Starting phenix.real_space_refine on Sun Jul 5 22:59:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mbq_23741/07_2026/7mbq_23741.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mbq_23741/07_2026/7mbq_23741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mbq_23741/07_2026/7mbq_23741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mbq_23741/07_2026/7mbq_23741.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7mbq_23741/07_2026/7mbq_23741.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mbq_23741/07_2026/7mbq_23741.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mbq_23741/07_2026/7mbq_23741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mbq_23741/07_2026/7mbq_23741.map" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 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 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 chiralities: 1 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 6.96, per 1000 atoms: 0.23 Number of scatterers: 30616 At special positions: 0 Unit cell: (144.55, 144.55, 154.462, 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: 2.65 Conformation dependent library (CDL) restraints added in 1.5 seconds 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7600 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 8 sheets defined 70.8% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 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: 3.812A 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: 3.533A 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: 3.509A 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: 3.848A pdb=" N ILE A 849 " --> pdb=" O LEU A 845 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE A 850 " --> pdb=" O GLY A 846 " (cutoff:3.500A) removed outlier: 4.052A 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: 4.777A 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: 3.865A 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: 3.663A 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: 3.671A 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: 3.848A pdb=" N ILE B 849 " --> pdb=" O LEU B 845 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE B 850 " --> pdb=" O GLY B 846 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE B 864 " --> pdb=" O PHE B 860 " (cutoff:3.500A) removed outlier: 4.389A 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: 3.550A pdb=" N VAL B 946 " --> pdb=" O ALA B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 979 removed outlier: 3.865A 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: 4.065A pdb=" N SER C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 119 removed outlier: 3.664A 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: 3.814A 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: 3.671A 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: 3.550A pdb=" N VAL C 946 " --> pdb=" O ALA C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 979 removed outlier: 3.867A 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: 3.663A 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: 3.588A 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: 3.813A 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: 3.961A 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: 3.950A 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: 3.551A 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: 3.524A 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: 3.636A 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: 7.615A pdb=" N LEU A 243 " --> pdb=" O CYS A 217 " (cutoff:3.500A) removed outlier: 7.412A 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: 6.233A 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: 7.411A 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: 7.548A pdb=" N HIS B 304 " --> pdb=" O TRP B 240 " (cutoff:3.500A) removed outlier: 6.317A 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: 7.412A 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: 3.760A 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: 7.412A pdb=" N LEU D 219 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.667A 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: 6.316A 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: 5.60 Time building geometry restraints manager: 3.46 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: 9429 1.34 - 1.46: 5385 1.46 - 1.58: 16290 1.58 - 1.69: 0 1.69 - 1.81: 292 Bond restraints: 31396 Sorted by residual: 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 2.08e+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 2.08e+00 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 2.05e+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 1.96e+00 bond pdb=" C1 NAG A1501 " pdb=" O5 NAG A1501 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.70e+00 ... (remaining 31391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 41890 1.60 - 3.20: 844 3.20 - 4.80: 143 4.80 - 6.40: 39 6.40 - 8.00: 12 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 112.59 118.40 -5.81 1.22e+00 6.72e-01 2.27e+01 angle pdb=" N GLN C 511 " pdb=" CA GLN C 511 " pdb=" C GLN C 511 " ideal model delta sigma weight residual 112.59 118.39 -5.80 1.22e+00 6.72e-01 2.26e+01 angle pdb=" N GLN A 511 " pdb=" CA GLN A 511 " pdb=" C GLN A 511 " ideal model delta sigma weight residual 112.59 118.38 -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 112.59 118.36 -5.77 1.22e+00 6.72e-01 2.24e+01 angle pdb=" N ARG D 513 " pdb=" CA ARG D 513 " pdb=" C ARG D 513 " ideal model delta sigma weight residual 108.41 101.11 7.30 1.61e+00 3.86e-01 2.06e+01 ... (remaining 42923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 16221 17.58 - 35.17: 1559 35.17 - 52.75: 348 52.75 - 70.34: 88 70.34 - 87.92: 20 Dihedral angle restraints: 18236 sinusoidal: 6556 harmonic: 11680 Sorted by residual: 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 180.00 159.27 20.73 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA LEU C 544 " pdb=" C LEU C 544 " pdb=" N ALA C 545 " pdb=" CA ALA C 545 " ideal model delta harmonic sigma weight residual 180.00 159.29 20.71 0 5.00e+00 4.00e-02 1.72e+01 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 180.00 159.31 20.69 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 18233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 4392 0.057 - 0.114: 685 0.114 - 0.170: 31 0.170 - 0.227: 8 0.227 - 0.284: 16 Chirality restraints: 5132 Sorted by residual: chirality pdb=" C41 YUY D3001 " pdb=" C40 YUY D3001 " pdb=" C42 YUY D3001 " pdb=" O7 YUY D3001 " both_signs ideal model delta sigma weight residual False -2.21 -2.50 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA ASN A 512 " pdb=" N ASN A 512 " pdb=" C ASN A 512 " pdb=" CB ASN A 512 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+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 -2.49 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 5129 not shown) Planarity restraints: 5240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1501 " 0.037 2.00e-02 2.50e+03 3.08e-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 D3002 " 0.037 2.00e-02 2.50e+03 3.07e-02 1.18e+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 A1501 " 0.037 2.00e-02 2.50e+03 3.06e-02 1.17e+01 pdb=" C7 NAG A1501 " -0.011 2.00e-02 2.50e+03 pdb=" C8 NAG A1501 " 0.029 2.00e-02 2.50e+03 pdb=" N2 NAG A1501 " -0.048 2.00e-02 2.50e+03 pdb=" O7 NAG A1501 " -0.007 2.00e-02 2.50e+03 ... (remaining 5237 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6276 2.78 - 3.31: 29990 3.31 - 3.84: 54255 3.84 - 4.37: 61822 4.37 - 4.90: 105283 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 2.246 3.040 nonbonded pdb=" O GLN D 771 " pdb=" OG1 THR D 775 " model vdw 2.247 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: 0.10 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.100 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: 0.050 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 26.480 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.060 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:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 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= 0.169 Angle : 0.590 8.003 42940 Z= 0.337 Chirality : 0.042 0.284 5132 Planarity : 0.005 0.077 5236 Dihedral : 15.268 87.924 10636 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.94 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 C 32 TRP 0.017 0.001 TRP A 984 HIS 0.004 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 (31396) covalent geometry : angle 0.58942 / 0.34 (42928) hydrogen bonds : bond 0.12397 / 8.64 ( 2072) hydrogen bonds : angle 5.08617 / 3.71 ( 6060) link_NAG-ASN : bond 0.00050 / 0.03 ( 4) link_NAG-ASN : angle 2.05932 / 1.55 ( 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 207 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 1.161 Fit side-chains REVERT: A 230 MET cc_start: 0.8867 (ttt) cc_final: 0.8651 (ttt) REVERT: B 230 MET cc_start: 0.8863 (ttt) cc_final: 0.8645 (ttt) REVERT: C 230 MET cc_start: 0.8867 (ttt) cc_final: 0.8649 (ttt) REVERT: D 230 MET cc_start: 0.8867 (ttt) cc_final: 0.8649 (ttt) outliers start: 17 outliers final: 0 residues processed: 203 average time/residue: 0.7673 time to fit residues: 180.3319 Evaluate side-chains 152 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0770 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.079806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.053701 restraints weight = 67941.782| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 2.24 r_work: 0.2656 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9163 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 31400 Z= 0.178 Angle : 0.552 10.175 42940 Z= 0.284 Chirality : 0.039 0.153 5132 Planarity : 0.005 0.059 5236 Dihedral : 4.557 50.398 4304 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.56 % Allowed : 16.26 % Favored : 82.18 % 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: 2.12 (0.14), residues: 3944 helix: 2.27 (0.10), residues: 2612 sheet: 0.51 (0.33), residues: 268 loop : -0.58 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1069 TYR 0.012 0.001 TYR A 995 PHE 0.011 0.001 PHE D 828 TRP 0.016 0.001 TRP A 620 HIS 0.004 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (31396) covalent geometry : angle 0.55185 / 0.28 (42928) hydrogen bonds : bond 0.04528 / 3.15 ( 2072) hydrogen bonds : angle 4.24233 / 3.08 ( 6060) link_NAG-ASN : bond 0.00089 / 0.04 ( 4) link_NAG-ASN : angle 1.04148 / 0.79 ( 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 198 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 152 time to evaluate : 0.790 Fit side-chains REVERT: A 1076 GLN cc_start: 0.9064 (tt0) cc_final: 0.8759 (tp-100) REVERT: A 1081 MET cc_start: 0.8562 (tmm) cc_final: 0.8306 (ppp) REVERT: B 1076 GLN cc_start: 0.9059 (tt0) cc_final: 0.8753 (tp-100) REVERT: B 1081 MET cc_start: 0.8565 (tmm) cc_final: 0.8302 (ppp) REVERT: C 1076 GLN cc_start: 0.9052 (tt0) cc_final: 0.8747 (tp-100) REVERT: C 1081 MET cc_start: 0.8563 (tmm) cc_final: 0.8301 (ppp) REVERT: D 1076 GLN cc_start: 0.9049 (tt0) cc_final: 0.8749 (tp-100) REVERT: D 1081 MET cc_start: 0.8563 (tmm) cc_final: 0.8305 (ppp) outliers start: 46 outliers final: 25 residues processed: 181 average time/residue: 0.6873 time to fit residues: 145.5975 Evaluate side-chains 178 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 493 MET Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 493 MET Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 633 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 89 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 332 optimal weight: 0.9990 chunk 266 optimal weight: 3.9990 chunk 295 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 chunk 290 optimal weight: 5.9990 chunk 257 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.079504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.053405 restraints weight = 67965.125| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 2.25 r_work: 0.2654 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9168 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31400 Z= 0.155 Angle : 0.504 9.660 42940 Z= 0.262 Chirality : 0.038 0.147 5132 Planarity : 0.005 0.060 5236 Dihedral : 4.446 49.618 4304 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.07 % Allowed : 15.34 % Favored : 82.59 % 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: 2.34 (0.14), residues: 3944 helix: 2.42 (0.10), residues: 2608 sheet: 0.41 (0.31), residues: 284 loop : -0.38 (0.20), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1069 TYR 0.011 0.001 TYR D 559 PHE 0.011 0.001 PHE D 567 TRP 0.014 0.001 TRP B 984 HIS 0.003 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (31396) covalent geometry : angle 0.50408 / 0.26 (42928) hydrogen bonds : bond 0.04292 / 2.98 ( 2072) hydrogen bonds : angle 4.02963 / 2.93 ( 6060) link_NAG-ASN : bond 0.00090 / 0.05 ( 4) link_NAG-ASN : angle 0.79959 / 0.61 ( 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 213 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 152 time to evaluate : 1.159 Fit side-chains REVERT: A 493 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.7915 (mmt) REVERT: A 974 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8066 (mp10) REVERT: A 1076 GLN cc_start: 0.9044 (tt0) cc_final: 0.8704 (tp-100) REVERT: B 493 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7916 (mmt) REVERT: B 974 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8049 (mp10) REVERT: B 1076 GLN cc_start: 0.9048 (tt0) cc_final: 0.8713 (tp-100) REVERT: C 493 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7944 (mmt) REVERT: C 974 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8063 (mp10) REVERT: C 1076 GLN cc_start: 0.9040 (tt0) cc_final: 0.8701 (tp-100) REVERT: D 493 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.8003 (mmt) REVERT: D 974 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8064 (mp10) REVERT: D 1076 GLN cc_start: 0.9039 (tt0) cc_final: 0.8702 (tp-100) outliers start: 61 outliers final: 32 residues processed: 190 average time/residue: 0.6960 time to fit residues: 155.0960 Evaluate side-chains 192 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 974 GLN Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 493 MET Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 974 GLN Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 493 MET Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 974 GLN Chi-restraints excluded: chain C residue 981 ASP Chi-restraints excluded: chain C residue 1068 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 974 GLN Chi-restraints excluded: chain D residue 981 ASP Chi-restraints excluded: chain D residue 1068 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 181 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 186 optimal weight: 0.7980 chunk 356 optimal weight: 0.7980 chunk 308 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.079463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.053514 restraints weight = 67613.633| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.24 r_work: 0.2657 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9170 moved from start: 0.1519 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= 0.144 Angle : 0.497 10.056 42940 Z= 0.257 Chirality : 0.037 0.144 5132 Planarity : 0.005 0.061 5236 Dihedral : 4.374 49.875 4304 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.35 % Allowed : 15.68 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.14), residues: 3944 helix: 2.49 (0.10), residues: 2608 sheet: 0.50 (0.31), residues: 276 loop : -0.39 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1069 TYR 0.011 0.001 TYR A 995 PHE 0.011 0.001 PHE A 567 TRP 0.013 0.001 TRP A 984 HIS 0.002 0.001 HIS C 882 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (31396) covalent geometry : angle 0.49715 / 0.26 (42928) hydrogen bonds : bond 0.04093 / 2.84 ( 2072) hydrogen bonds : angle 3.94108 / 2.86 ( 6060) link_NAG-ASN : bond 0.00063 / 0.03 ( 4) link_NAG-ASN : angle 0.72988 / 0.55 ( 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 220 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 151 time to evaluate : 1.133 Fit side-chains REVERT: A 493 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7916 (mmt) REVERT: A 1076 GLN cc_start: 0.9052 (tt0) cc_final: 0.8695 (tp-100) REVERT: B 493 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7926 (mmt) REVERT: B 1076 GLN cc_start: 0.9062 (tt0) cc_final: 0.8702 (tp-100) REVERT: C 493 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7906 (mmt) REVERT: C 1076 GLN cc_start: 0.9062 (tt0) cc_final: 0.8705 (tp-100) REVERT: D 1076 GLN cc_start: 0.9066 (tt0) cc_final: 0.8710 (tp-100) outliers start: 69 outliers final: 34 residues processed: 199 average time/residue: 0.7237 time to fit residues: 168.7604 Evaluate side-chains 188 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 493 MET Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 493 MET Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 1068 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 1068 LEU 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: 4.9990 chunk 235 optimal weight: 6.9990 chunk 371 optimal weight: 0.0870 chunk 375 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 165 optimal weight: 0.0170 chunk 219 optimal weight: 7.9990 chunk 168 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 277 optimal weight: 0.7980 chunk 202 optimal weight: 0.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.080918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.055316 restraints weight = 67985.590| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.25 r_work: 0.2707 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9141 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 31400 Z= 0.102 Angle : 0.461 9.750 42940 Z= 0.238 Chirality : 0.036 0.144 5132 Planarity : 0.004 0.062 5236 Dihedral : 4.193 49.439 4304 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.60 % Allowed : 16.70 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.14), residues: 3944 helix: 2.59 (0.10), residues: 2628 sheet: 0.54 (0.31), residues: 276 loop : -0.47 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1080 TYR 0.009 0.001 TYR D 559 PHE 0.008 0.001 PHE D 567 TRP 0.013 0.001 TRP C 984 HIS 0.003 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (31396) covalent geometry : angle 0.46061 / 0.24 (42928) hydrogen bonds : bond 0.03545 / 2.47 ( 2072) hydrogen bonds : angle 3.80752 / 2.76 ( 6060) link_NAG-ASN : bond 0.00156 / 0.08 ( 4) link_NAG-ASN : angle 0.65111 / 0.49 ( 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 202 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 155 time to evaluate : 1.226 Fit side-chains REVERT: A 779 MET cc_start: 0.7676 (mtp) cc_final: 0.6942 (mmp) REVERT: A 974 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8006 (mp10) REVERT: B 779 MET cc_start: 0.7700 (mtp) cc_final: 0.6935 (mmp) REVERT: B 974 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8007 (mp10) REVERT: C 779 MET cc_start: 0.7705 (mtp) cc_final: 0.6881 (mmp) REVERT: C 974 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8002 (mp10) REVERT: D 779 MET cc_start: 0.7714 (mtp) cc_final: 0.6884 (mmp) REVERT: D 974 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8000 (mp10) outliers start: 47 outliers final: 31 residues processed: 190 average time/residue: 0.7307 time to fit residues: 161.6021 Evaluate side-chains 186 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 974 GLN Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 974 GLN Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain B residue 1075 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 974 GLN Chi-restraints excluded: chain C residue 1068 LEU Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 974 GLN Chi-restraints excluded: chain D residue 1068 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 108 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 271 optimal weight: 3.9990 chunk 352 optimal weight: 3.9990 chunk 304 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 276 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 282 optimal weight: 0.8980 chunk 393 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 514 GLN B 514 GLN C 514 GLN D 514 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.078756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.052748 restraints weight = 68248.668| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 2.24 r_work: 0.2636 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9185 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31400 Z= 0.185 Angle : 0.523 10.326 42940 Z= 0.270 Chirality : 0.038 0.138 5132 Planarity : 0.005 0.060 5236 Dihedral : 4.371 50.360 4304 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.04 % Allowed : 16.67 % Favored : 81.29 % 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: 2.51 (0.14), residues: 3944 helix: 2.58 (0.10), residues: 2608 sheet: 0.61 (0.31), residues: 268 loop : -0.42 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1080 TYR 0.014 0.001 TYR A 995 PHE 0.011 0.001 PHE B 567 TRP 0.012 0.001 TRP A 984 HIS 0.004 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 (31396) covalent geometry : angle 0.52303 / 0.27 (42928) hydrogen bonds : bond 0.04375 / 3.03 ( 2072) hydrogen bonds : angle 3.93896 / 2.86 ( 6060) link_NAG-ASN : bond 0.00013 / 0.01 ( 4) link_NAG-ASN : angle 0.75262 / 0.55 ( 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 211 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 151 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 MET cc_start: 0.8439 (mmm) cc_final: 0.8042 (mmp) REVERT: A 779 MET cc_start: 0.7771 (mtp) cc_final: 0.6968 (mmp) REVERT: B 493 MET cc_start: 0.8439 (mmm) cc_final: 0.8042 (mmp) REVERT: C 493 MET cc_start: 0.8445 (mmm) cc_final: 0.7790 (mmp) REVERT: D 493 MET cc_start: 0.8437 (mmm) cc_final: 0.8039 (mmp) outliers start: 60 outliers final: 42 residues processed: 202 average time/residue: 0.7286 time to fit residues: 171.5311 Evaluate side-chains 193 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 151 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 974 GLN Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 974 GLN Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain B residue 1075 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 812 MET Chi-restraints excluded: chain C residue 974 GLN Chi-restraints excluded: chain C residue 1068 LEU Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 974 GLN Chi-restraints excluded: chain D residue 1068 LEU Chi-restraints excluded: chain D residue 1075 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 170 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 277 optimal weight: 0.9990 chunk 288 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 329 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.079276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.053204 restraints weight = 68261.982| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.27 r_work: 0.2652 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9174 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 31400 Z= 0.150 Angle : 0.499 10.862 42940 Z= 0.257 Chirality : 0.037 0.139 5132 Planarity : 0.005 0.061 5236 Dihedral : 4.346 50.116 4304 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.80 % Allowed : 16.56 % Favored : 81.63 % 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: 2.59 (0.10), residues: 2612 sheet: 0.55 (0.30), residues: 276 loop : -0.47 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1080 TYR 0.011 0.001 TYR D 995 PHE 0.012 0.001 PHE D 567 TRP 0.012 0.001 TRP A 984 HIS 0.003 0.001 HIS C 882 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (31396) covalent geometry : angle 0.49921 / 0.26 (42928) hydrogen bonds : bond 0.04061 / 2.82 ( 2072) hydrogen bonds : angle 3.87798 / 2.81 ( 6060) link_NAG-ASN : bond 0.00063 / 0.03 ( 4) link_NAG-ASN : angle 0.67875 / 0.49 ( 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 207 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 154 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7766 (mmp) REVERT: A 779 MET cc_start: 0.7787 (mtp) cc_final: 0.6943 (mmp) REVERT: B 493 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7766 (mmp) REVERT: B 779 MET cc_start: 0.7798 (mtp) cc_final: 0.6978 (mmp) REVERT: C 493 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7761 (mmp) REVERT: C 779 MET cc_start: 0.7756 (mtp) cc_final: 0.6944 (mmp) REVERT: D 493 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8040 (mmp) REVERT: D 779 MET cc_start: 0.7756 (mtp) cc_final: 0.6949 (mmp) outliers start: 53 outliers final: 42 residues processed: 192 average time/residue: 0.7045 time to fit residues: 159.1489 Evaluate side-chains 200 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 154 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 974 GLN Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 493 MET Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 812 MET Chi-restraints excluded: chain B residue 974 GLN Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain B residue 1075 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 493 MET Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 974 GLN Chi-restraints excluded: chain C residue 1068 LEU Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 974 GLN Chi-restraints excluded: chain D residue 1068 LEU 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: 1.9990 chunk 367 optimal weight: 3.9990 chunk 350 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 228 optimal weight: 4.9990 chunk 216 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 267 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 269 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.078943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.053041 restraints weight = 68182.606| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.24 r_work: 0.2643 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9182 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 31400 Z= 0.166 Angle : 0.517 11.065 42940 Z= 0.264 Chirality : 0.038 0.138 5132 Planarity : 0.005 0.061 5236 Dihedral : 4.370 50.104 4304 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.97 % Allowed : 16.46 % Favored : 81.56 % 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: 2.48 (0.14), residues: 3944 helix: 2.53 (0.10), residues: 2636 sheet: 0.57 (0.31), residues: 276 loop : -0.41 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1080 TYR 0.013 0.001 TYR A 995 PHE 0.011 0.001 PHE D 567 TRP 0.012 0.001 TRP A 984 HIS 0.003 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (31396) covalent geometry : angle 0.51729 / 0.26 (42928) hydrogen bonds : bond 0.04181 / 2.90 ( 2072) hydrogen bonds : angle 3.88161 / 2.81 ( 6060) link_NAG-ASN : bond 0.00051 / 0.03 ( 4) link_NAG-ASN : angle 0.70295 / 0.51 ( 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 208 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 150 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7758 (mmp) REVERT: A 495 ARG cc_start: 0.7968 (ttm170) cc_final: 0.7651 (ttm170) REVERT: A 779 MET cc_start: 0.7865 (mtp) cc_final: 0.7023 (mmp) REVERT: B 493 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8067 (mmp) REVERT: C 493 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7744 (mmp) REVERT: D 493 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8040 (mmp) outliers start: 58 outliers final: 48 residues processed: 192 average time/residue: 0.7136 time to fit residues: 161.3151 Evaluate side-chains 199 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 147 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 974 GLN Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 493 MET Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 812 MET Chi-restraints excluded: chain B residue 974 GLN Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain B residue 1075 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 493 MET Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 812 MET Chi-restraints excluded: chain C residue 974 GLN Chi-restraints excluded: chain C residue 981 ASP Chi-restraints excluded: chain C residue 1068 LEU Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 812 MET Chi-restraints excluded: chain D residue 974 GLN Chi-restraints excluded: chain D residue 981 ASP Chi-restraints excluded: chain D residue 1068 LEU 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: 4.9990 chunk 23 optimal weight: 7.9990 chunk 189 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 246 optimal weight: 0.9980 chunk 329 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.079511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.053580 restraints weight = 68132.565| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 2.26 r_work: 0.2660 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9170 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31400 Z= 0.137 Angle : 0.502 11.124 42940 Z= 0.256 Chirality : 0.037 0.140 5132 Planarity : 0.005 0.061 5236 Dihedral : 4.326 49.798 4304 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.84 % Allowed : 16.43 % Favored : 81.73 % 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: 2.57 (0.14), residues: 3944 helix: 2.63 (0.10), residues: 2612 sheet: 0.70 (0.31), residues: 276 loop : -0.47 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1080 TYR 0.011 0.001 TYR A 995 PHE 0.011 0.001 PHE D 567 TRP 0.012 0.001 TRP C 984 HIS 0.003 0.001 HIS D 882 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (31396) covalent geometry : angle 0.50165 / 0.26 (42928) hydrogen bonds : bond 0.03928 / 2.73 ( 2072) hydrogen bonds : angle 3.82147 / 2.77 ( 6060) link_NAG-ASN : bond 0.00087 / 0.04 ( 4) link_NAG-ASN : angle 0.66745 / 0.48 ( 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 204 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 150 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.7852 (mmp) REVERT: A 495 ARG cc_start: 0.7986 (ttm170) cc_final: 0.7668 (ttm170) REVERT: A 779 MET cc_start: 0.7802 (mtp) cc_final: 0.7037 (mmp) REVERT: B 493 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8109 (mmp) REVERT: B 779 MET cc_start: 0.7829 (mtp) cc_final: 0.7020 (mmp) REVERT: C 493 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.7769 (mmp) REVERT: C 779 MET cc_start: 0.7829 (mtp) cc_final: 0.7022 (mmp) REVERT: D 493 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8070 (mmp) REVERT: D 779 MET cc_start: 0.7770 (mtp) cc_final: 0.6999 (mmp) outliers start: 54 outliers final: 49 residues processed: 188 average time/residue: 0.7141 time to fit residues: 158.5645 Evaluate side-chains 202 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 149 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 974 GLN Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 493 MET Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 812 MET Chi-restraints excluded: chain B residue 974 GLN Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain B residue 1075 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 493 MET Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 812 MET Chi-restraints excluded: chain C residue 974 GLN Chi-restraints excluded: chain C residue 981 ASP Chi-restraints excluded: chain C residue 1068 LEU Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 812 MET Chi-restraints excluded: chain D residue 974 GLN Chi-restraints excluded: chain D residue 981 ASP Chi-restraints excluded: chain D residue 1068 LEU Chi-restraints excluded: chain D residue 1075 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 47 optimal weight: 2.9990 chunk 389 optimal weight: 0.9990 chunk 219 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 367 optimal weight: 3.9990 chunk 190 optimal weight: 0.4980 chunk 17 optimal weight: 10.0000 chunk 293 optimal weight: 1.9990 chunk 317 optimal weight: 0.9980 chunk 174 optimal weight: 5.9990 chunk 127 optimal weight: 0.0020 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.079962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.054010 restraints weight = 67689.815| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.27 r_work: 0.2673 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9161 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31400 Z= 0.122 Angle : 0.498 11.000 42940 Z= 0.253 Chirality : 0.037 0.140 5132 Planarity : 0.004 0.061 5236 Dihedral : 4.260 49.571 4304 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.80 % Allowed : 16.46 % Favored : 81.73 % 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: 2.66 (0.14), residues: 3944 helix: 2.71 (0.10), residues: 2600 sheet: 0.85 (0.31), residues: 272 loop : -0.46 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1080 TYR 0.010 0.001 TYR A 995 PHE 0.010 0.001 PHE B 567 TRP 0.013 0.001 TRP C 984 HIS 0.003 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (31396) covalent geometry : angle 0.49784 / 0.25 (42928) hydrogen bonds : bond 0.03778 / 2.63 ( 2072) hydrogen bonds : angle 3.76800 / 2.73 ( 6060) link_NAG-ASN : bond 0.00111 / 0.06 ( 4) link_NAG-ASN : angle 0.66203 / 0.48 ( 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 205 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 152 time to evaluate : 1.288 Fit side-chains REVERT: A 493 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.7868 (mmp) REVERT: A 495 ARG cc_start: 0.8011 (ttm170) cc_final: 0.7694 (ttm170) REVERT: A 779 MET cc_start: 0.7689 (mtp) cc_final: 0.6969 (mmp) REVERT: A 974 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8003 (mp10) REVERT: A 1080 ARG cc_start: 0.8662 (tmm-80) cc_final: 0.8390 (ttp80) REVERT: B 493 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8160 (mmp) REVERT: B 779 MET cc_start: 0.7701 (mtp) cc_final: 0.6968 (mmp) REVERT: B 974 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8005 (mp10) REVERT: B 1080 ARG cc_start: 0.8675 (tmm-80) cc_final: 0.8392 (ttp80) REVERT: C 493 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7856 (mmp) REVERT: C 779 MET cc_start: 0.7699 (mtp) cc_final: 0.6973 (mmp) REVERT: C 974 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8000 (mp10) REVERT: C 1080 ARG cc_start: 0.8671 (tmm-80) cc_final: 0.8388 (ttp80) REVERT: D 493 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8166 (mmp) REVERT: D 779 MET cc_start: 0.7695 (mtp) cc_final: 0.6974 (mmp) REVERT: D 974 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8000 (mp10) REVERT: D 1080 ARG cc_start: 0.8659 (tmm-80) cc_final: 0.8377 (ttp80) outliers start: 53 outliers final: 45 residues processed: 189 average time/residue: 0.7259 time to fit residues: 161.3999 Evaluate side-chains 202 residues out of total 3520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 149 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 974 GLN Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 493 MET Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 812 MET Chi-restraints excluded: chain B residue 974 GLN Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain B residue 1075 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 493 MET Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 812 MET Chi-restraints excluded: chain C residue 974 GLN Chi-restraints excluded: chain C residue 981 ASP Chi-restraints excluded: chain C residue 1068 LEU Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 812 MET Chi-restraints excluded: chain D residue 974 GLN Chi-restraints excluded: chain D residue 981 ASP Chi-restraints excluded: chain D residue 1068 LEU Chi-restraints excluded: chain D residue 1075 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 346 optimal weight: 4.9990 chunk 292 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 276 optimal weight: 4.9990 chunk 232 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.078147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.052096 restraints weight = 68233.403| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 2.24 r_work: 0.2620 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9199 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 31400 Z= 0.220 Angle : 0.564 11.227 42940 Z= 0.286 Chirality : 0.040 0.149 5132 Planarity : 0.005 0.062 5236 Dihedral : 4.496 50.361 4304 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.07 % Allowed : 16.22 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.14), residues: 3944 helix: 2.57 (0.10), residues: 2604 sheet: 0.69 (0.30), residues: 276 loop : -0.39 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1080 TYR 0.016 0.001 TYR D 995 PHE 0.012 0.001 PHE B 892 TRP 0.011 0.001 TRP B 984 HIS 0.004 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.22 (31396) covalent geometry : angle 0.56366 / 0.29 (42928) hydrogen bonds : bond 0.04526 / 3.14 ( 2072) hydrogen bonds : angle 3.92782 / 2.85 ( 6060) link_NAG-ASN : bond 0.00009 / 0.00 ( 4) link_NAG-ASN : angle 0.75046 / 0.53 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12560.97 seconds wall clock time: 214 minutes 5.46 seconds (12845.46 seconds total)