447 (mtm) cc_final: 0.8777 (mtm) REVERT: C 212 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7572 (pm20) REVERT: C 257 MET cc_start: 0.8794 (mmm) cc_final: 0.8398 (mmm) REVERT: C 917 MET cc_start: 0.9414 (OUTLIER) cc_final: 0.8825 (mtm) REVERT: D 194 MET cc_start: 0.9483 (mmm) cc_final: 0.9253 (mmm) REVERT: D 212 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7522 (pm20) REVERT: D 257 MET cc_start: 0.8785 (mmm) cc_final: 0.8389 (mmm) REVERT: D 917 MET cc_start: 0.9397 (OUTLIER) cc_final: 0.8816 (mtm) outliers start: 40 outliers final: 26 residues processed: 161 average time/residue: 0.1518 time to fit residues: 43.3155 Evaluate side-chains 162 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 324 CYS 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 917 MET Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1075 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 324 CYS 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 917 MET Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 212 GLU Chi-restraints excluded: chain D residue 324 CYS 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 917 MET 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: 0.4980 chunk 23 optimal weight: 8.9990 chunk 189 optimal weight: 40.0000 chunk 135 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 195 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 246 optimal weight: 0.9990 chunk 329 optimal weight: 9.9990 chunk 248 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.048911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.036138 restraints weight = 159778.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.037470 restraints weight = 76277.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.038340 restraints weight = 48380.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.038924 restraints weight = 36268.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.039220 restraints weight = 30028.662| |-----------------------------------------------------------------------------| r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 31400 Z= 0.111 Angle : 0.531 11.553 42940 Z= 0.264 Chirality : 0.037 0.145 5132 Planarity : 0.004 0.061 5236 Dihedral : 4.646 45.856 5252 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.88 % Allowed : 18.54 % Favored : 80.58 % 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: 2.62 (0.14), residues: 3944 helix: 2.83 (0.10), residues: 2572 sheet: 0.02 (0.27), residues: 300 loop : -0.55 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 552 TYR 0.009 0.001 TYR D 559 PHE 0.007 0.001 PHE C1005 TRP 0.014 0.001 TRP D 984 HIS 0.006 0.001 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00249 (31396) covalent geometry : angle 0.53043 (42928) hydrogen bonds : bond 0.03388 ( 2072) hydrogen bonds : angle 3.74762 ( 6060) link_NAG-ASN : bond 0.00105 ( 4) link_NAG-ASN : angle 0.95955 ( 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 164 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.985 Fit side-chains REVERT: A 136 MET cc_start: 0.9223 (ptp) cc_final: 0.8642 (pmm) REVERT: A 212 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7653 (pm20) REVERT: A 257 MET cc_start: 0.8767 (mmm) cc_final: 0.8343 (mmm) REVERT: A 538 MET cc_start: 0.8378 (mtt) cc_final: 0.8167 (mtp) REVERT: A 917 MET cc_start: 0.9397 (OUTLIER) cc_final: 0.8736 (mtm) REVERT: A 981 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8433 (p0) REVERT: B 136 MET cc_start: 0.9222 (ptp) cc_final: 0.8646 (pmm) REVERT: B 212 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7680 (pm20) REVERT: B 917 MET cc_start: 0.9428 (mtm) cc_final: 0.8764 (mtm) REVERT: B 981 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8434 (p0) REVERT: C 136 MET cc_start: 0.9217 (ptp) cc_final: 0.8645 (pmm) REVERT: C 212 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7686 (pm20) REVERT: C 257 MET cc_start: 0.8820 (mmm) cc_final: 0.8423 (mmm) REVERT: C 917 MET cc_start: 0.9403 (OUTLIER) cc_final: 0.8737 (mtm) REVERT: C 981 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8418 (p0) REVERT: D 136 MET cc_start: 0.9218 (ptp) cc_final: 0.8640 (pmm) REVERT: D 257 MET cc_start: 0.8773 (mmm) cc_final: 0.8350 (mmm) REVERT: D 538 MET cc_start: 0.8375 (mtt) cc_final: 0.8166 (mtp) REVERT: D 779 MET cc_start: 0.8098 (mpp) cc_final: 0.7642 (mpp) REVERT: D 917 MET cc_start: 0.9391 (OUTLIER) cc_final: 0.8728 (mtm) REVERT: D 981 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8432 (p0) outliers start: 26 outliers final: 14 residues processed: 158 average time/residue: 0.1531 time to fit residues: 42.1012 Evaluate side-chains 160 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 633 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 C residue 212 GLU Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 917 MET 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 859 VAL Chi-restraints excluded: chain D residue 917 MET Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 981 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 47 optimal weight: 5.9990 chunk 389 optimal weight: 5.9990 chunk 219 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 367 optimal weight: 2.9990 chunk 190 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 293 optimal weight: 5.9990 chunk 317 optimal weight: 9.9990 chunk 174 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.048170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.035310 restraints weight = 161473.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.036583 restraints weight = 77722.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.037463 restraints weight = 49902.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.038020 restraints weight = 37682.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.038341 restraints weight = 31444.921| |-----------------------------------------------------------------------------| r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31400 Z= 0.196 Angle : 0.569 12.218 42940 Z= 0.282 Chirality : 0.038 0.146 5132 Planarity : 0.004 0.060 5236 Dihedral : 4.650 48.710 5252 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.95 % Allowed : 18.54 % Favored : 80.51 % 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: 2.84 (0.10), residues: 2580 sheet: 0.02 (0.28), residues: 300 loop : -0.54 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 552 TYR 0.012 0.001 TYR A 995 PHE 0.012 0.001 PHE B1005 TRP 0.013 0.001 TRP D 240 HIS 0.006 0.001 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00443 (31396) covalent geometry : angle 0.56830 (42928) hydrogen bonds : bond 0.03497 ( 2072) hydrogen bonds : angle 3.81268 ( 6060) link_NAG-ASN : bond 0.00198 ( 4) link_NAG-ASN : angle 1.24495 ( 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 162 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 1.034 Fit side-chains REVERT: A 136 MET cc_start: 0.9228 (ptp) cc_final: 0.8975 (pmm) REVERT: A 212 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7723 (pm20) REVERT: A 257 MET cc_start: 0.8832 (mmm) cc_final: 0.8428 (mmm) REVERT: A 554 MET cc_start: 0.8664 (ptp) cc_final: 0.8454 (ptp) REVERT: A 917 MET cc_start: 0.9407 (OUTLIER) cc_final: 0.8781 (mtm) REVERT: A 981 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8443 (p0) REVERT: B 136 MET cc_start: 0.9230 (ptp) cc_final: 0.8979 (pmm) REVERT: B 212 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7755 (pm20) REVERT: B 726 MET cc_start: 0.9296 (mmm) cc_final: 0.9082 (tpp) REVERT: B 917 MET cc_start: 0.9433 (mtm) cc_final: 0.8809 (mtm) REVERT: C 136 MET cc_start: 0.9225 (ptp) cc_final: 0.8701 (pmm) REVERT: C 212 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7764 (pm20) REVERT: C 257 MET cc_start: 0.8889 (mmm) cc_final: 0.8513 (mmm) REVERT: C 798 MET cc_start: 0.8978 (mtm) cc_final: 0.8750 (mtm) REVERT: C 917 MET cc_start: 0.9415 (OUTLIER) cc_final: 0.8779 (mtm) REVERT: D 136 MET cc_start: 0.9228 (ptp) cc_final: 0.8977 (pmm) REVERT: D 212 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7720 (pm20) REVERT: D 257 MET cc_start: 0.8842 (mmm) cc_final: 0.8441 (mmm) REVERT: D 726 MET cc_start: 0.9132 (tpp) cc_final: 0.8911 (tpp) REVERT: D 798 MET cc_start: 0.8960 (mtm) cc_final: 0.8730 (mtm) REVERT: D 917 MET cc_start: 0.9401 (OUTLIER) cc_final: 0.8772 (mtm) REVERT: D 981 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8437 (p0) outliers start: 28 outliers final: 17 residues processed: 153 average time/residue: 0.1551 time to fit residues: 41.6467 Evaluate side-chains 160 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 917 MET Chi-restraints excluded: chain C residue 951 VAL 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 859 VAL Chi-restraints excluded: chain D residue 917 MET Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 981 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 346 optimal weight: 3.9990 chunk 292 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 276 optimal weight: 0.8980 chunk 232 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.048877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.036104 restraints weight = 159833.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.037427 restraints weight = 76142.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.038300 restraints weight = 48240.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.038823 restraints weight = 36186.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.039243 restraints weight = 30366.348| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3911 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= 0.117 Angle : 0.530 12.497 42940 Z= 0.262 Chirality : 0.037 0.136 5132 Planarity : 0.004 0.061 5236 Dihedral : 4.547 45.325 5252 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.95 % Allowed : 18.57 % Favored : 80.48 % 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: 2.68 (0.14), residues: 3944 helix: 2.87 (0.10), residues: 2572 sheet: 0.12 (0.28), residues: 300 loop : -0.53 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1080 TYR 0.009 0.001 TYR A 559 PHE 0.010 0.001 PHE C1005 TRP 0.012 0.001 TRP D 984 HIS 0.006 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00265 (31396) covalent geometry : angle 0.52972 (42928) hydrogen bonds : bond 0.03328 ( 2072) hydrogen bonds : angle 3.70843 ( 6060) link_NAG-ASN : bond 0.00042 ( 4) link_NAG-ASN : angle 0.95154 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3808.99 seconds wall clock time: 67 minutes 19.71 seconds (4039.71 seconds total)